Bridging Imaging Users to Imaging Analysis - 2022 (Responses) - Form Responses 1_copy.csv

Timestamp,I agree to these terms and conditions,Which of the following roles best describes you?,Which of the following do you have significant formal training in or experience with? Select all that apply.,Where do you currently primarily work?,How would you describe your work?,How would you rate your computational skills?,How would you rate your comfort in developing new computational skills?,How do you generally go about solving an image analysis problem? Check the approach(es) you use the most.,How frequently do you use scripting to solve image analysis problems?,"In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [Scholarly ""best practices"" article]","In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [Written step-by-step tutorial]","In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [Video tutorial]","In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [Interactive webinar]","In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [One-on-one ""office hours"" with an expert]","In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [In person seminar/tutorial lasting <1 day]","In regards to learning more about image analysis, how preferable do you find each of these instructional methods? [Multiday workshop]",How interested are you in learning more about the following topics? [Image analysis theory],How interested are you in learning more about the following topics? [General image analysis practices],How interested are you in learning more about the following topics? [Image analysis practices related to my (sub) discipline],How interested are you in learning more about the following topics? [Learning to use a particular software tool],How interested are you in learning more about the following topics? [Deep learning as applied to image analysis],How interested are you in learning more about the following topics? [Analyzing large images/large numbers of images],How interested are you in learning more about the following topics? [Visualizing image analysis results],The next question will ask you about particular image analysis tools and techniques. Do you want to answer questions about microscopy in the field/area of life sciences or physical sciences?,What image analysis tools have you used before? (check all that apply),What image analysis tools do you use the most?,What kinds of images do you commonly want to analyze (select all that apply?* [Brightfield/DIC/phase-contrast of cells or organisms from manually selected fields],What kinds of images do you commonly want to analyze (select all that apply?* [Brightfield/DIC/phase-contrast of cells or organisms from an automated microscope (such as a high content imager)],What kinds of images do you commonly want to analyze (select all that apply?* [Fluorescent images of cells/organisms from manually selected fields],What kinds of images do you commonly want to analyze (select all that apply?* [Fluorescent images of cells/organisms from an automated microscope (such as a high content imager)],What kinds of images do you commonly want to analyze (select all that apply?* [Histologically stained tissue sections],What kinds of images do you commonly want to analyze (select all that apply?* [Electron microscopy],What kinds of images do you commonly want to analyze (select all that apply?* [Imaging mass spectrometry],What kinds of images do you commonly want to analyze (select all that apply?* [Imaging flow cytometry],What kinds of images do you commonly want to analyze (select all that apply?* [Superresolution (PALM/STORM)],What kinds of images do you commonly want to analyze (select all that apply?* [Autofluorescence imaging (ie FLIM)],What kinds of images do you commonly want to analyze (select all that apply?* [Other],"What image analysis problems (i.e. finding nuclei, tissue analysis, analysis of super-resolution data, etc) do you think are generally well-solved?","What image analysis problems (i.e. finding nuclei, tissue analysis, analysis of super-resolution data, etc) do you wish had easier/better solutions?",What image analysis tools have you used before? (check all that apply),What image analysis tools do you use the most?,What kinds of images do you commonly want to analyze (select all that apply)? [Optical microscopy/DIC/fractography],What kinds of images do you commonly want to analyze (select all that apply)? [Scanning electron microscopy (secondary electron or back scattered imaging)],"What kinds of images do you commonly want to analyze (select all that apply)? [Transmission electron microscopy (including electron diffraction and STEM imaging, e.g. HAADF-STEM)]","What kinds of images do you commonly want to analyze (select all that apply)? [Spectroscopy/diffractive imaging in the SEM/TEM (eg. EDS, EBSD, EELS, CL)]",What kinds of images do you commonly want to analyze (select all that apply)? [Imaging with mass spectrometry (eg SIMS/APT)],What kinds of images do you commonly want to analyze (select all that apply)? [X-ray microscopy (including tomography)],"What kinds of images do you commonly want to analyze (select all that apply)? [FM imaging, force spectroscopy, single molecule force spectroscopy]",What kinds of images do you commonly want to analyze (select all that apply)? [Fluorescence microscopy],What kinds of images do you commonly want to analyze (select all that apply)? [Other],"What image analysis problems (i.e. segmenting particles, 3D reconstruction, spectroscopic analysis, extracting force/mechanical property measurements, etc) do you think are generally well-solved?","What image analysis problems (i.e. segmenting particles, 3D reconstruction, spectroscopic analysis, extracting force/mechanical property measurements, etc) do you wish had easier/better solutions?",Where did you hear about this survey? Please select all that apply.,Please select any of the following you have attended in the past,"Are there any image analysis workshops, tutorials, or conferences you are aware of and attended or considered attending? If so, how many?","How would you most prefer to be notified about image analysis workshops, sessions, or conferences being planned?","Are there any image analysis workshops, tutorials, or conferences that you have participated in and found particularly helpful?  If yes, what made them beneficial?",Are there any conferences you've attended in the past that you think would particularly benefit from the addition/expansion of image analysis offerings?,"What specific topics (i.e. overviews of a particular tool, comparisons between pieces of software, or how to use a certain tool for a certain kind of experiment) would you like to see prioritized for future image analysis workshop and tutorial offerings?",What do you think analysis tool CREATORS (such as software developers) could/should do to make image analysis better and more successful? How best could we encourage them to do it?,What do you think analysis tool USERS (such as microscopists) could/should do to make image analysis better and more successful?  How best could we encourage them to do it?,Any other thoughts?,"Would you be interested in subscribing to a mailing list (announcing workshops, new tools, collaboration opportunities, etc) for EITHER the Center for Open Bioimage Analysis OR Bioimaging North America OR the Royal Microscopical society? If yes, you will be taken to a page to subscribe, if not this form will submit."
5/6/2022 10:19,Yes,Research scientist,Chemistry/Biochemistry,North America,4,5,6,Look up solutions generally on the internet (Google),Most of the time,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Somewhat interested,Not at all interested,Somewhat interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,,,,,,,,2D,,,Word of mouth,,None,Word of mouth,,,,,,,No
5/6/2022 10:19,Yes,Undergraduate/Graduate student,"Statistics/Biostatistics, Deep learning",Europe,5,4,2,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Not at all preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Very interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,2D + time,,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,Conference session on imaging or image analysis,Few,My local microscopy facility,,,,,,,No
5/6/2022 10:20,Yes,Facility director,Cell/Molecular Biology,North America,3,3,3,Look up solutions generally on the internet (Google),Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",2D,2D,3D + time,3D + time,2D,,,,,,,segmentation and tracking,"automatic tracking, decon",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,ABRF,,,,,,Yes
5/6/2022 10:21,Yes,Principal investigator,Cell/Molecular Biology,North America,4,4,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",,2D,2D,,,,,,Basic segmentation esp in cell culture,Poor quality images! Segmenting overlapping cells or cells without clear boundaries or neurons with varying sizes,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,More extensive explanation of software options and resources regarding how to select the best ones for various scenarios,Learn how to apply best practices - too many awful examples in the literature of flawed analysis that's then replicated by other studies.,,Yes
5/6/2022 10:21,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Cell/Molecular Biology, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,6,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Moderately interested,Moderately interested,Not at all interested,Not at all interested,Moderately interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D (large volume),,,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume)",,"Edge detection, thresholding, pairwise distances",Clustering. I still don't trust a single clustering algorithm to be correct.,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Twitter,EMBL AMBA. Interaction with experts.,No,How to be sure you're using the correct tool. What is the underlying algorithm and why is this correct for my particular image analysis problem?,Better/more interactions with users.,"Understand what a traceback is/how to properly describe an issue with the software (don't just say, ""it didn't work"").",There's a lot of overlapping functionality between different open-source bioimage analysis software. Is there a good way to consolidate these by application and make sure the ones available are used/rigorously tested by more people? I feel that the best software is software that has been used by lots of people for a while. This is the only way to get rid of bugs.,No
5/6/2022 10:22,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Medicine, Statistics/Biostatistics",Europe,4,4,4,"Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all interested,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,,2D,,,,,nuceli segmentation,cytoplasmic segmentation,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum",,Few,Postings on image.sc forum or microforum,,,,,,,Yes
5/6/2022 10:24,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science",Europe,7,6,7,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"3D + time, 3D (SPIM/large volume)",3D + time,,,,,,,,,,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Twitter,,,,,,,Yes
5/6/2022 10:31,Yes,Postdoctoral fellow,Developmental Biology,North America,4,3,3,Sit down with a tool I know and start playing with the data,Sometimes,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)","3D (<3000x3000x100), 3D + time",,,,,,,,,3D segmentation/measure/analysis,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Conference session on imaging or image analysis,Few,Postings on image.sc forum or microforum,,i2k2020,build up customized plugin (imageJ or other powerful software),,,,Yes
5/6/2022 10:32,Yes,Facility director,Cell/Molecular Biology,North America,4,6,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",3D + time,,,,,,,"3D (<3000x3000x100), 3D (SPIM/large volume)","Segmentation, object classification, 2D analyses",General purpose (not lightsheet) 3D image registration,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,Workshop/tutorial on imaging or image analysis,Few,Postings on image.sc forum or microforum,,,"More software and plugin development, particularly ImageJ2/ImgLib2 development",,,Less python,Yes
5/6/2022 10:40,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology, Medicine",Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D large volume + time","2D, 2D + time, 3D large volume + time",2D,2D,,,,2D,,finding nuclei,"EM segmentation, whole slide analysis (qupath is great, more models included), multiplexing ",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,"Hands on, demos with practical examples of complex datasets and solutions, ",,,,,,Yes
5/6/2022 10:43,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology, Computer science",Europe,6,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"3D + time, 3D (SPIM/large volume), 3D large volume + time",,"2D + time, 3D (<3000x3000x100)",,,,,,,,segmentation validation practices are still widely lacking,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,"At the I2K conference, the interaction with others is outstanding. This benefits collaboration and use of tools in the long run.",Many biology/medicine focused conferences would benefit from a more analytical presence. ,"I think general image analysis workshops are lacking and sometimes the offers are ""too specific/niche/specialized"" which might be off putting for new attendees.","Personally, I'd suggest more financial and time support for creators to produce step-by-step guides, use cases, videos, webinars etc","Users could contribute to step-by-step guides, use cases, videos, webinars etc, but from a user perspective. Also, it is invaluable to see data analysis workflows applied to new data - so users sharing their data and testing workflows on their data is incredibly useful.",,Yes
5/6/2022 10:57,Yes,Facility staff,Developmental Biology,North America,5,3,7,Look up solutions generally on the internet (Google),Sometimes,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Very preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)",,,3D large volume + time,,,,,,,,,Finding nuclei,Segmenting filamentous structures,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,Workshop/tutorial on imaging or image analysis,Many,Postings on image.sc forum or microforum,,,Image analysis theory,Better tutorials ,,,Yes
5/6/2022 11:10,Yes,Image/data analyst,Cell/Molecular Biology,Europe,6,5,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","3D (<3000x3000x100), 3D + time",,"3D (<3000x3000x100), 3D + time",,2D,,,,,,,well separated objects of non varying intensity ,not well separated objects of varying intensity ,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,NEUBIAS Academy due to the variety of topics covered,ELMI,,,Being asked about the reproducible way of analyzing their images in submitting papers.,,Yes
5/6/2022 11:46,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,3,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Often,Very preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all preferable,Moderately preferable,Not at all preferable,Very interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","3D (<3000x3000x100), 3D + time",,"2D, 3D (<3000x3000x100)",,,2D,,,3D (<3000x3000x100),,,cluster analysis in STORM,denoise in STORM,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Twitter,None,ASCB,comparisons between pieces of software,"Please create better GUI in open-source software. It is still not competitive than commercial ones in this regard. Also optimize for for large data sets,.",,,Yes
5/6/2022 12:08,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science",Europe,6,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,2D,2D,,,,,,,,,,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,"Community event, hands-on hackathon",,,,,,No
5/6/2022 13:18,Yes,Image/data analyst,Cell/Molecular Biology,Europe,7,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",2D,,,,,,,nuclei segmentation,"dense cell segmentation 2D/3D, filament segmentation 3D",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,Simple explanation of the background algorithms,,,Find a common way communicating to users not experienced in programming or algorithms (simple language),Give constructive feedback to the forum and developers,,No
5/6/2022 14:09,Yes,Facility director,"Physics/Biophysics, Cell/Molecular Biology, Computer science, Computer vision",Europe,7,6,7,Sit down with a tool I know and start playing with the data,Most of the time,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,2D + time,"3D (<3000x3000x100), 3D + time, 3D large volume + time",2D + time,2D,,,,,,,,,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,No
5/6/2022 14:33,Yes,Postdoctoral fellow,Cell/Molecular Biology,Europe,5,4,2,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (<3000x3000x100),,3D (<3000x3000x100),,,,,,,molecule detection,time-consuming tasks into train the algorithms,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Email list,no,no,,Softwares based in machine learning  that do not require high programming skills,,,Yes
5/6/2022 15:16,Yes,Undergraduate/Graduate student,"Medicine, Deep learning",North America,6,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,2D,,2D,,,,,,,,,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,Conference session on imaging or image analysis,None,Postings on image.sc forum or microforum,,,,,,,No
5/6/2022 15:22,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",Europe,6,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (SPIM/large volume), 3D large volume + time",,3D (<3000x3000x100),,,,,,,,Segmentation of dense and diversely shaped nuclei,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,,,AI/DL approaches for segmentation,"""idiot-proof"" code/notebooks with over-abundant annotations",Staying up to date with current techniques. Showcasing possibilities and use-cases.,,Yes
5/6/2022 15:33,Yes,Image/data analyst,"Medicine, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,7,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,,,,,cell and nuclei segmentation,,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,Neubias,,,,,,No
5/6/2022 15:37,Yes,Image/data analyst,"Cell/Molecular Biology, Statistics/Biostatistics",Europe,6,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Not at all preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",,,,,"2D, 3D (<3000x3000x100)",,,segmentation of fluorescently-labelled nuclei,segmentation of objects in EM images,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,No
5/6/2022 15:37,Yes,Facility staff,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,7,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",,,,,,,,"Finding nuclei, finding cells","Organelle segmentation, tracking",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,,Better documentation,"Basic image analysis training, understanding of fundamental theory",,No
5/6/2022 15:42,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,2,5,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,2D,2D,,,,,,simple image enhancement; thresholding/segmentation; morphometry/measurement ,creating and training neural networks; 3d and spectral deconvolution; 3D rendering/movie creation; 3D mesh creation,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Postings on image.sc forum or microforum,i2k 2022; online (i.e. accessible without great expense),Developmental Biology conferences,not sure.,Make applications platform agnostic; easy to install on different platforms,learn basic coding in order to be able to adapt existing tools to specific needs,"I see innumerable exciting and interesting looking new tools being developed, but frequently struggle to implement them due to my limited expertise with programming.  And this is as someone who worked in the computer industry for years and is certainly in the top 5% of my colleagues (biologists) with respect to knowledge and comfort with computers (i.e. I'm not afraid of the command line).  So while it's great that someone's developed a python routine to do something useful with images, unless it's wrapped in a nice UI and easily downloaded installer (that works on Macs as well as Windows), it probably won't be used by many people.",Yes
5/6/2022 15:45,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology, Medicine",Asia,4,4,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Moderately interested,Somewhat interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,"2D, 2D + time",3D (<3000x3000x100),"2D, 2D + time","2D, 3D (<3000x3000x100)",,,,,,,Nuclei and foci counting,Cell segmentation ,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,My local microscopy facility,,,,,,,Yes
5/6/2022 15:54,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,4,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,,Finding nuclei/Roi,Biologically relevant coordinate systems allowing comparison between samples. Fast/High throughput robust analysis for non programmers. ,,,,,,,,,,,,,,"Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,"Neubias series, because they are comprehensive and widely accessible on YouTube. Meaning you can rewatch/ find a new one dependent on what expertise you need at any given time ",,,Identify the steps that take the most time in common workflows by wet lab biologists and recursively try to speed then up.,Think about analysis before the imaging happens. Talk to image analysis experts. Cost analysis into their grants,,Yes
5/6/2022 15:55,Yes,Image/data analyst,"Statistics/Biostatistics, Computer science, Deep learning",Europe,7,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D + time, 3D + time","2D + time, 3D large volume + time",2D + time,,,,,,,finding nuclei in 2D,analysis in 3d in general,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Email list,,ECCB (computational biology conference),,,,,Yes
5/6/2022 16:07,Yes,Research scientist,Cell/Molecular Biology,North America,3,4,2,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Not at all preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,"Segmentation, generating (from single images) or working with 5D stacks in python, tracking cells (but these are probably because I don't have time to find the right information online)",,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,"I'm agnostic to how I hear, but I often feel like I only hear about conferences that would've been perfect for me while they're happening or after they're over. Just wish there was one place I could check to see upcoming imaging conferences.","My company had an in-house course that used data generated at the company as examples for the course, with accompanying Jupyter notebooks and I found that very helpful. It was helpful to see the exact type of data I would use (confocal fluorescence microscopy) and how analysis was performed.",,"I'd love intermediate level. Most of the conferences I see are either very basic Fiji/python or full on heavy program development. Right now I'm trying to bridge the gap between those two spaces and finding it quite difficult to find the right resource. Or even a course/seminar on how to move from primarily lab-based to primarily computational and what roles are available.

I'd also love sessions on how to initiate image analysis. You've collected a dataset, how do you decide what to extract from your images. Or which existing script to adapt for your use. What are the best practices the experts in the field use for this?",Provide more information walking through how to use the software instead of just throwing things on github without much documentation.,Think about image analysis and talk with statisticians prior to starting experiments.,,Yes
5/6/2022 16:11,Yes,Facility director,"Physics/Biophysics, Cell/Molecular Biology",Europe,1,1,2,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Not at all preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,,,,Ask asap users for feedback and adapt the tools ,Contact image analysis specialist before doing the experiment ,,No
5/6/2022 16:11,Yes,Principal investigator,Cell/Molecular Biology,North America,4,2,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)",2D,2D,,,,,Gross structural analysis,"Qualitative antibody labelling - i.e., determining whether labelling is more intense in some areas compared to others. Identifying subtle strctural differences between samples. ",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"I learned a lot from the CLMC, probably the best training I've had. I wish i knew more about simple coding but I couldn't keep up with the one session in a conference I attended. ",A lot of labs could benefit from proper microscopy and imaging practice independent of the conference.  ,"How to use tools, very basic coding for beginners (thresholding, simple calculations to increase throughput instead of manual calculations).","Have a forum where users can submit feedback, give better access to training. ",Get training! Attend conferences and workshops. I was able to attend my imaging conferences due to professional development funding from my university and one was free to attend (online). ,No,Yes
5/6/2022 16:13,Yes,Image/data analyst,"Cell/Molecular Biology, Computer vision",North America,7,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,"2D, 2D + time",,,"nucleus segmentation, cell counting, cell segmentation","visualization, 3d annotation, 3d segmentation",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Allen Institute for Cell Science Bioimage Informatics was a good mix of workshops and relevant talks,Biophysical Society,,Include better documentation and focus on improving existing software instead of only creating new software.,We should give analysis tool users guidelines and make it easy for them to organize their data and include experiment and microscope information.,"Adding any guides or standards for developers (e.g., documentation, interaction on image.sc) would be great. ",Yes
5/6/2022 16:20,Yes,Undergraduate/Graduate student,"Computer science, Computer vision, Deep learning",Europe,7,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Moderately interested,Moderately interested,Somewhat interested,Very interested,Somewhat interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,Word of mouth,Workshop/tutorial on imaging or image analysis,None,Email list,Hackathon for tracking. Really great to compare each others methods and approachs on the same datasets. And it's fun. ,,"I am not used to conferences so that might actually be common. I would say some kind of presentation of a particular field, like a review, and then a debate/discussion between experts. ","I'm always interested in visualising the results in a meaningful way. And step by step written examples of how to analyse this or that. Multiple different examples. Most of the time I'm using a new tool, I just want to do something simple and quick, so I don't want to spend hours understanding everything about the software. ",Report their use case.,,Yes
5/6/2022 16:36,Yes,Research scientist,"Computer science, Computer vision",Europe,6,7,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,detecting (not segmenting) nuclei,accurate segmentaion of nuclei + membranes,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/6/2022 16:48,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,4,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Moderately preferable,Very preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,"2D analysis, we seem to hit a hurdle when moving to 3D",Adjusting relative movement of structure of interest within a tissue/cell to take into account movement/morphogenesis/growth of entire tissue,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Word of mouth,EMBO 3D developmental imaging in Oeiras. Take your own sample and have experts help you to optimise the imaging.,n/a,n/a,"Every commecial software (imaris,volocity) that I have used could be 100x more user friendly. It;s also often difficult to adapt one solution to another problem - eg: tool X will find and track nuclei but not Golgi complex. (I understand why this is the case, but not everyone wants to track nuclei!)",Standardised methods sections in papers perhaps? Some journals already have them.,n/a,No
5/6/2022 16:55,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,3,3,3,"Ask on forum.image.sc, Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D + time",,,,,3D (<3000x3000x100),,,nuclei,"Co-incidence, unsupervised track analyses, time based analyse",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Twitter,When detailed and practical enough to imply in running projects. ,"Seeing is believing, gordon conf etc.","Comparisons, highlight software that replaces old packages, ","Have open source software instead of Matlab, have intuitive GUIs or stand alone pakages, have Napari working equally well as installable unit as is cellprofiler.  ","Take more time and effort to get analysis working, it should more commonly known that analyses takes resources",,Yes
5/6/2022 17:01,Yes,Research scientist,Cell/Molecular Biology,Europe,4,3,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D + time, 3D (<3000x3000x100), 3D + time",2D + time,"2D + time, 3D (<3000x3000x100)",,,,,,,"finding nuclei, qunatitative analysis",subcellular structure recognition and tracking,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,,Few,Twitter,,,,,,,Yes
5/6/2022 17:29,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Most of the time,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately interested,Somewhat interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,3D (<3000x3000x100),,,,,,3D (<3000x3000x100),,,Segmentation of cells,Noise reduction ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,"Small tutorials, great overview talks lots of time to meet and chat",,"Comparisons, challenges ","Better tutorials with pictures, explaining terms they use in the software and letting it get tested by users ",Need to think about analysis before running the experiment ,,Yes
5/6/2022 17:29,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,finding and tracking round high snr objects,Tracking of neuron protrusions (segmentation is okish but visualizing changes over time tedious)  ,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,Robert Haase's YouTube course was a great resource to start with!,,,,,,Yes
5/6/2022 18:09,Yes,Principal investigator,"Physics/Biophysics, Medicine, Statistics/Biostatistics, Deep learning",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Very interested,Somewhat interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,,,,"2D, 3D large volume + time",Normal tissue segmentation ,"Super-resolution; transfer learning between modalities (MRI, CT)",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,"MICCAI, ISMRM","RSNA, ASTRO,AACR",Improved DICOM workflows for batch processing,More public deposition of benchmark open-access datasets to use for QA/model calibration by (re)users. ,Improved data descriptors (eg Nature Scientific Data) for describing datasets and open access GitHub code publication.  ,,Yes
5/6/2022 20:18,Yes,Facility staff,"Cell/Molecular Biology, Computer science",North America,5,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",2D,,,,"2D, 3D (<3000x3000x100)",,,Counting dapi-labeled nuclei is generally well solved until your application is particularly hard or your sample prep is bad or your images are dim or etc...,everything about SMLM quantification; segmentation of oddly shaped cells; tracking cells in phase contrast; normalization of staining batch differences; image alignment,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Postings on image.sc forum or microforum,AQLM- in depth explanation of theory; AIM- hands on practice; Neubias- detailed workflows; SciPy- introduction to new libraries I was unfamiliar with,experimental biology- there are booths from vendors but it would be a great place for open-source software to advertise.,,work directly with the intended users (biologists) to see what mistakes are commonly made and what features are commonly wanted. ,"Understand (and teach, when appropriate) how to set up a scope for reproducible analysis; Understand the limitations of an analysis method and what metrics can be reliably measured and reported; think about and test the analysis BEFORE getting very far in image acquisition","I wish journals had stricter reporting standards for microscopy images and analysis methods. Too many papers say ""images were analyzed in ImageJ"" with no further explanation (and no citation for the software).  ",Yes
5/6/2022 20:27,Yes,Facility staff,Cell/Molecular Biology,North America,4,3,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D + time, 3D + time, 3D (SPIM/large volume)","2D + time, 3D + time","2D, 3D (<3000x3000x100)",,,,,,,,"There are good solutions example Cellpose, stardist, ilastik. It’s about time commitment to master the available tools. ",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Postings on image.sc forum or microforum,"I2K, NEUBIAS",EMBL,Start with making people an expert in 2D and then expand upon 3D and time. ,Most are actively engaging users. Examples to learn from are Pete Bankhead (QuPath),,Engage with imaging cores. Let the facility scientists become the voice for your tools. Train them for them to train others. Facility scientists are the folks that see most traffic of users. ,Yes
5/6/2022 21:52,Yes,Research scientist,Developmental Biology,South America,4,4,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,,,,,,,,,"2D, 2D + time",,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,,,,,No
5/6/2022 22:37,Yes,Image/data analyst,"Physics/Biophysics, Cell/Molecular Biology, Computer vision",North America,7,6,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,2D,,,,,,,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Word of mouth, Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Postings on image.sc forum or microforum,,,,,,,No
5/7/2022 0:36,Yes,Research scientist,"Cell/Molecular Biology, Medicine",Europe,4,4,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Moderately interested,Somewhat interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)","2D, 3D (SPIM/large volume)",,,,,,,Nuclear and cellular segmentation and separation in cell culture images,Nuclear and cellular segmentation and separation in tissue sections images,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,,,,,,,Yes
5/7/2022 1:03,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics",Asia,4,3,2,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,,,2D,,,,,,Finding nuclei,Thresholding,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Many,Email list,"C-CAMP, India, image analysis workshop.",Not yet,AI in bioimage analysis,,,,Yes
5/7/2022 2:19,Yes,Principal investigator,"Computer science, Computer vision, Deep learning",Europe,7,6,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,3D (SPIM/large volume),,,,,,,neuron reconstruction in em,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,Mix of talks (for tool discovery) and workshops (how to use tools),,,"Focus on making their software beginner-friendly, funding for UX work",Learn some scripting,,No
5/7/2022 4:03,Yes,Principal investigator,"Physics/Biophysics, Developmental Biology, Medicine, Statistics/Biostatistics, Computer science",Europe,6,7,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time",,,,,,,,,"Segment nuclei and segment cells, counting nuclei/cells","Measurements, visualization of measurements",,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Postings on image.sc forum or microforum,Pete Bankheadsl's online tutorials are great because he explains things super well,NEUBIAS symposium,Data science,"Better tutorials, documentation; easier to use software; intuitive graphical user interfaces","Learn the basics, learn scripting",We need a dictionary to translate between computational and biological terms (e.g. cell segmentation => instance segmentation),No
5/7/2022 4:50,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Computer science, Deep learning",Europe,7,4,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Most of the time,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Very interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 3D (<3000x3000x100)",,,,,,,,,Twitter,Conference dedicated to imaging or image analysis,Some,Twitter,,,,,,,No
5/7/2022 7:58,Yes,Principal investigator,Physics/Biophysics,Europe,5,6,6,Sit down with a tool I know and start playing with the data,Most of the time,Somewhat preferable,Very preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Somewhat interested,Not at all interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,"2D + time, 3D + time",,"2D, 2D + time, 3D + time, 3D large volume + time",,,,,,,,,"Segmentation for standard imaging techniques (DIC and Fluorescence, more so 2D than 3D), particle tracking, ",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Word of mouth,"Sample sessions with pre-built code (collab), small group session with bring your own data",,"Estimating error (computational and experimental) of methods when applied to my own data, discussion of pitfalls, available test data sets, getting started guides","Money. E.g. permanent staff funding for image analysis attached to microscopy cores or HPCs, more mechanisms like Chan Zuckerberg to improve and maintain code, support venues for publication of significant releases (difficult as subsequent release often seen as lacking novelty)","Take better images, which means software tool should describe clearly which data feature are essential, nice to have or not important. Users don't know if e.g. 8 bit or 12 bit matters, if additional noise from gain is a problem, what are reasonable resolutions,...",,Yes
5/7/2022 8:39,Yes,Facility staff,Cell/Molecular Biology,Asia,5,3,3,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Often,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,"2D, 2D + time, 3D (SPIM/large volume)",2D,,,2D,,,,Finding Nuclei,"Tight junctions, cell boundaries, solutions for metadata association for the open source image analysis software with the local storage of the commercial HCI",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Twitter,Ilastik and Cell profiler ,I2K2022,Use of Cellprofiler-Analyst in addition to the cellprofiler database properties,More tutorials for the users,Post the challenges in the forum regularly ,,Yes
5/7/2022 9:29,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Medicine",Europe,2,2,1,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Not at all interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)","2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,Outlining single round cells and detecting tissue outline,Identifying cells over 3D stacks,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,My local microscopy facility,,,,,,,No
5/7/2022 9:34,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,6,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Not at all interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 3D (<3000x3000x100)",,2D,2D,,2D,,,,"Cell counting, gel semi quantitation, AUD analysis ",Multiple marker fluorescence analysis ,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,None,Email list,,,,,,,Yes
5/7/2022 9:53,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Medicine",North America,4,4,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc",Often,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",2D,2D,,,,,,,finding nuclei,finding cells,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter",Conference dedicated to imaging or image analysis,Many,Postings on image.sc forum or microforum,I2K,no,,They should keep in mind that many life scientists are not too comfortable with coding.  ,They should be gently reminded that learning to code is beneficial to their research.,,No
5/7/2022 10:47,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,2,3,3,Ask a friend or colleague to help me,Often,Somewhat preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D + time, 3D (<3000x3000x100)",,,,,3D (SPIM/large volume),,,,,,,,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Email list,,,,,,,No
5/7/2022 11:31,Yes,Facility director,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",North America,5,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Often,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,"2D + time, 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,2D,,,"2D, 2D + time, 3D + time","2D, 2D + time, 3D + time",,finding most structures that are well defined using fluorescent biomarkers,"Segmentation of brightfield, phase contrast and DIC images",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,,,"Comparisons between software, deep learning approaches that are accessible to life scientists with moderate experience with coding;   deep learning approaches that can be made available to users of a core facility",Perhaps publish how to articles?,"Try to grapple with the growing literature in the field; finding reliable pipelines for learning about new developments, encourage more life scientists who use microscopy to incorporate mage analysis approaches in their experimental paradigms. ",,Yes
5/7/2022 12:01,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science, Deep learning",Europe,4,6,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc",Often,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,2D + time,2D + time,2D + time,2D + time,2D + time,2D + time,2D + time,2D + time,Finding nuclei,"Cell Classification, data viz",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/7/2022 12:35,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Deep learning",North America,4,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Not at all preferable,Very preferable,Very preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Somewhat interested,Moderately interested,Not at all interested,Somewhat interested,Very interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,"2D, 2D + time","2D, 2D + time",,"I wish it was easier to get intensity vs time trajectories from movies (drift correction, background identification, segmenting particles, fitting with 2D Gaussians, and sometimes normalizing to an individual fluorophore)",Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,General theory,"Grants/awards/recognition/speaking opportunities. There are a lot of resources available, but I think creators need to be incentivized to make the code user friendly or port their code to a FIJI/ImageJ addon",Users need to provide more feedback. It would be nice if there was a wishlist section on image.sc or other forums where users could request software features and creators can identify which feature they can work on. ,,Yes
5/7/2022 13:35,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,7,4,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time",,,,,,,,,,Biological polymeric structures single filament dynamics analysis (eg cytoskeleton),,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/7/2022 13:56,Yes,Principal investigator,Developmental Biology,North America,7,2,1,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",2D,,3D (SPIM/large volume),,3D (SPIM/large volume),,,,"2D, 3D (<3000x3000x100)",,,,I wish there was a public software to do image segmentation of 3D datasets followed by quantification. Something similar to Imaris,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,Not really,,Imaris vs public software,Can we talk to them?,,,Yes
5/8/2022 12:37,Yes,Facility director,Cell/Molecular Biology,Europe,3,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"3D (<3000x3000x100), 3D + time",,,"3D (<3000x3000x100), 3D (SPIM/large volume)",,,3D (<3000x3000x100),,,Cell & nuclear segmentation,"Super-resolution data, complex 3D structure segmentation & quantification ",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,A discipline-specific society or network,N/a,N/a,Difficult to prioritise as all topics can be useful.,"Everything that overcomes initial barriers for users, such as intuitive GUIs and interactive/video tutorials. ","Make sure the data is of best possible quality, and that the selected analysis approach is appropriate to address a specific question.","Quantitative image analysis needs to be recognised as an integral part of any imaging workflow, essential to unlock new insights into biological processes. With advanced analysis software tools being very time-consuming to learn and to appropriately apply for 'typical' experimental researcher, this calls for support by dedicated image data analysts, e.g. to develop bespoke analysis workflows and data visualisation solutions. Imaging facilities would be ideal to provide this support. However, when operating as SRFs with full cost recovery, funding such positions is almost impossible. In addition, bioinformaticians are highly seeded after in the industry and academic jobs are comparably unattractive. Thus, I fear a lot of potential for better-quality higher-impact research goes to waste. Funders should consider this. ",Yes
5/9/2022 6:49,Yes,Image/data analyst,"Cell/Molecular Biology, Medicine, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",Europe,6,6,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 3D (<3000x3000x100), 3D + time, 3D large volume + time",2D,"2D, 2D + time, 3D + time, 3D large volume + time",,,2D,,,2D,2D,"2D, 3D (<3000x3000x100), 3D + time","finding nuclei, some forms of tracking",all of them,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,"Hands on, reverse engineering of problem, call4help sessions",,"segmentation, counting, tracking",funding for tutorials and online learning,share our data so they have something to test it on,Central organisation as N/EUBIAS would be great to have (again),Yes
5/9/2022 7:09,Yes,Facility director,Cell/Molecular Biology,North America,2,3,3,Sit down with a tool I know and start playing with the data,Never,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/9/2022 8:05,Yes,Facility director,Cell/Molecular Biology,Europe,3,2,3,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Never,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Not at all preferable,Not at all interested,Not at all interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 3D (<3000x3000x100), 3D + time",,2D,2D,,,"2D, 3D (<3000x3000x100)",,,Finding mammalian cell nuclei,"samples with high background or ""noisy"" staining",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,Neubias ones,MMC,specific use of tools or challenging datasets,better users interfaces and better step-by-step sheets,better sample preparation and awarness of data for image aalysis,,Yes
5/9/2022 9:34,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics",Europe,3,4,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Not at all preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time",,"2D, 3D + time",2D,,,,2D,,,Finding nuclei and not complex shapes,Segmenting complex and often not uniform structures (i.e. intestinal villi),,,,,,,,,,,,,,Word of mouth,Workshop/tutorial on imaging or image analysis,Some,Email list,,"NorMIC Biological Optical Microscopy Workshop (BNMI, UiO, NCMM, Oslo)","In depth tutorial with examples of scikit-image, OpenCV, tools and modules available in Python","Relatable terms to end users, as in Find Nuclei, Define Cytoplasm. Not everyone wants to get knee deep into understanding what is going on behind the scenes or knows the names of segmentation/filtering algorithms by heart. Also previews of the different outputs that might come out from a particular pipeline/analysis.","Keep spreading the word, teaching and sharing. Sometimes it feels its is a very niche field where it is difficult to access without prior knowledge (as a degree in Computer Science or Engineering)",,Yes
5/9/2022 10:59,Yes,Facility staff,"Cell/Molecular Biology, Medicine",Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",2D,,,,2D + time,,,"finding nuclei, finding spots, ","segmentation in low SNR or crowded images, spot detection (always can get better, even if it's pretty good), mitochondria segmentation, image filtering/restoration prior to segmentation",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,"NEUBIAS was excellent, and on the practical side, one-to-three days workshops are best at getting to grips with the subject",,"what to use for difficult datasets (for high quality images there are many existing solutions), strategies for data pre-processing for segmentation, training NN for segmentation and communicating between platforms (sending results from one to be used in another)","Have idiot-proof guides and help pages to support beginners in using their tool. If there was proper credit given to a developer for a plugin for example (I mean authorship, clear from the start), it might help.","Have journals request full, comprehensive, reproducible details of how the analysis was done. ",,No
5/9/2022 11:26,Yes,Research scientist,Cell/Molecular Biology,North America,3,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D large volume + time",2D,,,,2D,"2D, 3D (<3000x3000x100)",,,"Deconvolution, single-molecule localization",Segmentation of noisy 3D data; Tracking of fast-moving cells in 3D when the time interval is suboptimal; Handling large 3D+time SPIM datasets that have been compressed without needing to decompress the data being analyzed first (so that you can easily feed them to a standard gaming-grade GPU without ridiculous amounts of RAM),,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,LSFM workshop at MBL,,"How to use python to process large volume imaging data (e.g. segmentation, tracking)",Improve utilization of CPU multithreading and GPU wherever possible!,Make backups...,,No
5/9/2022 11:40,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,3,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,3D (SPIM/large volume),,,"2D, 3D (<3000x3000x100)",,,"Nuclei tracking, cell border segmentation, filopodia segmentation, organelle segmentation",Organelle tracking (especially organelles that undergo fission/fusion like mitochondria or are highly dynamic like ER).  ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,I2K 2021 - lots of really solid tutorials and a wide enough selection of topics that I could choose tutorials that were relevant to me,ascb could use more image analysis sessions,"I would love to see more theory on how to solve a particular problem with different software.  So, less like ""this is how you segment endosomes in ilastik,"" and more like: ""here are some concepts to bear in mind when trying to segment endosomes, and here are five different workflows in different programs to do it."" That way I can develop an idea of the strengths and weakness of various approaches (and not simply use the method that I was taught because it's the only think I know).","Make it AS EASY AS POSSIBLE to download/use.  I can't tell you the number of cell biologists I know who have shunned amazing computational tools because they couldn't figure out how to even get the program to open on their computer.  It's so frustrating.  If you need to go onto github to download it and the instructions are even remotely complicated, you have just lost a huge fraction of your potential audience.  Once the obstacle to use is lowered, people will invest time.  Also, youtube tutorials from creators would be great. These can show off different features of the tool.  ","Users can also make tutorials! Whether video or written, tutorials from users with very specific use cases would be amazing. I learned Blender by watching endless youtube videos of people modeling chairs, or cars, or (of course) donuts.","A huge number of cell biologists feel like they are too busy to learn new computational tools.  However, most of them are comfortable with ImageJ/Fiji.  If you make it an easy plugin in Fiji, people will use it.  If they need to download the latest version of python, chances are a big chunk of them will stick with the worse but easier to run existing solution.",Yes
5/9/2022 12:29,Yes,Research scientist,"Physics/Biophysics, Developmental Biology, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,5,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Moderately preferable,Moderately preferable,Somewhat interested,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",,,,,"2D, 3D (<3000x3000x100)",,Most basic cell and tissue segmentation problems where contrast is high,"Low contrast segmentation, most kinds of classification, segmentation of complex cell shapes or dense cell clusters. Time series analysis",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,Focus on tools and hands-on workshops that let me get started processing real data quickly,,Overviews of particular tools and in-depth explanations of image processing workflows are the most useful tutorials,"Tools need to have user friendly interfaces for non-coding scientists, but should also have hackable APIs/macro languages/scripting interfaces so that coding scientists can extend them. Best practices around separating processing workflow from UI elements should be encouraged. Easy interfaces to standard scripting languages should be promoted more heavily","Microscopists should develop image analysis plans BEFORE acquiring images, so that the entire acquisition to data analysis pipeline can be properly designed. Easier and more seamless interaction between acquisition software, QC/QA tools, and analysis tools would encourage this workflow. Demanding microscope manufacturers use standard, open source image and metadata formats would make this process easier. Collecting best-of-breed processing tools under standard interfaces (Fiji, Napari, etc) so that microscopists have a one-stop-shop for their analysis would also help",,Yes
5/9/2022 12:32,Yes,Postdoctoral fellow,Physics/Biophysics,Asia,4,6,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,"2D, 2D + time, 3D + time, 3D (large volume), 3D large volume + time",,"Localize spots, find spots, low frequency background removal",3D nuclei or cellular segmentation ,Twitter,Workshop/tutorial on imaging or image analysis,Few,Word of mouth,,,Python and napari ,"Test data, examples, step by step guide","Follow a simple checklist of ""things to do or check""","We need checklists for image analysis pipelines (like list out metadata and parameters, don't just say you used a package)",No
5/9/2022 14:47,Yes,Image/data analyst,"Physics/Biophysics, Cell/Molecular Biology",North America,4,4,4,Look up solutions in the scientific literature,Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Not at all preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all interested,Not at all interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",3D + time,3D + time,3D + time,3D + time,3D + time,2D,2D,2D,3D + time,3D (<3000x3000x100),,?,?,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Twitter,,,,,,,Yes
5/9/2022 15:24,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",,2D,,,,,,,,allowing overlapping objects in segmentation,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,napari ,"easier automation in fiji, e.g. a plugin that applies a workflow on a folder, similar to cellprofiler",,,No
5/9/2022 15:37,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,7,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",,,,2D,,,,"Segmentation of fluorescent images, morphological analysis of segmented images","Motion tracking, brightfield imaging analysis",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,,None,Email list,,I think most large life science or medicine conferences could benefit from a session on tools and image processing - it can be tricky to get tools into the hands of the people that would benefit most,More topics on best practices for development would be useful to me,"I see a need for more standalone tools, especially in medicine-adjacent fields - I design tools for clinicians who have no hope of learning any kind of scripting but whose work could really benefit from more quantitative analysis. I also see a need for tools that give interpretable metrics related to a specific experiment workflow - e.g., I design hematology tools, so adaptations of computer vision that calculate blood flow velocity profiles. I think a major component of developing standalone tools is something that's interactive - perhaps workshops on designing a successful user interface experience would be useful?","I wish there was a better ""practical knowledge"" guide I could hand to the experimentalists and clinicians who collect data I'm tasked with analyzing - topics like avoiding overlap in events you'd like to quantifying (cell density), adjusting microscope settings so that no pixel values equal 255, choosing appropriate image resolution, and reducing noise and background in images. In my own work, I'm trying to include a ""tips and tricks from the developers"" sort of guide. I also think that we as developers should encourage reaching out for help - image.sc is great for this. I've helped researchers who have already taken months of poor-quality data by the time they get to me, and it would have been easier to help them if I could have guided them to take high-quality images first.",Thanks for holding this conference! I've learned a lot.,Yes
5/9/2022 15:41,Yes,Facility staff,"Cell/Molecular Biology, Computer science",North America,6,5,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)","2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time","2D, 2D + time","3D (<3000x3000x100), 3D large volume + time",,,,,,,,,,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,,,,,,,Yes
5/9/2022 16:04,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,3,5,4,Sit down with a tool I know and start playing with the data,Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D + time,,,,,,,,,,colocalization,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/9/2022 17:30,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Developmental Biology, Statistics/Biostatistics, Computer vision",Europe,5,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,3D + time,,3D + time,,,,,,,,,,,,,,,,,,,,,,,Twitter,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,,,,,Yes
5/9/2022 17:37,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology, Computer science, Computer vision, Deep learning",Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Sometimes,Not at all preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Not at all interested,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,Denoising ,EM segmentation in a streamlined way,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,Lowering learning floor,Yes,,Jupyter notebooks and horrible to install plugins and github links are not appropriate for general audiences. That's why software that works out of the box from companies hasn't died yet. ,Users making tools and leaving them unsupported. See trakEM2 for example. ,"Jupyter notebooks are closer to what can work for general audiences. Needs some more streamlining.

Boo for Fiji, image.sc is not friendly for non coders and not interactive, should be more like discord",Yes
5/9/2022 17:55,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",North America,4,3,5,Look up solutions generally on the internet (Google),Never,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",2D,,"2D + time, 3D + time",,,,,,,,,Cell segmentation (single cells in culture),"Segmenting cells in a tissue in 3D, quantifying changes in fluorescent intensity on a 3D cell surface ",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,My local microscopy facility,Imaris online workshops. They show every step using the software and it’s easy to try the things yourself.,,How to use a certain tool for a certain experiment.,Collaborate with scientists and imaging core facilities directly to help developing tools where they are needed. ,Learn about image analysis prior planning an experiment and acquiring data. Encourage by entry level workshops.,,No
5/9/2022 23:01,Yes,Research scientist,Cell/Molecular Biology,South America,4,4,3,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 3D (<3000x3000x100)",,,,,,,,,2D,3D,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"I2K2020 was amazing, and helpful in every way! It was awesome to participate in different tutorials and to be able to view the recordings available for everyone",,tutorials on new tools are always helpful,"Tools that only work for a publication won't be used further, tools should be easy to find, friendly to use and to tweak for the user's own problem. Written tutorials in detail or links to video tutorials are very useful. Including common errors and how to avoid them is very helpful too. These tools should be well cited to encourage creators to do all this work for the users.","sharing their problems and solutions in image.sc forum could be very helpful for other users. users can share their image analysis workflow as a macro from imagej or describe it in detail, with correct citations to creators whenever created tools are used.",,Yes
5/10/2022 2:43,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Asia,5,5,3,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,2D,,,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,Email list,Yes Ihave attended one last year conducted by JNCASR Bangaluru India . workshop conducted by them was benificial,No,how to analyze organelle shape and size from a confocal image using image analysis software.,by providing detail pipeline and ease to use those pipeline can make any analysis tool more better,by sharing pipeline which can help novice user in this field,,Yes
5/10/2022 2:59,Yes,Principal investigator,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,6,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Often,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately interested,Somewhat interested,Moderately interested,Not at all interested,Moderately interested,Very interested,Not at all interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,"Finding nuclei, identifying isolated objects",Complex time tracking problems e.g. mitochondrial transport,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,My local microscopy facility,ESRIC super resolution school - immersive experience with high quality technical lectures combined with hands on experience ,BSCB spring meeting ,Comparisons / different routes to solving similar problems.,The best analysis is achieved when image acquisition and analysis technique are optimised together in an iterative process. You need to stop students going off and acquiring a tonne of data before they’ve thought how to analyse it. Lost count of the number of times I’ve been presented with large data sets and asked how to analyse it - it’s already too late for anything other than manual tracking at that point.,Get them to think about analysis sooner,,Yes
5/10/2022 5:36,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,2,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Not at all interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,2D + time,,,,,,,,,finding nuclei,tracking motile small things that cross over (such as organelles etc),,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,,,,step-by-step how-to guide that has been proof-read by non-specialist,helpful checklist of simple best practise that is not too onerous?,,Yes
5/10/2022 9:36,Yes,Image/data analyst,Cell/Molecular Biology,Europe,6,5,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",2D,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Postings on image.sc forum or microforum,ABRF ,"ELMI can be pretty variable when it comes to image analysis, I think they should have separate analysis and data management sessions (often combined currently)","Napari (and other Python offerings), QuPath",Fund them properly (and long term!) to allow for stuff like writing documentation and being available for help ,Learn how to report bugs/errors and how to ask for help,,No
5/10/2022 15:51,Yes,Facility director,Cell/Molecular Biology,North America,3,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 3D (<3000x3000x100)",2D,2D,,,,,,,"finding nuclei, puncta detection",cell boundaries for confluent samples,,,,,,,,,,,,,,"Twitter, BINA","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,"neubias youtube series - i could watch, pause, rewatch, etc as necessary and they went in depth on topics",ABRF,"how to choose which open source software(s) to use, i.e. pros and cons of each","user friendly documentation. Because many users are NOT programmers, some documentation does not really explain what the tools do well.",consider image analysis BEFORE collecting data. Grad school programs should emphasize the importance of discussing experimental design with experts such as core facility personnel PRIOR to attempting any experiments at the bench,Thank you for all you do. You are appreciated.,Yes
5/10/2022 15:57,Yes,Image/data analyst,"Cell/Molecular Biology, Computer science",North America,6,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,Image visualization in 2D and 3D,"The ability to find the tools that already exist more easily, lots of solutions exist but they can be hard to find if you aren't connected to the bio imaging community.",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,,None,My local microscopy facility,,,"Generalist tutorials on segmentation - a wide overview of the many tools and techniques, from classical non-ML approaches to the deep learning approaches, would be immensely valuable to many people who are beginners.","We need a better central repository of the catalog of imaging tools. Ideally prominently connected to the GUIs of ImageJ and Napari. More like an ""App Store"" for the various tools, with good searchability and filtering to find exactly the tools you want. Also, documentation is key.
","Seek out help from the imaging community on the image.sc forums, (but they first have to discover the forums!)",,Yes
5/10/2022 23:21,Yes,Undergraduate/Graduate student,Physics/Biophysics,North America,4,4,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,Localization microscopy imaging,3D reconstruction,Colleague,Conference session on imaging or image analysis,Few,Email list,Some sessions of Focus on Microscopy Conference,Focus on Microscopy Conference,How to use a certian tool for a certain kind of experiment,Know more precise about the needs from users and fix the bug promptly,Try some experiments on their own after learning about an analysis tool,No,No
5/11/2022 0:02,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Medicine, Computer science",North America,4,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Often,Somewhat preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",2D,2D,2D,,,2D,,,"Many 2D problems, especially in cultured eukaryotic cells or monotypic tissue types. Colocalization of two signals.",Anything dealing with microbes (cell diameters ~ 1um). Complex tissue types. Bacterial biofilms. Microscopy flow cells. Cell tracking (esp. In 3D). Anything analysis with more than 4 fluors. Any analysis with an ML training component. Easy transitions between aquisition and analysis software. Image database management. Portable image metadata. Reliable metadata management. ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,"I2K (practical, reliable, cutting edge).",Pretty much all of them 🙃,Managing image data for scientific reproducibility. Designing image analysis pipelines. How to deal with giant data datasets in the age of high throughout/semi-automated imaging. Why No One is Willing to Fix the UI/UX problems in imageJ. Why you should stop trying to do image analysis on a crappy laptop screen. Deconvolution for Those Who Don't (Apparently) believe in Math.,"Be scientists. Lacking that, spend a couple days a month for a year trying to deal with the mess that is imaging data and the wonky tools we have to deal with them.","Image analysis has changed. It's not going to be ""try a few things in ImageJ and slap a cool looking LUT on it"" any more. ML-based training and ID is the future: get used to it.

Teach microscopist how to code. At least a little.",Great study. Thanks for doing it.,Yes
5/11/2022 2:31,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,2,2,6,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Very preferable,Very interested,Very interested,Very interested,Not at all interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,Automatic selection of filamentous structures within cells. Generally analysis of structures that are not roundish blobs.,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,Does Robert Haases bioimaging intro course count? If yes - the amalgamation of theory and immediate hands on  experience. Also Robert and his collegues make the environment of the course very welcoming and safe for asking questions.,I think every conference could benefit from showcasing image analysis methods related go the conference topic.,,,,,Yes
5/16/2022 11:22,Yes,Research scientist,Computer science,Europe,6,2,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all interested,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,,,,,,,2D,,segmentation ,counting ,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,,,,,,,,Yes
5/16/2022 11:25,Yes,Undergraduate/Graduate student,Physics/Biophysics,Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Very preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Very interested,Very interested,Moderately interested,Somewhat interested,Not at all interested,Somewhat interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,2D,3D + time,3D + time,,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,Few,Twitter,,,,,,,No
5/16/2022 11:33,Yes,Facility staff,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science",Europe,4,5,5,Sit down with a tool I know and start playing with the data,Often,Moderately preferable,Very preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,2D,,,"2D, 2D + time",,none that work across all datasets,tracking of objects within objects in multichannel 3d timeseries,,,,,,,,,,,,,,RMS,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,Neubias.  Very hands-on with a good teacher: pupil ratio,no,deep learning implementation in analysis pipelines using something that actually works on hardware available to general users ,robust segmentation and easy ways of testing/ visualising while writing analysis scripts,educate them in terms of expectations based on signal to noise and resolution of their data- plan image capture and tlak to analysts BEFORE imaging,,No
5/16/2022 11:39,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,3,3,1,Sit down with a tool I know and start playing with the data,Never,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Somewhat preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,,,,finding nuclei,tissue analysis and cell tracking,,,,,,,,,,,,,,Email list,Conference session on imaging or image analysis,Few,Email list,,,"specific pipelines to solve specific problems, especially for 3D segmentation",,,,Yes
5/16/2022 11:41,Yes,Facility director,Cell/Molecular Biology,North America,1,3,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,2D + time,3D (SPIM/large volume),"2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,"2D + time, 3D (<3000x3000x100)","2D, 3D + time",,"Counting cellls, mean fluorescence intensity, distance between 2 spots","lineage tracing, segmentation in dense monolayers, spectral  unmixing, high content imaging in conditions were there are drastic changes (ie fluorescent signal changes, cell death, morphological changes), ",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Word of mouth,,,,better guis ,,,Yes
5/16/2022 11:42,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,2,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Not at all preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,2D,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,deconvolution,"finding nuclei, cell tracking",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,"i2k; great combination of talks, workshops and time to ask questions",any life science conference,"deep learning, scripting",open-access,reproducibility,,Yes
5/16/2022 11:43,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,3,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Not at all preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,2D,,2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"segmenting cells in 2D fixed images, counting objects etc",anything live and in 3D!,,,,,,,,,,,,,,"A discipline-specific society or network, Email list",Conference session on imaging or image analysis,Few,Email list,,,How to use current tools for live cell data - segmentation of objects and analysis of intensities over time etc,"Often the image analyssi papers are rpetty hadrcore and teh code can be challenging to use for non-experts - would be super helpful if these could be made more accessible, recognising that you should not need to be a coding expert to use these tools!",,,Yes
5/16/2022 11:49,Yes,Facility staff,Cell/Molecular Biology,North America,5,5,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",2D,"2D, 2D + time, 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,"2D, 2D + time","2D, 2D + time",,Simple segmentation counting things is cell profiler is easy to show people an get off the ground,3d analysis and large data sets,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,AIM at Berkeley,i don't know,"I need to learn python so I can use napari, ",,"I think getting basic tools out there like cell profiler has been helpful, when I show people it and get them started it seems to help open new avenues for people. ",I think also just getting people to realize that images are data is a big challenge. and there is always just the challenge of stopping people from making their images small jpgs (shudder -.-) and getting them to realize how the destroy their data.,Yes
5/16/2022 11:54,Yes,Principal investigator,Cell/Molecular Biology,North America,4,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time","3D (<3000x3000x100), 3D + time",,,,3D (<3000x3000x100),,,,,,,,,,,,,,,,,,,Email list,,None,Email list,,,,,,,No
5/16/2022 12:00,Yes,Postdoctoral fellow,Physics/Biophysics,Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Often,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D + time",,,,,,"2D, 2D + time",,,finding nuclei and particle size in a sparse sample,Keratinocytes segmentation,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,Clearliness and practical examples,Focus on Microscopy,Deep learning and artificial intelligence,,,,Yes
5/16/2022 12:05,Yes,Undergraduate/Graduate student,Computer science,Europe,7,7,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Often,Moderately preferable,Very preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Very preferable,Very preferable,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,well-separated non-overlapping objects,"low contrast images, clusters, complex overlaps (e.g. fungal hyphae)",,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,NEUBIAS about the communication between experimentalists and image analysts,,"data management (!), properties of a ""good"" image for analysis, limitations of image analysis, limitations of deep learning, overview of tools AND how they relate to each other",share functions between software to minimize switching environments,"closely collaborate with image analysts (for example discuss preliminary results ), so situations can be avoided where images are generated that are insufficient to analyze. learn about the image analysis tools and processes (sessions with image analysts) to gain an understanding of the available tools",,No
5/16/2022 12:05,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology",Europe,4,5,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Moderately preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Not at all interested,Very interested,Moderately interested,Not at all interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,3D (<3000x3000x100),,2D,2D,,,,,,"Nuclei segmentation seems to be well-solved... but even for that, finding the right tool is not so easy, the vastness of the field (and the high number of solutions) is confusing.",Segmenting cells ,,,,,,,,,,,,,,Email list,Conference dedicated to imaging or image analysis,Few,Email list,"EMBO course on plant imaging; highly beneficial because good ration of theory/hands-on, and personalized advice on our specific issues. Also liked ELMI meetings in which there was a session to teach ImageJ macro writing for total beginners, this was really helpful.",,,One thing that is difficult for users is to navigate the vastness of this field. It would be great to have a place where one could look and see which tools are available for each problem and what are the specifics/advantages/drawbacks of each tool.,,,No
5/16/2022 12:09,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,2,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D + time,"3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100), 3D + time",2D,2D,,,,,,,,,,,,,,,,,,,,,Email list,Conference session on imaging or image analysis,Few,Email list,,,,,,,Yes
5/16/2022 12:13,Yes,Clinician,Medicine,Europe,6,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Very preferable,Very preferable,Not at all preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,,,,,,,finding nuclei,,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Twitter,,,,,,,No
5/16/2022 12:14,Yes,Postdoctoral fellow,"Physics/Biophysics, Computer science, Computer vision, Deep learning",Europe,4,6,7,Sit down with a tool I know and start playing with the data,Most of the time,Not at all preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)","2D + time, 3D + time, 3D (SPIM/large volume)",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",2D,"2D, 3D + time",2D,2D,2D,"2D, 3D (<3000x3000x100)",2D,,,,,,,,,,,,,,,,,"Word of mouth, Postings on image.sc forum or microforum","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,,"FOM, ELMI",,,,,Yes
5/16/2022 12:22,Yes,Facility director,Cell/Molecular Biology,Europe,4,3,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,,,,,"2D, 2D + time, 3D + time",,finding nuclei,"specific object segmentation, denoising, deconvolution",,,,,,,,,,,,,,"Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"NeuBias, ",,Machine learning training,,,,Yes
5/16/2022 12:28,Yes,Principal investigator,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics",North America,4,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,3D + time,,2D,,,,,,3D + time,Finding nuclei,"Extracting quantitative descriptors from highly multidimensional data (X,Y,Z,t,lambda)",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Email list,"Janelia (several years ago), some of the subevents at Photonics West",,,,,,Yes
5/16/2022 12:29,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,2,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D,2D,3D large volume + time,3D + time,2D,2D,,,2D,3D + time,,Tissues background,improve SNR,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,None,A discipline-specific society or network,"SAPOM congress, RMS courses",I don't know now,"Tutorials about how to use Fiji plugins, Icy or video tutorials",Being in touch with users could be helpful,Maybe creating a basic package tool to learn in courses,,Yes
5/16/2022 12:37,Yes,Principal investigator,Physics/Biophysics,Europe,4,5,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time","2D, 2D + time","2D, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time","2D, 2D + time",,,segmentation,Correlative microscopy/data atlas- matching datasets across techniques,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,"APT&M, MTEX workshop",,,,,,Yes
5/16/2022 12:42,Yes,Facility staff,"Physics/Biophysics, Computer science, Computer vision",North America,5,6,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",3D (SPIM/large volume),2D,,,,,,"nuclei segmentation, intensity analysis that follows.","Tissue analysis, colocalization analysis",,,,,,,,,,,,,,Email list,Conference dedicated to imaging or image analysis,Few,Email list,"I2K 2020 from Jenelia. This introduced me to a number of image analysis tools that helped me at my job, where we have users from different departments requiring varied solutions for their projects. ",EMBL course on Super-resolution (STED). It would have been helpful if they had a session dedicated to image analysis/ deconvolution. ,Deep-learning based solutions,"Sharing the code (open source), conducting workshops/ courses.",reporting the image analysis workflow in a descriptive way. ,,Yes
5/16/2022 12:43,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,5,4,4,Look up solutions generally on the internet (Google),Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time",,,3D (SPIM/large volume),,,,,,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,,,,,,,No
5/16/2022 12:47,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",North America,3,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,2D,,,,,,,,,,,,,,,,,,,,,BINA,,Few,Email list,,,,,,,Yes
5/16/2022 12:50,Yes,Facility director,Physics/Biophysics,Europe,3,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Other commercial software (Avizo, Imaris, Volocity, etc)",2D,"2D + time, 3D (<3000x3000x100)","2D, 2D + time",2D,,"3D (<3000x3000x100), 3D (large volume), 3D large volume + time",,,2D + time,"segmenting particles, spectroscopic analysis, 3d recons",handling large datasets/automation,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,A discipline-specific society or network,"John C. Russ workshop many years ago, also commercial Image Ro Plus course provided at my lab.","Most I attend (e.g MMC, SEMT, TOSCA, etc. seem to have a selection of workshops and sessions related to Image Analysis",advanced segmentation and automation functions.,Adopt common language for I.A. processes. ,"Attend courses, workshops and conference sessions.",,No
5/16/2022 12:56,Yes,Facility director,Cell/Molecular Biology,Europe,2,4,2,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",2D + time,"2D, 3D (<3000x3000x100)",,,,,,,"puncta analysis, nuclei analysis, filament tracing","spine analysis, colocalisation analysis",,,,,,,,,,,,,,"A discipline-specific society or network, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,"Yes. I think it is very helpful to provide a data set and time so peaple can apply what is being explained. Also, recording of the sessions are very useful to come back later on.",,Different approaches to perform the same analysis (pros and cons).,To make analysis more intuitive and properly documented. ,,,Yes
5/16/2022 13:04,Yes,Image/data analyst,"Computer science, Computer vision",Europe,6,6,5,Sit down with a tool I know and start playing with the data,Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very interested,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,2D + time,3D + time,3D + time,2D,"3D (<3000x3000x100), 3D large volume + time",,,,,,,,,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,A discipline-specific society or network,,,,,,,No
5/16/2022 13:05,Yes,Facility staff,Cell/Molecular Biology,Europe,2,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Not at all preferable,Very preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100)",,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,Email list,Conference session on imaging or image analysis,,,,,,,,,No
5/16/2022 13:18,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",Europe,4,3,3,Ask a friend or colleague to help me,Sometimes,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,finding nuclei and other fluorescent labelled organelles,Not sure,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,FiJi workshop ,No,How to use certain tools,Good idea - not sure how to encourage it - find funding....,More video tutorials with specific tasks,,Yes
5/16/2022 13:20,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",Europe,4,3,3,Ask a friend or colleague to help me,Never,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,2D,,,"2D, 3D (<3000x3000x100), 3D large volume + time",,,,,,Nuclei detection /high contrast tissue selection,Tissue selection based on substructure rather than gray values /borders,,,,,,,,,,,,,,Email list,Conference session on imaging or image analysis,Some,Email list,,,,These complex processes have to be explained well with examples and tutorials on relevant specimen (not an ideal specimen),"Share knowledge, not just with early career scientist. If the PIs don’t unterstand it they can’t advise, criticise or integrate into projects ","I have first hand experienced that anything more advanced than a post doc is not accepted to image analysis workshops. In addition, basic coding experience is required. That excludes most junior group leaders and older PIs. That means their labs are naturally not using advanced techniques.",Yes
5/16/2022 13:31,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,4,6,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,"2D, 3D (<3000x3000x100)",,,,"2D, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/16/2022 13:45,Yes,Facility staff,"Cell/Molecular Biology, Computer vision",North America,5,4,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",2D,,,,,,,nuclei segmentation,cytoplasm segmentation and watershed seperation,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,I2K,NEUBIAS type conferences,teaching Python/Napari based scripting,foster a more interdisciplinary network between developers and biologist and microscopists  to help them 'speak the same language',foster a more interdisciplinary network between developers and biologist and microscopists  to help them 'speak the same language',Core facilities need to act as nodes to facilitate communication between biologists and developers ,Yes
5/16/2022 13:46,Yes,Facility staff,Cell/Molecular Biology,North America,2,6,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)",,,,,,"2D, 3D (<3000x3000x100)",,,Segmentation,Colocalization,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,"The ABRF segmentation online workshop held recently following their reproducibility survey. We submitted our segmentation strategies and results, then attended the workshop and had two sessions with breakout rooms so we could see representatives of different image analysis software companies demonstrate the same exercises with their software. This allowed beginners to try and solve it ourselves, then see how the experts did it, and we could do so for multiple platforms. Recordings were also uploaded to youtube so we could see full workflows for the same problems on multiple platforms (5 I think). As a beginner who works in a core and is helping users with their own acquisition this was very helpful as it gives beginners a solid grounding for image analysis workflows and the differences between analysis platforms.",,,,,,No
5/16/2022 14:12,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,4,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Email list,hands on experiences with scopes/ image analysis software with local expert support and training.,,,Better integration of lossless image compression tools to allow for opening and storage of massive images on relatively light software. ,,,No
5/16/2022 14:17,Yes,Undergraduate/Graduate student,Chemistry/Biochemistry,Asia,6,4,1,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Not at all preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","2D, 2D + time, 3D + time",,"2D, 2D + time, 3D + time",,,,,,"2D, 2D + time, 3D + time",,,Finding nuclei,"analysis of super-resolution data, basic cell intensity and shape measurement analysis",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,Twitter,None,none,"overview of tool for complete beginner, step-by-step use of the software regarding image analysis from
basic to advance analysis. Include cell count, flourescence intensity measurement, cell shape, organelle shape ( like mitochondria in my case!), etc Tutorial with example taking an image and doing the analysis! 
'Help' could be more in layman language when introducing the functions of the software.","step by step image analysis tutorial with basic to advance analysis
'Help' section could be more in layman language when introducing the functions of the software.","Make the tool easy to understand and fun to use! 
direct working email contact for queries",,Yes
5/16/2022 14:17,Yes,Facility staff,"Cell/Molecular Biology, Computer science",North America,3,6,6,Sit down with a tool I know and start playing with the data,Most of the time,Moderately preferable,Moderately preferable,Not at all preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",2D,"2D, 3D (<3000x3000x100)",,,2D,2D,2D,"very little is ""generally"" solved",identifying cells in tissues and reporting intensities of multiple channels,,,,,,,,,,,,,,supervisor said to do it,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"Many years ago, training in John Russ's course",ASCB/EMBO meeting,people need to learn how to take data properly and save it properly for analysis and learn it is a give and take between imaging and analysis,"Stop making so many new tools.  Everybody seems to think their tool is better than everybody else's.  For instance, I've played with Napair and it's not better; it's just distracting from tools like ImageJ.",What should happen is that they learned to be more computer savvy.  It's not going to happen.,"if it cannot be installed by a computer illiterate person, then it's not a friendly tool for biologists.  If more than one thing has to be downloaded from github, forget about it. ",Yes
5/16/2022 14:45,Yes,Image/data analyst,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics, Computer science",North America,7,7,7,Sit down with a tool I know and start playing with the data,Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D,"2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,nuclei counting is well solved. ,membrane segmentation is poorly solved,,,,,,,,,,,,,,"Postings on image.sc forum or microforum, A discipline-specific society or network","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,No
5/16/2022 14:45,Yes,Facility director,"Physics/Biophysics, Computer science",North America,2,6,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,"2D, 3D (<3000x3000x100)",finding nuclei,tissue analysis,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,ABRF,Automated image analysis,,,,Yes
5/16/2022 14:46,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Computer science",North America,5,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,"2D, 3D (<3000x3000x100), 3D + time",2D,,2D,,,"2D, 2D + time",,"Tissue detection, Nuclei detection within defined image types/cell types (multinucleated macrophages don't count)","Cell border estimation, overlapping cell within a Z plane deconvolution, compression for large images",,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,"QuPath workshops, LSFM2020, I2K2020,2022. Access to expertise, access to multiple types of software and collected data to compare and contrast software capabilities *when there are experts for each software available*. ",,"A waterfall /workflow of recommendations for analysis tools, starting from particular imaging modalities.","Emphasize inputs and outputs. What data types go in? What modalities are recommended? What formats can you handle, and what formats can be output. What other software can you link up with.","Read about the basics of image analysis, Pete Bankheads interactive bioimage analysis handbook. Maybe a list of common pitfalls per image analysis general type.",,No
5/16/2022 15:00,Yes,Facility staff,Cell/Molecular Biology,North America,6,5,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",2D,"2D, 3D (<3000x3000x100)",,,,,,Nuclei segmentation and analysis,Python-based software with GUIs for people with no coding experience,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,I2K 2022. I learned about new software and solutions.,I2K 2022 - more training sessions for beginners,"napari, cellfinder, cellpose",More GUIs and less coding/scripting for beginners,"Tell us what problems need solving, what questions they have, what they want to accomplish",,Yes
5/16/2022 15:07,Yes,Research scientist,"Physics/Biophysics, Cell/Molecular Biology",Europe,4,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D + time",,,,,,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/16/2022 15:12,Yes,Research scientist,Cell/Molecular Biology,North America,4,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Not at all preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,"2D, 2D + time, 3D + time","2D, 2D + time, 3D + time",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,automated segmentation of fluorescence imaging,automated segmentation of 2D electron microscopy images,,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,MIcroscopy and Microanalysis; vEM; Women in Microscopy,Microscopy and Microanalysis,how to get started with using scripts/macros in FIJI and other open source software for non-coding people,make it more user friendly/packaged for non-coding people (microscopists only),discuss best practices and standardization more,,Yes
5/16/2022 15:16,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,4,6,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,"2D, 2D + time",,,background subtraction and automated cell counting/sorting,,,,,,,,,,,,,,"Email list, From Dr. Cimini's post on the Confocal Microscopy list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,No
5/16/2022 15:24,Yes,Facility director,"Physics/Biophysics, Chemistry/Biochemistry",North America,1,1,2,"Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Not at all interested,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,None,None,,,3D (<3000x3000x100),,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,Email list,,Few,Email list,,,"aligning SEM images to create 3D volume, how to segment cells or organelles in 2D and 3D",,,,Yes
5/16/2022 15:44,Yes,Postdoctoral fellow,Cell/Molecular Biology,Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",2D + time,2D,2D,,,,,,Finding nuclei,Cell segmentation from brightfield images ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,"Yes, deep learning methods","Yes, RNA imaging and analysis",,,,,Yes
5/16/2022 16:05,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",Europe,4,6,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately interested,Somewhat interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D + time, 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D + time, 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,"nuclei segmentation, particle tracking",3D deconvolution,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,My local microscopy facility,workshops at the LSFM conference for light sheet data,,Deep learning,"Better documentation, GUIs with intuitive design ","More dialogue, post answers and short blogposts/forum postings on new challenges/techniques",,Yes
5/16/2022 18:46,Yes,Image/data analyst,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics, Computer science",Europe,6,6,6,Sit down with a tool I know and start playing with the data,Most of the time,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,"2D, 2D + time",fluo quantifications,segmentations,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,"yes, thanks to enhanced interactivity",yes,focus on new tools and new approaches,gui is the key,understanding fundamental principles first, ,No
5/16/2022 19:28,Yes,Principal investigator,Cell/Molecular Biology,North America,5,1,1,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,,,2D,,,,"Segmentation, measuring signal intensity","Identifying cells positive for multiple factors, identifying inter-cell and spatial relationships",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,"CellProfiler workshops, QuPath workshops",AAI's annual meeting,"analysis of complex images factoring in single cells, region-based, and spatial factors ",Make it less dependent on scripting - intuitive software that works without needing to know programming,"learn scripting, understand how the importance of capturing a the right factors in an image that will be analyzed rather than just 'taking pictures'",,Yes
5/16/2022 19:59,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Computer science",Europe,7,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very interested,Moderately interested,Somewhat interested,Not at all interested,Very interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,3D (<3000x3000x100),,,3D (SPIM/large volume),,,,,,,finding nucleus in high resolutions 3D stacks ,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,No
5/16/2022 22:26,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology, Computer vision",Europe,5,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",2D,,,,,,,finding nuclei,Finding annotated image sets for deep learning,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,introduction to latest version of tools,,machine learning and deep learning,,,,Yes
5/16/2022 22:29,Yes,Image/data analyst,Cell/Molecular Biology,North America,3,2,2,"Sit down with a tool I know and start playing with the data, Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,2D object identification,"3D spatial analysis (distance, shape, volume, etc)",,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/16/2022 23:20,Yes,Principal investigator,Physics/Biophysics,North America,3,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,,,,,,,,,confocal listserv email,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,all of the above,,,,,,,Yes
5/16/2022 23:27,Yes,Research scientist,"Physics/Biophysics, Chemistry/Biochemistry, Computer science, Computer vision",North America,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time","2D, 2D + time",,,"2D, 2D + time","2D, 2D + time","2D, 2D + time",,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,It is often very hard to judge if an approach is obsolete and there may be a newer more fitting tool that may be out there. Coming up with the best search terms is a big hurdle.,,,There is often a Bio-imaging focus that obscures the usefulness of many approaches in other disciplines.,No
5/16/2022 23:58,Yes,Principal investigator,Cell/Molecular Biology,North America,2,4,2,"Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,2D,2D,,2D + time,2D,,,finding nuclei,"co-localization, ",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Email list,none,I haven't attended any conference/workshop,how to improve image resolution,I think they are doing a good job,practice,,Yes
5/17/2022 0:28,Yes,Image/data analyst,"Physics/Biophysics, Computer science, Computer vision, Deep learning",Australia,7,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,3D (SPIM/large volume),,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,My local microscopy facility,,,,,,,No
5/17/2022 0:49,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,5,2,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,,3D large volume + time,"3D + time, 3D large volume + time",,,,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Email list,Robert Haases online tutorials are easy to follow for beginners,,,,,,No
5/17/2022 1:42,Yes,Facility staff,"Cell/Molecular Biology, Medicine",Europe,5,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D + time, 3D large volume + time",3D (SPIM/large volume),3D (<3000x3000x100),,,,,3D + time,,counting and tracking in 2D,counting and tracking in 3D+time,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,"More basics of how to get in Napari and scripting. I miss some brige - its either using commercial tools and GUI or coding, the jump between that is big and we are expected to learn ourselves",talk to people totally new to the field (e.g. teach undergrad course),,,Yes
5/17/2022 1:53,Yes,Principal investigator,Cell/Molecular Biology,Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Very interested,Moderately interested,Not at all interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100)",,"2D, 2D + time",,,,,,,,"recognition of heterogeneous subcellular features, such as developing vacuoles in plant cells",,,,,,,,,,,,,,Postings on image.sc forum or microforum,,Few,Postings on image.sc forum or microforum,,,,,,,Yes
5/17/2022 1:57,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",Australia,3,4,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,,,,,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,,,,,,,,,Confocal Microscopy Listserv,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,,,,,,,Yes
5/17/2022 2:11,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",North America,5,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"3D (<3000x3000x100), 3D + time",,,,,,,,,Most things in 2D seem better solved than in 3D or higher dimensions (e.g. cell or nucleus segmentation of sparse 2D cells in culture),"In my experience, 3D+ images are generally harder to work with. There are fewer out-of-the-box solutions that work for those, especially if your samples are a bit unusual/specific. Segmenting tightly packed cells in 3D feels much harder than sparse cells in 2D.",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Postings on image.sc forum or microforum,,,"Appropriate use of machine learning models for biologists would be good, there is a lot of power there but it's not always the most accessible.","Community engagement is incredibly helpful, I think. I've had great experiences being able to interact with people who develop napari, for instance, they are really responsive and helpful. My impression is that a lot of people who develop these tools want them to be successful and used by many people, but they don't always have the money and resources to make them the best they can be. I think pushing institutions to recognize how dedicated image analysts and contributing to open source can help everyone so that they will fund it and make positions along those lines would be good, but maybe that's a pipe dream.","Make your code and workflows as transparent to others as possible. Provide feedback, report bugs, and so forth... I think we need to tell people they are not being a burden in doing so, they are helping! I used to feel self-conscious, like I didn't know enough to be able to report issues or ask questions. I wish I had realized sooner that being more engaged as a user can be helpful for the creators as well!",,Yes
5/17/2022 3:08,Yes,Research scientist,Cell/Molecular Biology,Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Very preferable,Very preferable,Not at all preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D (<3000x3000x100)","2D + time, 3D (<3000x3000x100)",,,,,,,,"spot detection, tracking, ","cell outline detection (yeast), ",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,My local microscopy facility,ImageJ/FIJI course by Kota Miura; great script that I have handed on to many.,,,,,,No
5/17/2022 3:09,Yes,Facility staff,Chemistry/Biochemistry,Europe,2,3,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,"2D, 2D + time",,"Finding, counting, measuring clearly defined structures. Automating analysis of datasets with limited variability.","Reliable, reproducible processing and analysis of datasets with large variability.",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,"Yes, real-life examples fully processed. Summarizing tips and tricks or best practices.",/,How to use a certain tool for a certain kind of experiment. Challenging dataset examples. What is good enough?,A variety of examples. Best practices lists or videos. ,Document and annotate workflows. Keep some example data with processing workflow for future reference.,/,Yes
5/17/2022 3:16,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,5,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,"2D + time, 3D + time",,"2D + time, 3D + time",,,,,,,,Cell segmentation,Cell tracking,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,ELMI 2021 ImageJ workshop,AACR,,Clear instructions for use and limitations (i.e. if it will definitely not work on a certain image type),,,Yes
5/17/2022 3:17,Yes,Research scientist,Chemistry/Biochemistry,Asia,3,2,2,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,2D + time,,,,,,,,,Denoising,Tracking of fluorescence spots precisely,,,,,,,,,,,,,,Twitter,,None,Twitter,,,How to use libraries of codes opened through deposit such as Github,,,,Yes
5/17/2022 3:24,Yes,Image/data analyst,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,7,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,"2D, 3D (<3000x3000x100)",,,"Nuclei/cell segmentation, object tracking","image registration, data visualization",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"Neubias, Global BioImaging image analysis course",,Course on image analysis using Python and Napari for beginners.,"I think creators are doing a good job when they know the biological relevance. If biology is forgotten, analysis often is compromised. ","Users should learn more about basics of images such as what is a pixel, resolution, bit depth etc. These should be included in the microscopy training. ",,Yes
5/17/2022 3:32,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology, Computer science, Deep learning",Europe,4,6,6,"Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"3D (<3000x3000x100), 3D large volume + time","3D (<3000x3000x100), 3D large volume + time","2D, 3D (<3000x3000x100)",,,"3D (SPIM/large volume), 3D large volume + time",,,,"finding nuclei, finding cells",tubular structures reconstruction,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,I2K,,comparisons between pieces of software,Manage to facilitate access to the solutions,Giving more info about sample preparation,,Yes
5/17/2022 3:39,Yes,Facility director,Cell/Molecular Biology,Europe,3,5,3,Ask a friend or colleague to help me,Never,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,,,,clear tutorials/instructions and user-friendly GUI,active interaction with software developers,,Yes
5/17/2022 3:46,Yes,Facility director,Cell/Molecular Biology,Europe,4,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,"2D, 2D + time","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D + time",2D,,,,,,2D + time,"Does that not depend on image quality, labelling etc?","Does that not depend on image quality, labelling etc?",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,Introduction of updates of existing software we use; use of open source software; having recordings available after the sessions;,,Depends on ongoing projects,Better documentation and keep it updated; for open source software continuation is sometime a problem; ,"Talk to the creators to resolve problems, add additional functionality ; ",,Yes
5/17/2022 3:50,Yes,Facility staff,Cell/Molecular Biology,Europe,1,6,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","2D, 2D + time",2D + time,"2D, 2D + time, 3D (<3000x3000x100)",2D,2D,,,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,Email list,,Few,Email list,,Manchester Microscope Congress,,,,,No
5/17/2022 4:13,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,2,6,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,2D,,,,,,,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,Napari,,,,Yes
5/17/2022 4:17,Yes,Postdoctoral fellow,Cell/Molecular Biology,Europe,6,6,6,Ask a friend or colleague to help me,Sometimes,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D + time","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,N A,N A,,,,,,,,,,,,,,"My local microscopy facility, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,hand on trainings,yes,step by step image analysis guide.,N A,N A,No,Yes
5/17/2022 4:31,Yes,Facility staff,Cell/Molecular Biology,Europe,5,5,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,,,,"2D, 3D (<3000x3000x100)",,,"nuceli + spot counting, confluency (growth rates)","STED coloc analysis, 3D neuron architecture, ",,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Word of mouth","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,NEUBIAS - great community,,deep learning,,,,Yes
5/17/2022 4:41,Yes,Facility staff,Physics/Biophysics,Europe,3,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)",,,2D,,,,"2D, 2D + time, 3D (<3000x3000x100)",,Segmentation and quantification.,3D segmentation for electron microscopy. ,,,,,,,,,,,,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"Bioimage Analysis with Python, a course at Cambridge University. It was a five-day in-person course replete with hands-on exercises that could immediately be applied to the problems your normally face. By the end of the course, my image analysis skills had been taken to a whole new level.",,More Python coding. ,,Yes. More training. ,,Yes
5/17/2022 4:42,Yes,Facility director,"Physics/Biophysics, Statistics/Biostatistics",Asia,2,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,"2D, 3D (SPIM/large volume)",,,,,"3D + time, 3D (SPIM/large volume), 3D large volume + time","3D + time, 3D large volume + time",,"Segmentation (neuronal, vascular, axonal) of two-photon imagery with photon-deprived imaging conditions (most segmentation methods fail when the features of interest contain many dark voxels)",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,,,,,,"Multi-photon microscopy is the primary workhorse of many neuroscience labs, yet markedly different from conventional wide-field fluorescence microscopy. Please keep it on your radar.",Yes
5/17/2022 4:52,Yes,Image/data analyst,Developmental Biology,Europe,7,4,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,,,,,,,Yes
5/17/2022 4:53,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,1,5,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)",,,,,,3D large volume + time,,,,,,,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/17/2022 5:14,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology",Europe,4,5,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D (<3000x3000x100),3D (<3000x3000x100),3D large volume + time,3D large volume + time,3D (SPIM/large volume),3D (SPIM/large volume),,3D large volume + time,,,,Hard to answer this ~ Image analysis can always be improved and it depends largely on the image,Same answer above applies. ,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"Yes ~ Simple, but in depth explanations. Most principles in image analysis are simple to follow if explained correctly. It is easy to go to quickly through a concept, or over complicate it. I enjoy learning from people who are passionate and expert. ~ Lots of diagrams!","Most biological questions now need image analysis pipelines to produce results, but I think image analysis conferences should be distinct from biology.","My job at the moment involves a lot of tomogram processing so I'll say: tomogram pre-processing (motion correction, alignment, CTF estimation, CTF correction, noise filtering), particle picking, feature extraction, and sub-tomogram averaging.

I'm also very interested in neural networks and machine learning to data mine/ classify."," More instructions and manuals! ~ There is a BIG learning gap for someone with no background in computing in being able to understand what developers are talking about in their read me files. Understandably it isn't their job to teach, but it would certainly help bridge the gap if there were more accessible and detailed descriptions.

 Active community for answering difficult questions.","Users have a responsibility to immerse themselves in the image analysis topics and try to learn/ understand. The most frustrating thing as a developer is to instruct someone how to do something that is clearly described in the manual/info.

Voice any blank spaces in the manual.","As someone who has learnt image analysis independently, I can see why there is such a learning gap between biologists and image analysts. It is something you either have to spend a lot of time reading up on, or have a dedicated image analyst on team. The midpoint is being instructed/ taught, but to be honest I think if someone wants to learn all they need is on the internet and ready. ",Yes
5/17/2022 5:31,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,2D,,,,,,,,,,,,,,,,,,,,,Our research group's PI,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/17/2022 5:47,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,6,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D (<3000x3000x100),,"3D (<3000x3000x100), 3D + time",3D (<3000x3000x100),,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,Writing scripts to identify differently shaped objects by contrast,,,,,,,,,,,,,,Email list,,None,My local microscopy facility,,,,Better instructions/help pages,,,No
5/17/2022 5:53,Yes,Facility staff,Cell/Molecular Biology,Europe,1,3,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Not at all preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,2D,,,,,,,,,,,,,,,,,,,,,Email list,,None,Email list,,vEM,,Better explanations of terminology/more user friendly interfaces,,,Yes
5/17/2022 6:13,Yes,Facility director,Physics/Biophysics,Europe,2,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc)",,,2D,2D,,,,2D,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Neubias school,,,give more ewxamplary images,First do imaging right,,Yes
5/17/2022 6:21,Yes,Research scientist,Chemistry/Biochemistry,Europe,3,3,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 2D + time","2D, 2D + time",,2D,,,,,,counting nuclei,"SEM segmentation (particles, fibers, porous structures)",,,,,,,,,,,,,,"Postings on image.sc forum or microforum, Twitter",Workshop/tutorial on imaging or image analysis,Some,Twitter,"napari plugin hackathon/workshop, very hands on with great support from experienced devs",,,"Docs and easy to run examples (notebooks, sample data, etc.)","Better descriptions of problems (notebooks, sample data), greater engagement with devs.",,No
5/17/2022 6:26,Yes,Image/data analyst,Physics/Biophysics,Europe,6,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Moderately preferable,Moderately interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",2D,"2D, 3D (<3000x3000x100)",,,"2D + time, 3D + time",,,nuclei segmentation,membrane segmentation and cell labeling in 3D,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,Neubias offers a large quantity of options,ASCB ,Image analysis without coding for beginners,Build a repository of available tools,Communicate more with the devs,,Yes
5/17/2022 7:40,Yes,Facility director,Developmental Biology,Europe,2,2,1,Look up solutions generally on the internet (Google),Never,Not at all preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,,,,2D,2D,,,,"3D (<3000x3000x100), 3D large volume + time",,Segmentation from micro-CT volumes or noisy confocal datasets,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,,,,,,,No
5/17/2022 7:51,Yes,Facility director,Cell/Molecular Biology,Europe,3,4,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D + time,2D + time,2D + time,2D + time,2D,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,,,,Yes
5/17/2022 7:54,Yes,Facility staff,"Cell/Molecular Biology, Statistics/Biostatistics",Europe,3,6,6,Sit down with a tool I know and start playing with the data,Sometimes,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100)",2D,2D,,,,,,,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,Embrace open file formats. Not sure how to persuade them...,,,Yes
5/17/2022 8:00,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",Asia,5,2,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D large volume + time,,3D (<3000x3000x100),3D large volume + time,,,,,,,,,,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
5/17/2022 8:03,Yes,Facility staff,"Cell/Molecular Biology, Medicine",Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100)",,,,,,finding nuclei,intracellular segmentation,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Interaction with tutors,N/A,overviews and comparisons between software,much better and clearer documentation that is up to date. providing with training datasets where you can detect mistakes/errors during learning,"participate and share in mailing lists, forums etc. about image analysis",,No
5/17/2022 8:03,Yes,Facility director,Cell/Molecular Biology,Europe,2,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,2D,2D,,,,"2D, 2D + time, 3D + time",,finding uclei if threshhold is possible,machine learning,,,,,,,,,,,,,,Email list,Conference session on imaging or image analysis,Few,Email list,,ELMI,big data,communicate with users,communicate with developers,,No
5/17/2022 8:13,Yes,Image/data analyst,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,7,7,Sit down with a tool I know and start playing with the data,Often,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,3D (<3000x3000x100),,2D,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,2D,,,nuclei and mitochondria,ER,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,NEUBIAS Conference,ASCB,,,Contact local imaging facility before starting a project,,Yes
5/17/2022 8:20,Yes,Facility director,Cell/Molecular Biology,North America,4,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D + time,"2D, 3D (<3000x3000x100)","2D + time, 3D + time",2D,,,,,,,basic segmentation of large objects,"basically everything - even problems with ""well-solved"" solutions often have so many different solutions (e.g. how many different software platforms are there to segment 3D objects?) that making the choice of which one to use is very frustrating",,,,,,,,,,,,,,"Twitter, confocal listserv","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,A discipline-specific society or network,the workshops at i2k this year were especially good - very interactive and with recordings,ASCB,"basic introduction to scripting in, e.g., python/napari","Make it easier to install python - sort of joking, sort of not - part of the reason Matlab was great was because it was a stable environment where most things were always forward and backward compatible - didn't depend very much on what version you were using (which libraries would work with what version, etc.). But I don't think there is really any hope of achieving this. Also - for the novice image analysts I train - help files/text written in plain English with no image analysis or programming jargon. Finally - better cross-compatibility between analysis platforms - i.e. the ability to link multiple steps in a pipeline that take place in different programs.",Attend workshops/courses - get educated,"I really think that a major issue at this point is the abundance of image analysis solutions. There are SO many! It's great that there are so many options, but it makes it really difficult to choose - especially when each one is in its own little ecosystem with its own interface, libraries, etc. ",Yes
5/17/2022 9:03,Yes,Facility staff,Developmental Biology,Europe,4,4,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,,2D,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,,,No
5/17/2022 9:05,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,3,3,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,3D + time,,,,,,,,,,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,No
5/17/2022 9:16,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,5,3,2,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time, 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,2D,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,counting nuclei,thresholding/segmentation of low-contrast images,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Postings on image.sc forum or microforum,,,scripting for beginners,manuals,share images,,No
5/17/2022 9:28,Yes,Research scientist,Cell/Molecular Biology,South America,5,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,3D (<3000x3000x100),,,,,,,,,Segmenting,Determining distance to the nuclei in 3d (z stacks) images,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"I2k conference, amazing free and virtual (for everyone in the world) detailed tutorials of tools made by the great people who created them in the best environment ever with YouTube (for ever) recordings ",All of them,,,,,Yes
5/17/2022 9:49,Yes,Facility staff,Cell/Molecular Biology,Europe,5,3,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100)",,,,,,measuring in 2D,"segmentation of the organelles, conversion between different microscopy formats ",,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,None,Email list,To obtain info about the methods for image analysis,,,"Make the software userfriendly, have one common image format",,,Yes
5/17/2022 9:53,Yes,Facility staff,Cell/Molecular Biology,South America,4,5,6,Look up solutions in the scientific literature,Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,3D + time,,,,,,3D large volume + time,,,Finding nuclei,Thresholding and Segmentation ,,,,,,,,,,,,,,"A discipline-specific society or network, Twitter",Workshop/tutorial on imaging or image analysis,Few,Email list,I didn't have any background and the workshops helped me a lot to understand many concepts that I had read but it was in practice where I realized about the real meaning ,Yes,"I would like to learn how to better use ImageJ tools, especially for 3d image analysis",,"having more options to learn, go to workshops and have the possibility to interact with experts who can help them solve specific doubts",I would like to propose special programs that offer training and scholarships particularly to Microscopy facility staff,Yes
5/17/2022 10:50,Yes,Principal investigator,Physics/Biophysics,Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,,,,"2D, 3D + time",Optical imaging data,"I'm interested in niche microscopy data: Atomic Force Microscopy. Specifically, locating and classifying molecular conformations which may change over time",,,,,,,,,,,,,,"Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,,"I'm organising a data analysis in AFM conference (or session) with the RMS and am excited to see that being integrated into MMC. I don't think this exists for any AFM conferences and would like it to e.g. AFMBiomed, iSPM, SPMonSPM, ",ImageJ for AFM (maybe too niche for this). Scikitimage/Python interactive tutorials/workshops,sharing data and software when its not perfect! Talking to each other about software. Platforms/persuasion to co-develop software. Encouragement to develop online and openly so people aren't doing the same thing at the same time separately. ,Sharing open datasets which are clearly annotated with metadata openly. We could help them by explaining how and why we'd like the data labelled/formatted/organised/strutcured and how best to do this via e.g. figshare,"It would be great to try and include some of the SPM/AFM community, who are traditionally not good at developing or sharing data analysis tools!",Yes
5/17/2022 10:54,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Sometimes,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D, 2D + time, 3D (<3000x3000x100), 3D (SPIM/large volume), 3D large volume + time","2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,"2D + time, 3D + time",,Finding nuclei,"Tracking, time-series analysis",,,,,,,,,,,,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,My local microscopy facility,,,,,,,Yes
5/17/2022 11:16,Yes,Facility staff,Cell/Molecular Biology,Europe,3,6,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat interested,Somewhat interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",,"2D, 3D (SPIM/large volume)",,,,3D (<3000x3000x100),,,,"Cell detection from brightfield images for calculating transfection efficiency, for instance.",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,NEUBIAS course,,Colocalisation,,,,Yes
5/17/2022 11:42,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,South America,3,3,5,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Moderately preferable,Not at all preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D,2D,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time",2D,2D,,,"2D, 2D + time",,,Finding nuclei,Reliability of co-localization analysis,,,,,,,,,,,,,,Word of mouth,Workshop/tutorial on imaging or image analysis,None,My local microscopy facility,,,Co-localization tools e fluorescence quantification,"Step by step manual for processing images
And step by step hardware dealing",,,Yes
5/17/2022 11:49,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",South America,4,3,3,Ask a friend or colleague to help me,Never,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,3D (<3000x3000x100),3D (<3000x3000x100),2D,2D,2D,2D,2D,2D,2D,moving cells,Intranuchear christaloids,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,No lastly.,No.,,"May be, not always.",Yes.,,Yes
5/17/2022 12:18,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",South America,6,5,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D (<3000x3000x100),3D (<3000x3000x100),3D + time,2D,2D,,,,,,,finding nuclei,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,None,Email list,,,,,,,Yes
5/17/2022 12:21,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,2,2,2,Ask a friend or colleague to help me,Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Not at all interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,No
5/17/2022 14:09,Yes,Research scientist,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,4,5,Sit down with a tool I know and start playing with the data,Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D + time, 3D (<3000x3000x100)","2D + time, 3D (<3000x3000x100)",,2D,,,,,,segmenting nuclei,denoising,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,Yes
5/17/2022 15:53,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology, Developmental Biology",North America,4,6,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc",Often,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Moderately preferable,Moderately preferable,Not at all preferable,Not at all interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,,2D,,,,,,,,,,,,,,,,,,,,,,Email list,Conference dedicated to imaging or image analysis,None,Email list,,,Quantitative analysis of fluorescence ; imageJ,"Make it simpler to learn how functions work and, most important , provide a way to test that your images satisfy the assumptions underlying functions. ",Not use software they don’t understand,,Yes
5/17/2022 16:55,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,3,5,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Not at all preferable,Moderately preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Not at all interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D + time, 3D (<3000x3000x100), 3D + time",,2D,"2D, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,,,,Yes
5/17/2022 17:13,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology",Australia,2,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100)",,2D,2D,,,,2D,,Quantifying things that are easily to isolate and identify,Quantifying things were segmentation is difficult ,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,None,Email list,A general introduction to ImageJ.  Helped to showcase what is possible.,Any microscopy related conference,Anything around ImageJ because everyone has access to it,Information to understand the processes that are occuring,"Discuss image analysis needs/problems, or desirable workflows",,Yes
5/17/2022 18:15,Yes,Postdoctoral fellow,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,4,2,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Not at all preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time",,,,,,"2D, 2D + time","2D, 2D + time",,,,,,,,,,,,,,,,,My local microscopy facility,Conference dedicated to imaging or image analysis,None,Email list,,,,,,,Yes
5/17/2022 18:15,Yes,Research scientist,Cell/Molecular Biology,North America,4,4,5,Sit down with a tool I know and start playing with the data,Most of the time,Not at all preferable,Moderately preferable,Moderately preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Not at all interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time",,,,,,"2D, 2D + time",,,,,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,,,,,,,No
5/17/2022 18:20,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Medicine",Europe,3,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time",,2D,,,,,,,2D in vitro cell segmentation,"Segmentation of tissue data, especially in 3D+ (e.g. nuclei in cleared samples in Lightsheet), deconvolution of lightsheet images, spectral separation of channel bleedthrough and autofluorescence in conventional (i.e. not FLIM or hyperspectral) detectors",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,3D tissue segmentation,Make them accessible to non coders (e.g. through Napari),Share ground truth data for AI training,,No
5/17/2022 18:27,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",North America,4,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,nuclei segmentation,foci identification; tracking,,,,,,,,,,,,,,My local microscopy facility,,Few,My local microscopy facility,,,,,,,No
5/17/2022 18:30,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,3,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D + time, 3D + time",,"2D + time, 3D + time",,2D + time,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Some,My local microscopy facility,,,,,,,Yes
5/17/2022 18:31,Yes,Research scientist,Cell/Molecular Biology,North America,1,3,4,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100)",,2D,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,None,My local microscopy facility,,,"Automating workflows, best practices/methods of reducing investigator bias",,,,Yes
5/17/2022 18:34,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Medicine, Statistics/Biostatistics",North America,4,4,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions on a particular website (please list below)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Not at all interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,2D + time,,,,,,2D + time,,,cell segmentation based on bright field,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
5/17/2022 18:35,Yes,Research scientist,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology",North America,2,4,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Not at all interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,,,,,,2D,,finding nuclei ,identifying unique phenotypes,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,None,Email list,N/A,N/A,How to use certain tools and comparisons between different tools,More friendly GUIs and more video tutorials!!! Open source video tutorials by the creators,Not sure there,N/A,No
5/17/2022 18:56,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,2,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,2D,,,,,,,,,,,,,,,,,,,,,,,,Email list,,None,Email list,,,,,,,Yes
5/17/2022 19:34,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,4,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,2D,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,None,My local microscopy facility,,,,,,,No
5/17/2022 21:32,Yes,Facility staff,Cell/Molecular Biology,Australia,5,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat interested,Not at all interested,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time",,,,,2D + time,2D + time,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,Yes
5/17/2022 23:35,Yes,Research scientist,Physics/Biophysics,North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,3D (SPIM/large volume),,,,,,Counting mono-nucleated cells,Object relationships that include cell-cell borders,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,I2K conferences. Well curated recordings on YouTube,,,"I'm annoyed whenever I see resources being devoted to creating one-off software solutions (""islands"") when it could have been trivially implemented through Fiji/CellProfiler.",Make sure people take good data,,No
5/18/2022 1:52,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology",Europe,4,3,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,None,Email list,,,,,,,Yes
5/18/2022 4:22,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology",Europe,5,6,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,"2D, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,,,,"finding nuclei, tracking spots/cells in 2D, measuring intensities within nuclei","extracting cell shapes in epithelial tissues (touching cells), 3d cell tracking in large datasets",,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,"Robert Haase's YouTube tutorials - good background to image analysis and well demonstrated use of these principles for analysis in Fiji. Also had more in-depth analysis with additional plugins (Clij, Qupath etc.).","EMBO Seeing is Believing, lightsheet microscopy conferences (LSFM)","Comparison between different software for cell segmentation (and cell shape analysis) in epithelial tissues. Comparison of free and commercial software for 3D cell tracking analysis - similar to the various ""analysis challenges"" that have been performed in previous years but showing off the findings as a workshop/webinar.","I think a lot of creators already are highly active in the community and do a lot to make analysis better (added features, helping users with problems etc.). The image.sc forum is a valuable resource for this purpose and I would encourage software creators to announce software via the forum and offer advice/support via that medium also.","As above, use various forums (particularly image.sc) to seek help/advice for their needs. If enough people have the same needs, it will encourage software developers to engage with the community and will drive the need for better (easier to use?) software.",,Yes
5/18/2022 5:44,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",Europe,2,5,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,"2D, 2D + time","2D, 2D + time",,,,,,"2D, 2D + time",,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,hands-on tutorial,,"using open source software - extracting data and inputing/formating in such a way to work with opensource. Advanced applications - FLIM with phasor approach, FCS",accessible with plugins for use with opensource tools,write full methods desrciptions within publications. Make published data available,,Yes
5/18/2022 6:03,Yes,Facility director,Developmental Biology,Europe,4,2,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc",Most of the time,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",2D,,2D,,,,,"None, though finding nuclei in 2D works well.",3D analysis of large data,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,"Neubias webinars: theory then practice, and viewable on YouTube later on.",,Workflows that use different software.  E.g. Fiji to Ilastik to CellProfiler,Assume *complete* lack of computing knowledge from the user,Ask about analysis prior to acquire images.  We ask users before they even touch their microscope what they want to do with their images.,"I'm an amateur analyst, I run a facility, I wish there was someone who would be happy to remotely run an analysis when it's clear what is asked for is beyond my capability.",No
5/18/2022 6:43,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Medicine",Europe,4,2,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Not at all preferable,Not at all interested,Somewhat interested,Very interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,,,,,,,"Every tissue has a different challenge, sometimes even finding the nuclei can be difficult ","More options to find nuclei, we work with liver tissue and it`s hard to get the software to identify reliably both hepatocyte nuclei and all other nuclei",,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,Some InForm video tutorials were very helpful,N/A,,,,,No
5/18/2022 6:49,Yes,Image/data analyst,"Physics/Biophysics, Computer science, Computer vision, Deep learning",Europe,7,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,fluorescence nucleus segmentation,EM organelle segmentation,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,NEUBIAS,,Sustainable development,"Lowest possible initial barriers, e.g. installation",Speak to developers about needs etc. Stop reinventing the wheel. Communication via strong community,,Yes
5/18/2022 7:24,Yes,Facility staff,Cell/Molecular Biology,Europe,5,5,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc",Most of the time,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","3D (<3000x3000x100), 3D + time",2D,,,,,,,"segmentation in 2D , tracking , color deconvolution, machine learning with random forest,","annotation in 3D for Deep learning, 3D segmentation, Denoising self-supervised, detection neurone in 3D,  easy way to use the Deep learning model in FIJI for the biologist (cell pose, stardist, N2V, CARE are ok but we need a better solution like DeepImageJ)",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"all the NEUBIAS school and workshop, EMBL session",,"Deep learning for microscopy, napari, 3D annotation, CLIJ, Clesperanto",A solution easy to use in FIJI or Napari (use DL model). documentation on youtube,"share there knowledge, worshop, ",,Yes
5/18/2022 7:26,Yes,Image/data analyst,"Physics/Biophysics, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",Europe,6,6,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Not at all interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,automatic segmentation,,,,,,,,,,,,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"X Computer Optimized Microscopy course (Barcelona, June 2018)",only attended of image analysis/ microscopy,,tools that are understandable and easy to apply for regular users,learn the basics and meaning of what is an image,,Yes
5/18/2022 7:26,Yes,Facility director,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D + time, 3D large volume + time",2D,,,,,2D,3D + time,,,"SIM, STORM, airyscan",,,,,,,,,,,,,,"Twitter, Email list",Workshop/tutorial on imaging or image analysis,Few,Postings on image.sc forum or microforum,,ELMI,,,,"Image analysis is very complex. From a facility perspective, it would be helpful if there is a common repository where pipelines/workflows could be shared with examples (CellProfiler's webpage on tutorials is excellent). That makes the average user more likely to run analysis by themselves.  ",Yes
5/18/2022 10:15,Yes,Image/data analyst,"Chemistry/Biochemistry, Computer science",Europe,6,5,7,Sit down with a tool I know and start playing with the data,Most of the time,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D large volume + time,3D large volume + time,3D + time,3D + time,2D,2D,2D,2D,2D + time,2D + time,3D (<3000x3000x100),,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,,,,,,,No
5/18/2022 10:23,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics, Deep learning",Europe,4,5,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D + time",,,,,,,,finding nuclei,"segmentation, particle tracking, co-occurrence analysis, colocalisation",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,I2K. Principles of fluorescent microscopy @ pastuer institut. Online python for image analysis courses. ,No. The field needs to improve it's user friendly-ness. ,"Advanced FIJI. Cellprofiler (and others) - top tips, compare and contrast. ","With analysis software, the most off putting thing is when the options window pops up with a bunch of parameters that mean nothing to you. Each parameter should have a lil ? button which provides a link to what this means. More integration of statistical analysis. Biologists love a slide bar. *everyone loves a slide bar. Particularly with real-time update of what happens to the analysis in response to changing said parameter. ",Be properly trained. Particularly in appropriate statistical analysis. ,"Every analysis tool should have a clear pipeline which you can fiddle with in an informed manner. Most biologists are broadly asking the same thing from image analysis and ultimately a single package should be able to achieve this. 

Oh! better integration of python with Fiji. Fiji macro language is whacky. 

Finally, not a fan of being lumped in with undergrads. undergrads and postgrads have very distinct different needs. ",Yes
5/18/2022 10:32,Yes,Facility staff,Cell/Molecular Biology,Europe,2,3,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all interested,Very interested,Very interested,Very interested,Moderately interested,Not at all interested,Not at all interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 3D (<3000x3000x100)",,2D,,,,,,,finding nuclei,"avoiding autofluorescence signals in tissue samples, coping with low SNR",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,BioVoxxel seminar on site - tailored themes to our problems,,,Explain how to adapt particular tools/pipelines for samples that don't behave as well as the example data set. ,Pay more attention to dynamic range than what looks pretty to human eyes,,Yes
5/18/2022 10:42,Yes,Facility staff,"Physics/Biophysics, Cell/Molecular Biology, Developmental Biology",Europe,3,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Most of the time,Not at all preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D + time,"2D, 3D + time",,,,,,,,"finding nuclei, localiying dots","time point alignement down to the pixel. More than an analysis problem, installation of tools is a huge issue. Depending on your OS you need different versions, different libraries. It is so painful for people not well versed in command line/bash/python... An a real issue for tool propagation",,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,My local microscopy facility,"When the tutorial had a pdf or slides we could follow, we were shown a few steps, then did them in small beakout rooms with a helper, and back and forth like this between the main session and the little breakout groups where we could share our screen if there were issues","Yes, ELMI",all of it. How toos are particularly useful,"Package things so that the installation is easier, document tools with users in mind (not other developers) ",give feedback to creators on what the major hurdles are and why some tools are not used,,Yes
5/18/2022 11:19,Yes,Facility staff,"Physics/Biophysics, Chemistry/Biochemistry, Statistics/Biostatistics, Computer science, Computer vision",Europe,3,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc)","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time",,"2D, 3D (<3000x3000x100), 3D (large volume)","2D, 3D (<3000x3000x100)",,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,,,,,,,Yes
5/18/2022 11:28,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,1,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat interested,Very interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D,"2D, 2D + time","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",2D,2D,,,,,,"Finding cells, tracking cell nuclei over time, counting nuclei","Analysis of super-resolution images,  Analysis of 3D brightfield images, manipulating large data sets including time-courses and large tiling experiements",,,,,,,,,,,,,,Email list,Conference session on imaging or image analysis,Few,Email list,None come to mind,MMC; ,"overviews, using specific tools for specific questions, how to choose the best software tool or package for your data. ",good user interface; easy to understand and logical protocols; online resources and help,engage more from the start of experiments. ,,No
5/18/2022 12:39,Yes,Research scientist,Cell/Molecular Biology,North America,4,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Very interested,Not at all interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,2D,,,,,,,,,analyzing multiple parameters in multiple images at the same time,,,,,,,,,,,,,,"My local microscopy facility, Email list",,,Email list,,,,,,,No
5/18/2022 14:27,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,1,2,2,Look up solutions generally on the internet (Google),Never,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Somewhat interested,Not at all interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (<3000x3000x100),,,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Postings on image.sc forum or microforum,,,,,,,No
5/18/2022 15:04,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat interested,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 3D (<3000x3000x100)","2D, 2D + time",2D,,,,,,,cell counting,3D and time,,,,,,,,,,,,,,"Postings on image.sc forum or microforum, slack","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,i2K,,Napari and pyhton,encourage with dedicated funding,,,Yes
5/18/2022 15:56,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,1,3,4,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Somewhat interested,Not at all interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",None,,,,,,,,,,,,DAPI staining,"Analysis of small organelles, dust in an expensive microscope ruining images, easier how-to for beginners. ",,,,,,,,,,,,,,Email list,,None,Email list,,,,,,,Yes
5/18/2022 16:07,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,2,5,6,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D (<3000x3000x100),,3D (<3000x3000x100),,,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Some,My local microscopy facility,,,,,,,No
5/18/2022 16:29,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,3,2,2,"Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Not at all interested,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,2D + time,3D (<3000x3000x100),2D + time,2D,,,,,,,,automated tracking of migrating cells,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,None,My local microscopy facility,We had to solve a problem in the lab. Usually my postdocs or students do the actual analysis,this wasn't on offer at any meeting I've attended yet. ,analysis of chemotaxis and polarisation,publish open access papers,Really important - good facility staff should mention this during introduction to microscopy,,No
5/18/2022 17:03,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,7,3,2,Ask a friend or colleague to help me,Never,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,2D,,,2D,2D,,"segmentation, finding nuclei, tracking cells (neutrophils). ",SPT and super-resolution ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,,,Napari and Python,,,,No
5/18/2022 17:08,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Computer vision",Europe,4,6,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,"2D + time, 3D + time",,,,,,,,Nuclei segmentation,Tissue analysis,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,,,,,,,Yes
5/18/2022 17:10,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",Europe,2,5,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Not at all preferable,Moderately preferable,Not at all preferable,Not at all preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,3D + time,,,,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,Twitter,,,,,,,No
5/18/2022 19:52,Yes,Facility director,Cell/Molecular Biology,North America,2,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",2D,,,,,2D + time,,segmenting basic cell compartments,"particle tracking, ",,,,,,,,,,,,,,"Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,Attended a Cell Profiler workshop that was great for getting started. It just got everyone to point where you could explore the software,ABRF,Comparisons between software and how they can work together would be useful,"Easy to follow GUI interface, documentation of tools, highlight when data doesn't meet requirements, output files that could be used for reporting of methods ","incorporation/maintenance of metadata in image files, reporting of methods used",,Yes
5/18/2022 21:41,Yes,Postdoctoral fellow,Cell/Molecular Biology,Asia,4,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",,,,,,,,Segmentation of fluorescence images,Segmentation of bright-field / phase-contrast images,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Conference dedicated to imaging or image analysis,Few,Postings on image.sc forum or microforum,Overview of various image analysis tools which gives an idea of current state of the field and allows to find a new tool for solving your problem.,No,"Overview of ""failure"" stroies when describes ability of tool to do its job - this will show the limits of this specific tool and users would be prepared for such outcome in curtain scenarios. Description of validation workflow for the tool would be useful.","1. For point-and-click tools - introduce ""recording"" functions. This would allow improve reproducibility of analysis and from these recorded macros/scripts creators might see how actually end-users apply their tools. 2. Provide a sample scripts / pipelines for some generic analysis. 3. Provide an workflow for results validation (especially for high-throughput tools)","Scripting or at least recording macros for the analysis they perform. This would ease the  troubleshooting and improve reproducibility. To encourage users to do so, I think we should communicate with journals about these ideas. Journals are interested in the transperent and reproducible results; thus, they can use their power to push authors implementing a good practice in the research workflows.",,No
5/19/2022 2:12,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",Europe,2,5,5,Ask a friend or colleague to help me,Sometimes,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,,"2D, 3D (<3000x3000x100)",,2D,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,Few,My local microscopy facility,,,"regional segregation of tissues, point distance measures, thickness measures, focal vs regional signal intensity",,Better experimental design and replication. Discuss experiments / best practice guidelines for standard preparations prior to starting.,,No
5/19/2022 2:36,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",Europe,4,6,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Not at all interested,Somewhat interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D + time","2D, 2D + time, 3D + time","2D, 2D + time, 3D + time","2D, 2D + time, 3D + time",2D,"2D + time, 3D + time",,"2D, 2D + time, 3D + time","2D, 2D + time, 3D + time",,,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,,,,,No
5/19/2022 4:36,Yes,Image/data analyst,Physics/Biophysics,Europe,6,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"3D + time, 3D (SPIM/large volume), 3D large volume + time",,2D,,,,2D,2D + time,,"nuclei segmentation, enumerate objects within other objects, distances between objects","Co-localisation, brightfield segmentation, shape analysis",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Email list,"collegiality of attendees, everybody was genuinely interested in helping each other out, irrespective of the base level which were widely varied, avid exchange of contact details for future communication","Lighst sheet microscopy conference (but I attended in 2014, so long time ago...)","machine learning, it's such a hot topic but so hard to establish. There needs to be a: this is how to set it up from scratch/establish a pre-trained model locally. Usually everything is prepared and one can dive into coding but that is not the only learning curve. The second learning curve is not available if one does not get over the first hump.",Things that are not supported anymore should disappear from the options list. Things that are actively supported should be easily identifiable (easier with the forum.image.sc these days),"Giving feedback to developers about issues/problems - not everybody dares to and at times the feedback is in a format that does not help the developer identify what the problem might be, i.e. saying ""it does not work"". Then it is difficult to delineate between user error and genuine problems (hardware, software bug, file format). ","I am a big fan of the open-ness of the BioImage Analysis community. However, in all its proliferative glory, I find it difficult to keep up to date with all the new developments at the moment, and this is only going to get worse... ",Yes
5/19/2022 4:41,Yes,Undergraduate/Graduate student,Physics/Biophysics,Europe,5,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Not at all preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Not at all interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,,,,3D (<3000x3000x100),"Training with large datasets, counting in low density images, easy segmentation of different image parts","High-density counting, shape classifying for low training image data, defect localisation ",,,,,,,,,,,,,,"Word of mouth, Email list",Conference session on imaging or image analysis,Few,Email list,,,General data labelling - not only bboxes and class labels for CNN's but also those for GNN's. Also gaussian processes and auto encoders as I've heard they could be quite useful,Be more open for communication and work with (not for) others to build on their software to stop others reinventing the wheel.,More communication with the software developers to understand different problems. Courses in github issues might help bridge this. ,,Yes
5/19/2022 6:17,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Medicine, Statistics/Biostatistics, Computer science, Deep learning",Europe,4,5,7,Sit down with a tool I know and start playing with the data,Sometimes,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Not at all preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,"2D, 2D + time",,,"2D, 2D + time",,,,,,,Tissue analysis,Allways wishing for better solutions,,,,,,,,,,,,,,"Word of mouth, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Hands on ,Not sure,Nothing in particular,Co-authorship ,Not sure,Nope,Yes
5/19/2022 8:59,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics",Europe,3,4,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Somewhat preferable,Very preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D + time,,,,,,,,,"counting number of dead cells/nuclei/spheres, determining % of area that is occupied by cells","cell tracking specifically when: (1) cell nucleus is not stained, (2) cell morphology changes in time, (3) cells interact (come too close to each other).",,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,None,Email list,ones conducted by the local microscopy facility,no,"basic procedures/scripts, something that provides you with the basic skillset that you can use later to solve your own problems.","we need better tutorials with multiple examples of how the software can be used. Ideally, step-by-step tutorials.","It would be great if we start shearing our knowledge in more organized fashion. For example, it could be useful to create a some sort of registry of detailed procedures/step-by-step protocols/scripts used for image analysis with a link and a name. So that we could refer to them in our papers.",,Yes
5/19/2022 9:53,Yes,Clinician,Medicine,Europe,6,2,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,2D,,,,,,,,,,,,,,,,,,,,,Word of mouth,,None,My local microscopy facility,,,,,,,Yes
5/19/2022 10:09,Yes,Facility director,Cell/Molecular Biology,North America,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,2D + time,3D + time,2D,,,2D + time,,,Segmentation,Multi-variate analysis such as Linear Discriminant Analysis applied to imaging,,,,,,,,,,,,,,BINA,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,,,,Yes
5/19/2022 10:14,Yes,Facility director,Physics/Biophysics,North America,3,6,3,Sit down with a tool I know and start playing with the data,Most of the time,Moderately preferable,Moderately preferable,Not at all preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Moderately interested,Somewhat interested,Moderately interested,Not at all interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,"2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",,"Everything depends on segmentation, which is always problematic in real samples",Segmentation,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Dragonfly ran a great series during the pandemic.  What made them particularly exciting was that they were pretty advanced and yet hands-on. . . ,"Segmentation of real images with advanced concepts, not just thresholding",A comparison of deep learning with more standard techniques for doing similar tasks,"Keep things logical, with displayed parameters so users actually know what is going on.  Make an easy way for pipelines to be carried out on similar datasets.  ","One of the things I find so powerful about scripting is that it naturally provides accountability and transparency to science.  If you apply the same script to many images, there is a record of what you did and presumably the same thing was done to all images in the study.  The script can be submitted as part of the analysis documentation, and can be used when reproducing the study.",ImageJ scripting is an incredibly powerful tool that can be used for free by anyone.  I think organizations such as this should support its use (and other tools like it).,No
5/19/2022 10:34,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics",North America,6,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Most of the time,Very preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,2D,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",,,,,,,"Finding nuclei, manual thresholding for area/percent calculation, manual counting","Unbiased/automated segmentation of objects, pixel classifier and AI quality metrics/controls",,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Some,Email list,Ones that discuss the principles of optimizing images for analysis and appropriate image precessing steps,,Principles of and rigor in image shelties. Quality control and bias. ,"Keep lowering the learning curve for accessibility to serious/high-throighput analysis tools (e.g. graphical interfaces instead of scripting). Stop trying to replace everything with AI, instead expand opportunities to integrate AI tools with conventional methods (with proper controls and QC).","Make every effort to avoid manual thresholding/selections/counting and other potential sources of bias. Think critically about appropriateness of certain image processing and analysis tools. Appropriately use the quantitative range of their camera/detector and the highest bit depth available, and stop exporting images in formats that lose data. Report processing and analysis methods thoroughly in publications.",,Yes
5/19/2022 10:59,Yes,Postdoctoral fellow,"Physics/Biophysics, Computer science",North America,3,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D + time,,,,,,,,,,,,,,,,,,,,,,,,Email list,,None,Email list,,,,,,,Yes
5/19/2022 11:02,Yes,Facility director,Cell/Molecular Biology,North America,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Very preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,2D,,,"2D, 3D (<3000x3000x100), 3D large volume + time",,,"finding sparse nuclei, tracking puncta in 3D + time",automatic segmentation and analysis of TEM micrographs,,,,,,,,,,,,,,A discipline-specific society or network,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/19/2022 11:22,Yes,Postdoctoral fellow,Chemistry/Biochemistry,North America,4,2,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100), 3D + time",2D,2D,,,,,,,Quantification of intensity with thresholding (defining parameters in a clear way),,,,,,,,,,,,,,My local microscopy facility,,Few,My local microscopy facility,no,no,Using ImageJ/FIJI.  MatLab scripts + ImageJ,,,,No
5/19/2022 13:16,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",Europe,3,4,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,"2D, 3D (SPIM/large volume)",,,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,,,,,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,A discipline-specific society or network,"Image Analysis for Biologists, Cambridge, was really helpful at the start of my PhD and getting me started off in my imaging career. Covered Icy, FIJI and MATLAB and gave a good grounding in basics and best practises. 3 day residential course, IIRC.",,,,,,No
5/19/2022 13:55,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,3,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",2D,,,,,,,Classification based on cytoplasmic stains,Nuclei counting and membrane segmentation for dense tissues,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,Email list,Workshop on using Imaris for segmenting 3D objects,,,Standardizing image formats and integrations between softwares would be very helpful.,,,Yes
5/19/2022 14:02,Yes,Image/data analyst,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Medicine, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,7,6,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,3D (<3000x3000x100),,3D (<3000x3000x100),,,,,,Classifying cellular types,3D processing,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,3D processing,,,,No
5/19/2022 14:09,Yes,Principal investigator,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)",,,3D + time,,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,"2D CLEM, connectomics wiring diagrams","automated segmentation of organelles, 3D CLEM, analyzing large 3D volumes",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,These are rarely useful - best case results or generic solutions are often presented. ,"M&M, Zeiss CLEM.",Objective comparisons between various software for segmentation of objects from EM and volume EM data,"THIS is a critical point - creators often underestimate how intimidating any ANY coding is for biologists. Simple slip-ups (dependencies, file types etc) are trivial for creators but are game-enders for biologists. It is imperative that documentation (thorough AND updated) + videos + trials (best case AND troublesome data) + caveats/assumptions is included. Be crystal clear of what the inputs/variables and arguments are, and how they alter outputs. Encouragement = have more people use your work! If in industry, please be honest with your users re. capabilities, and have clear agreements re. deliverables if developing something new.","Accept that there is no universal ""point-and-click"" solution, and that there is great payoffs for always looking out for newer solutions. Also please stop reflexively panicking/shutting down if you see code. Right from grad school MUST have simple but mandatory programming modules - they at least need to know how to install and use packages from command line.",MONEY FOR DATA ANALYSIS. There are no real dedicated funding streams or career paths for data analysts (ARISE is a welcome change),No
5/19/2022 14:36,Yes,Principal investigator,Chemistry/Biochemistry,Europe,3,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","2D, 2D + time, 3D (<3000x3000x100)",2D,2D,2D,,3D (large volume),3D (<3000x3000x100),"2D, 2D + time, 3D (<3000x3000x100)",,,,My local microscopy facility,,None,My local microscopy facility,,,,,,,No
5/19/2022 14:58,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,2,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,2D,,,,,,,,"Finding nuclei, basic automated quantification of fluorescence","Colocalization analysis, spot detection, finding the edges of cells",,,,,,,,,,,,,,My local microscopy facility,Conference session on imaging or image analysis,Few,My local microscopy facility,,,,"Improve user interface to require less scripting, simplify/integrate explanations of imaging principals to discourage bad practices ",Learn more about the physics and other principals behind imaging to understand potential sources of problems or misleading data. Ideally integrate it more with life science education,,No
5/19/2022 15:11,Yes,Facility staff,Cell/Molecular Biology,North America,4,5,5,Sit down with a tool I know and start playing with the data,Sometimes,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",,2D,,,,,,identifying discrete objects from low background,separating objects,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,,ASCB,,,,,No
5/19/2022 17:16,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,3,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately preferable,Not at all preferable,Not at all preferable,Somewhat interested,Somewhat interested,Moderately interested,Not at all interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (<3000x3000x100),,2D,,,,2D,,,,RNAscope/ISH quantification,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,,,,GUI,,,No
5/19/2022 17:24,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,4,4,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time",,2D,,,,,,"2D + time, 3D + time","Finding spots/features/cells/nuclei/puncta, measuring sizes/volumes.",Calcium imaging,,,,,,,,,,,,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,A discipline-specific society or network,"We did an in-house Nikon Elements course that was really good, particularly because we had real data samples to analyze.","The AQLM course at the MBL in Woods Hole is top notch, fantastic instructors and cutting-edge equipment, and we collected amazing images but the analysis portion of it was lacking. ","Not sure, we definitely need to know how to handle massive amounts of calcium imaging data.",User-friendly interfaces are always helpful.,Give better details on image analysis in the methods sections of publications.,nope,Yes
5/19/2022 17:33,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Not at all preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,2D,2D,2D,,,3D + time,,,,Finding nuclei,Everything else,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,ISAC SESSIONS,ISAC ,How to improve use of specific tool,,Request more personalized training,,No
5/19/2022 19:17,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,3,2,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,2D,2D,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"3D & 4D visualization, stitching & image registration","Feature segmentation, deconvolution, contrast enhancement, AI, Machine learning",,,,,,,,,,,,,,"Postings on image.sc forum or microforum, Email list",,None,Email list,not yet,,I don't know,"More tutorials, help lines ",,,Yes
5/19/2022 23:33,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,4,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time",,,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,Few,My local microscopy facility,,,,,,,Yes
5/20/2022 3:32,Yes,Facility staff,Cell/Molecular Biology,Europe,1,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,"2D, 3D (<3000x3000x100)",,,,,,finding common organelles,tracing membranes or less common organelles,,,,,,,,,,,,,,"A discipline-specific society or network, Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,EC-CLEM workshop at CLEM COMULIS training scholl,any microscopy conference should have a dedicated image analysis session,open source tools for 3D data analysis,improve dialogue with end users ,improve dialogue with creators,,No
5/20/2022 4:41,Yes,Research scientist,Cell/Molecular Biology,Europe,3,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,2D + time,,,,,2D,,,,fluorescence segmentation and analysis,Time lapse imagery,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,Email list,N/A,Cyto,Using open source tool for image analysis,"Make things open source, in proprietary software make API to integrate user written scripts ",Make things open source ,,Yes
5/20/2022 4:48,Yes,Principal investigator,Physics/Biophysics,Europe,2,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,2D,,,,,,"2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Twitter,,,,,,,No
5/20/2022 4:54,Yes,Facility staff,"Physics/Biophysics, Chemistry/Biochemistry",Europe,3,4,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Never,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Somewhat interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc)",2D,2D,,,"2D, 3D (<3000x3000x100)",,,,,,"Image autocorrelation for SIMS, 3D imaging in SIMS.",Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,"AVS, SIMS",,"Understanding the needs of the customer is key, but there needs to be a commercial incentive to do it.",Very often new functions and tools are first made by the users in the lab and eventually find their way into commercial instruments or software. Spreading the word on excellent user-made tools can accelerate this process. ,,Yes
5/20/2022 5:13,Yes,Facility staff,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science",Europe,7,7,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,,"2D, 3D + time",,,,,finding nuclei for well separated cells,finding nuclei for dense cell areas and visualization after neighbourhood analysis or clustering,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,all,none,,,,,No
5/20/2022 5:49,Yes,Facility staff,Physics/Biophysics,Europe,2,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Not at all preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,,,,,,,,"2D, 3D (<3000x3000x100)",," Collect statistical data on artefacts shape, size, volume etc on a large number of AFM images.",Word of mouth,Workshop/tutorial on imaging or image analysis,Few,Email list,"Hands on time, applying skills to my images with expert support",,Topostats!,"Excellent documentation, user instructional videos with good production values, forums to ask questions to experts. Have clearly defined analysis pathways to allow users to recreate images from others/their past selves.",Report the use of the tools and feedback to developers/creators,,Yes
5/20/2022 6:23,Yes,Image/data analyst,Cell/Molecular Biology,Europe,5,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,"2D, 3D (<3000x3000x100)",,3D (<3000x3000x100),3D (<3000x3000x100),,3D (<3000x3000x100),,nuclei segmentation,remove bits of crap',,,,,,,,,,,,,,Email list,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,n/a,Yes. Digital pathology and AI congress. Though this seems more geared towards clinicians and pathologists rather than 'basic research',"standards, standards, standards (like NGFF, but more tools and workflows that work with it)","I like it when 'basic users' can train a model, then hand over the 'scaling' to an experienced user",BE aware of the controls to collect at the time they do their imaging,"I work in industry, where it feels they are also playing catch up on how to store, share and analyse images. They have different priorities (would love to just buy the solution to their problems), but I think it is clear the field moves faster than industry, and often we would like to use opensource/published tools. I wonder how industry coul dbe better involved support this (btw, happy to be contacted, i am Merrick Strotton @ UCB)",Yes
5/20/2022 8:23,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,5,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Often,Somewhat preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,analysis of images with high dynamic range,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,Training schools and webinars organized by NEUBIAS. They made image analysis available to me when I was a total newby and had nobody to ask in my close environment. They introduced a wide range of analysis tools/softwares to use and explained how to access them and how to proceed to learn more.,,Best approach/software for different types of problems. Overviews of new tools.,,I think users with experience in image analysis should spread their knowledge and acknowledge open source image analysis tools so that less experienced colleagues get access and start using image analysis,,Yes
5/20/2022 11:42,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Computer science",Europe,4,6,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D + time","2D, 2D + time, 3D + time",2D,,,,,,,nuclei segmentation in fluorescence images,segmentation and analysis and objects in brightfield images,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,When people show concrete example solutions for their image analysis problems that can give me ideas for my own image analysis problems (or for my colleagues),,"I would love to see more about tracking over time -- but not only about the tracking itself, more about the subsequent analysis of the data and visualization. Especially detection of similarity profiles over time and cluster detection.",,"Users should design their experiments so that image analysis works well, and not perform the experiment and then wonder how to analyze them, and actually realizing that their scientific question cannot be analyzed with the given setup (of dyes, etc.)",,No
5/20/2022 12:49,Yes,Image/data analyst,Statistics/Biostatistics,North America,7,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,,,,3D (<3000x3000x100),"Small image analysis (<50 Mb), nuclei detection, marker-based watershed, denoising","Mostly object detection and separation; detecting cell boundaries and cytosol when there is not a dedicated fluorescent marker for this, object separation when the objects are not spherical and clearly not touching; overlapping object detection in 2D images; object separation without having to worry about installing external software such as very specific versions of python libraries; file format interoperability between software; there is a huge skill gap between working with large data locally and then working with extremely large data with asynchronous data loading in a server-based or cloud environment; skeletonization with discontinuous information such as a weakly stained neuron; combining image data with sequencing information such as spatial transcriptomics",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,"ToScA North America, FIB-SEM Annual Meeting, XCT, M&M - each is dedicated to microscopy and I learn much by speaking with attendees about their favorite tools","Many commercial shows: The Battery Show, Ceramics Expo, TMS, ASBMR, Neuroscience",Gentle introductions for non-experts. Application-specific workflows that do not dwell much on theory and instead focus on insight (key in commercial).,"There are many interesting applications of Deep Learning, but usually I am interested in evergreen problems of separating features of interest. These could be bones, cells, layers of a battery, etc. It is exciting to do what is new, but recognize that the 'old' problems are still here and troublesome for non-experts. If a Deep Learning tool is a better fit, say so in plain language and try to make the barrier to entry as low as possible. Explain what steps are needed to install the tool and do not assume that the end user is also versed in how to install custom code through pip/conda/apt/brew, etc.","Especially in materials science microscopy we need more raw and annotated data sharing. It is almost non-existent! Dedicated portals for uploading data would be useful, but more broadly a culture of sharing must be fostered.","I work for a commercial image analysis product's sales team. I would say most people come to us with 'traditional' image analysis problems that are not easily addressed by tutorials. Object separation and segmentation are the most common needs. Visualization and measurements are also crucial, but require the segmentation to be good. There are some very exciting recent advancements to object detection and separation, but these are generally published in a rapid prototype manner that are not easily ported to commercial tools. For example, these environments are downloaded as Jupyter or ipynb notebooks. It is difficult to port such code to another tool. Breaking down a useful method like stardist or PolarMask++ into components that can be ported is very helpful when one tries to integrate these tools into other programs.",No
5/20/2022 14:15,Yes,Clinician,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Medicine, Statistics/Biostatistics, Computer vision",Europe,4,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Very interested,Moderately interested,Moderately interested,Somewhat interested,Not at all interested,Moderately interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100)",,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",Basic manual quantitation (none of the above listed problems),All the above listed problems,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Postings on image.sc forum or microforum,People explaining the results of their published work.,Yes. The meetings of the Pathological Society of GB and I,Image analysis theory. Limitations of pre-made tools. Pros and Cons of Open source vs commercial tools. Dangers of closed source tools. Importance of study design to include analysis methods from prior to any hardware selection and image capture.,"They must understand the problems that experimenters need to solve inpractical and contextual detail and not make tools that solve 'problems' they think exist (just because they can 'solve' them) without such background. Also, good documentation and open source.",Learn image analysis theory and take this into account when designing experiments from scratch instead of looking for a tool to solve a problem they come across after image capture. They should learn to code and not just 'script'.,"The survey is biased against coders and in favour of scipters, library useers and tool users. You only give choices about what tools or libraries are used - but i mostly code my own solutions from image analysis theory using C. Me and others like me don't get an appropriate box to tick. Your responses will therefore be biased to tool/library users - unless of course that is your intended audience in which case it doesn't matter.",No
5/20/2022 15:02,Yes,Research scientist,Chemistry/Biochemistry,North America,3,3,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,,,,,,,,2D,Integrated Density ,Integrated Density,Email list,Workshop/tutorial on imaging or image analysis,None,Email list,No,"Yes, ",Low cost densitometry image information.,Look at different scientific disciplines for opportunities.,Make findings more available through open source means.,N/A,Yes
5/20/2022 15:08,Yes,Principal investigator,"Developmental Biology, Statistics/Biostatistics",North America,4,6,6,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Very preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,,2D,,,,,,,,,finding nuclei,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,Email list,,"Evolutionary Developmental Biology, Society for the study of evolution",not sure,,get all of their images into public repositories!,,Yes
5/20/2022 15:58,Yes,Clinician,"Medicine, Statistics/Biostatistics",Europe,1,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Never,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,2D,,,,,,,finding nuclei,"tissue analysis, tumor defining",,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,A discipline-specific society or network,,,,,,,Yes
5/20/2022 16:57,Yes,Facility staff,Developmental Biology,Europe,1,6,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100)",,,,,,,nuclei detection and tracking,finding and tracking cells based on membrane labeling,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,None,Email list,,,,more detailed documentation and tutorials," learn basics of image analysis, participate in workshops etc. ",,Yes
5/21/2022 10:32,Yes,Facility staff,Cell/Molecular Biology,North America,3,3,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",2D,"2D, 2D + time",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,,,,Count cells,Multi marker detection,,,,,,,,,,,,,,Slack-BINA,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Imaris workshop - able to work with our own images + few people attending (more efficient),NA,How to do « good » image analysis / integration of the AI in image analysis,Explain the impact of each step/filter on the image with a preview and correction steps,Know the impact of each step/filter on their image. Are they allowed to do that or this?,,No
5/21/2022 16:02,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",Europe,2,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,3D (<3000x3000x100),3D (<3000x3000x100),,,,,,,,image segmentation,"automated labelling and annotation, automated quantification of precise structures",,,,,,,,,,,,,,Email list,,None,Email list,have not attended,have not attended,,,,,Yes
5/22/2022 8:13,Yes,Research scientist,"Statistics/Biostatistics, Computer science, Computer vision",North America,7,7,7,Look up solutions generally on the internet (Google),Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,3D (SPIM/large volume),,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,,Postings on image.sc forum or microforum,,,acceleration of of algorithms using gpus ,,,,Yes
5/22/2022 13:41,Yes,Facility director,Medicine,North America,4,2,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions on a particular website (please list below)",Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,2D,,,,,,,Detecting cell nuclei,Accurately detecting cell border (cytoplasm) in histology/IHC/IF on tissues. ,,,,,,,,,,,,,,image.sc,Workshop/tutorial on imaging or image analysis,Some,Postings on image.sc forum or microforum,"Well targeted to audience, interactive, engaging speakers",No,Image analysis for research pathology,Engage with pathologists,Provide feedback to creators in forums such as image.sc,"I am a pathologist using image analysis in my research pathology service. I was surprised by the lack of mention of pathology in this survey, given the critical role pathology plays in tissue based image analysis and the common use of image analysis by many research pathologists. Pathologists often do not feel represented in organizations and efforts such as those represented by this survey, which tend to focus more on biologists, therefore we tend to work among ourselves to discuss and learn about image analysis and develop new methods, but I think pathologists and biologists could benefit from more interactions between each groups on image analysis. This is already happening in some places, for example the image.sc Qupath forum.",No
5/23/2022 5:14,Yes,Image/data analyst,"Physics/Biophysics, Chemistry/Biochemistry, Computer science, Computer vision",Europe,7,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Sometimes,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,3D (<3000x3000x100),,,"2D, 2D + time",,,,Open source multidimensional visualisation,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Email list,Neubias - included many examples of different image analysis solutions,,,,"Standardise imaging conditions - too often given images with varying settings (e.g. exposures, laser powers, channel orders)",,Yes
5/23/2022 5:50,Yes,Image/data analyst,"Cell/Molecular Biology, Medicine, Statistics/Biostatistics, Deep learning",Europe,6,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,"2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time","2D, 2D + time",2D,"2D, 3D (<3000x3000x100)",2D,2D,"2D, 2D + time",,,"Segmenting Nuclei, single particle tracking, shallow learning (e.g. Weka)","3D cell tracking, single plane confocal segmentation, ",,,,,,,,,,,,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,The Microscopy Society of Ireland always holds fantastic conferences with a huge range of modalities. It's great to see approaches for image analysis from non-biological fields as they provide a completely different grounding for approaching certain tasks,"Honestly, I think every biology conference could benefit from this, especially just in getting the researchers to actively think about alternative imaging/analysis approaches that might be more applicable for their research","For my personal work, a topic on making high-level image analysis techniques and pipelines accessible for users (e.g. using GUIs, or guidance on how to structure instructions) would be greatly beneficial for myself, and a lot of other analysts that perform similar roles to me)","Providing access to source code and good documentation would help a lot, lots of time is spent trying to figure out coding options for specific software (more often commercial than open-source)",Thinking about the analysis stage when they're planning their experiments,,Yes
5/23/2022 6:07,Yes,Facility staff,Physics/Biophysics,Europe,2,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Moderately preferable,Very interested,Moderately interested,Moderately interested,Very interested,Not at all interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,,,,,,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,,,,,,,No
5/23/2022 6:08,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,4,5,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,2D,,,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,None,My local microscopy facility,,,,Make the tutorials more accessible for people without compsci backgrounds. ,,,No
5/23/2022 6:11,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,2,2,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all interested,Somewhat interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",2D,2D,2D,,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,None,Email list,,,,more user guides to analysis and software outputs,,,No
5/23/2022 6:19,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,3,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Often,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,,,,,,,,"Cell counting, tissue analysis",Data normalization,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,None,Word of mouth,"Yes, a 3 day workshop that showed multiple tools and image types",No,"More script orientated tools (Python, R, ...)",,,,Yes
5/23/2022 6:42,Yes,Undergraduate/Graduate student,Medicine,Europe,4,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Moderately preferable,Moderately preferable,Somewhat interested,Somewhat interested,Not at all interested,Not at all interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,,,,,,,,Automated selection and analysis of tissue areas ,,,,,,,,,,,,,,Word of mouth,,None,Email list,,,,,,,No
5/23/2022 7:20,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,2,5,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,,,,,2D,,"3D (<3000x3000x100), 3D (SPIM/large volume)","Cell segmentation (cellpose, KNIME workflows w/training data, etc. - lots of options and documentation out there).","Analysis of non-SMLM super resolution data/ considerations to be taken when adapting epi techniques to say, SIM or STED outputs ",,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,My local microscopy facility,ESRIC summer school - good balance between theory lectures and practical workshops. ,,SPT analysis - there are a lot of tools available but choosing the right one is very intimidating for a new user!,"Especially for open source tools, better documentation!! Even some very popular tools have documentation that assumes a relatively high baseline of coding knowledge which can either scare away new users or lead them to applying the tool incorrectly. Perhaps a documentation best practice guide?",Consider analysis needs before starting data collection!! ,,No
5/23/2022 7:47,No,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
5/23/2022 8:12,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Not at all interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)",2D,,,,,,,,finding nuclei,Foci analysis - DNA damage,,,,,,,,,,,,,,My local microscopy facility,,None,My local microscopy facility,,,,"Good supporting information, tutorials available on how features can be used.",,,No
5/23/2022 10:38,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,,,2D,,,,,,,,,,,,,,,,,,,Email list,,None,My local microscopy facility,,,,,,,No
5/23/2022 10:54,Yes,Facility director,Physics/Biophysics,Europe,3,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Other commercial software (Avizo, Imaris, Volocity, etc)","2D, 3D (<3000x3000x100), 3D (large volume)","2D, 3D (<3000x3000x100), 3D (large volume)","2D, 3D (<3000x3000x100), 3D (large volume)","2D, 3D (<3000x3000x100), 3D (large volume)",,,,"2D, 3D (<3000x3000x100), 3D (large volume)",,,,Email list,,None,A discipline-specific society or network,,,,,,,Yes
5/23/2022 10:55,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,3,3,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D + time","2D + time, 3D + time",,,,"2D + time, 3D + time",,,,,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/23/2022 12:50,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",Europe,4,5,3,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",None,"2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,,,,finding nuclei,"tissue analysis, analysis of super-resolution data",,,,,,,,,,,,,,My local microscopy facility,,None,Email list,,,how to use a certain tool for a certain kind of experiment,Be User Friendly,,,Yes
5/23/2022 12:52,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",North America,6,7,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D (SPIM/large volume), 3D large volume + time",,,,,"2D, 2D + time",,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,Twitter,,,,,,,Yes
5/23/2022 12:57,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,4,2,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions on a particular website (please list below)",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,A discipline-specific society or network,,,,,,,No
5/23/2022 12:58,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,3,2,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all interested,Somewhat interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,"Colocalization for 3 channels, colocalization in 3D, cell tracking in time",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,My local microscopy facility,,,Coding for image analysis of high content/high number,GUI with explanations similar to PRISM for statistics,,,Yes
5/23/2022 13:07,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",Europe,4,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Somewhat preferable,Not at all preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,,,,,,,Nuclei detection (yay stardist),"Multiplex membrane detection in tissue sections, digipathology, cell tracking in fast moving cell cultures, 3D intravital 2 photon tracking",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,All of the above,Neubias training school -Imaris webinars,ELMI,Multiplex analysis,Provide training to facility staff as they can train researchers at the institute. Like a positive pyramide scheme,Interact with tool developers and send problematic datasets/problems,It’s difficult to stay up to date of all the tools. Training the people using them is essential. Really enjoyed the in person neubias training where as a microscopist you interact with tool developers. The online trainingschools were also very useful but in-person is more bidirectional. ,Yes
5/23/2022 13:14,Yes,Principal investigator,Cell/Molecular Biology,Europe,2,4,4,"Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Not at all preferable,Moderately preferable,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time",,,3D (<3000x3000x100),,,,,,,segmenting 3D EM data,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/23/2022 13:18,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",Asia,5,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,,"2D + time, 3D (<3000x3000x100), 3D large volume + time",,,,,,,,,Nucleus segmentation is pretty good.,"Image segmentation - both brightfield and fluorescence images, especially segmentation of 2P calcium/voltage imaging data.",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,,,More detailed video tutorials of tools like ImageJ as well as how to process images to make them ready for publication would be great.,"I think there should be easy ways of going between different platforms - MATLAB/Python interfacing with ImageJ, for instance. Certain things are easier and more visual in ImageJ (like drawing regions of interest). Writing complicated analysis code and batch processing is much easier in MATLAB, in my opinion. And certain things like DeepLabCut selectively work in Python. If there were ways to easily import and process images between these softwares, I think it would facilitate testing out new analysis plugins, for example.
I don't know how to encourage developers to do this, unfortunately. 😅 But maybe getting funds to specifically hire interdisciplinary team of both biologists/experimentalists and computer scientists to work on this would help.","I think they should be clearer about how they did their analysis and be more consistent and objective about analysis. I think guidelines of ""good practice"" would help. Like ""good practices for coloc analysis"" or ""good practices for saving intermediate analysis images"" etc. I think it would improve reproducibility.",,Yes
5/23/2022 13:23,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",North America,2,3,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,"2D, 3D (<3000x3000x100)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,,,,Yes
5/23/2022 13:43,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,5,3,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Not at all preferable,Somewhat interested,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Not at all interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,3D + time,,,2D,,,,,,Finding nuclei,,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Twitter,,,,,Developing curricula that non CREATOR faculty could implement to teach in grad school,,No
5/23/2022 14:01,Yes,Facility staff,Chemistry/Biochemistry,North America,2,2,2,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,,"2D, 3D (<3000x3000x100)",,,"2D, 3D (<3000x3000x100)",,,Cells,Super resolution ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,,,,,,,Yes
5/23/2022 14:07,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",Europe,4,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,"co-localization of multiple channels (3D for two colors and 2D for more then 2 colors), 3D segmentation",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,,,,,Yes
5/23/2022 14:11,Yes,Postdoctoral fellow,"Physics/Biophysics, Statistics/Biostatistics",North America,7,6,6,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","plenty, but always room for improvement",quantitative platform that contains everything,,,,,,,,,,,,,,Twitter,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,Yes
5/23/2022 14:16,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Not at all interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Very interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",2D,"2D, 2D + time","2D, 2D + time",2D,,,,,,,finding nuclei,"Threshold decision, foci analysis, stripe analysis",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,no,no,how to use a certain tool for a certain kind of experiment,Use more accessible language and more comprehensive tutorials,Acquire images in best resolution possible,,Yes
5/23/2022 14:19,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,3,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,"3D + time, 3D large volume + time","3D + time, 3D large volume + time",,,,,,,,,,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,A discipline-specific society or network,,,,,,,Yes
5/23/2022 15:13,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology, Computer science",North America,4,6,7,Sit down with a tool I know and start playing with the data,Most of the time,Somewhat preferable,Somewhat preferable,Not at all preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all interested,Not at all interested,Not at all interested,Moderately interested,Somewhat interested,Not at all interested,Not at all interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,2D,,,,,3D (<3000x3000x100),2D,Nuclear segmentation; particle tracking; registration/alignment,"cytoplasm/whole-cell segmentation; tracing/tracking of broken lines from imperfect staining (e.g., filaments, cell membranes)",,,,,,,,,,,,,,"Postings on image.sc forum or microforum, A discipline-specific society or network, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Email list,Easy illustrative examples that can be followed in real time during webinar.,American Society for Cell Biology (ASCB),napari,,"Learn basic scripting, perhaps facilitated by providing simple templates, e.g., loops to process all images in a folder or all images that are currently open.",,No
5/23/2022 16:13,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",North America,6,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,,"2D, 3D (<3000x3000x100)",,,,,,,,,"counting cells, 2D cell shape analysis","analysis of cell orientations, analysis of cell stress fibers",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,"Summer Biomechanics, Bioengineering, and Biotransport Conference",,"Better documentation/examples of final results from image analysis, describe how to interface outputs from image analysis with commonly used statistical analysis software (PRISM, MATLAB, R, etc.)",Add more image analysis code/pipelines to repositories (ie GitHub),,Yes
5/23/2022 17:08,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","2D, 2D + time",,"2D, 2D + time, 3D + time",,"2D, 3D (<3000x3000x100)",,,,,,,Finding nuclei and well stained organelles,"Segmentation, cell motility, high noisy images",,,,,,,,,,,,,,Twitter,,Few,Email list,,,Basic scripting and coding,Wygiwys approach,Standardize procedures and describe them in detail in m&m sections,,Yes
5/23/2022 17:45,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",North America,4,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Not at all interested,Very interested,Moderately interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time",,,,,,,,,,Neurite tracing in noisy background with quantification of characteristics,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,"often tools can be inaccessible because I don't understand the basics (like I couldn't figure out how to download a program or don't know how to modify a macro to make it more general). Or like, I don't know how to get someones code on github into a thing I can use. What do I click on, what do I need to download? These are SUPER basic but are huge limiting factors for me and many of my labmates. ",,,,No
5/23/2022 18:04,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Medicine",North America,4,4,5,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time","2D, 2D + time",,2D,,,,,,,analysis of multichannel fluorescent temporal data,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,Email list,,,,,,,Yes
5/23/2022 18:17,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology, Computer science",Europe,2,4,2,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,"2D, 3D large volume + time",,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,Neubias schools,Neubias conferences,,,,,No
5/23/2022 18:18,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,4,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time","2D, 2D + time","2D, 2D + time",2D,2D,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,,,Yes
5/23/2022 18:46,Yes,Facility staff,Cell/Molecular Biology,Australia,3,4,6,Ask on forum.image.sc,Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,3D (<3000x3000x100),3D (<3000x3000x100),,,,,,3D (<3000x3000x100),,Finding nuclei,tissue analysis,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,Youtube tutorials,,All listed suggestions would be useful ,Have examples of real world data sets when developing analysis tools,Use correct data acquisition settings- education is key,,Yes
5/23/2022 19:05,Yes,Postdoctoral fellow,"Medicine, Computer science",North America,3,5,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time",2D,"2D, 2D + time",2D,,,,,,,n/a,n/a,,,,,,,,,,,,,,Twitter,,None,Twitter,"honestly, I do not think biologists need to or want to go to a conference solely dedicated to imaging. such workshop should however be a part of conference.",n/a,n/a,basically just streamlining it for people w/o comp background,provide feedback to creators? that would require have them as testers I guess,,No
5/23/2022 19:30,Yes,Facility staff,Developmental Biology,Europe,4,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Somewhat preferable,Very preferable,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",2D,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,"2D, 3D (<3000x3000x100)",2D + time,,finding nuclei,Object classification (more on the clarity and user interface side),,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,Yes. The great tutors and their availability for the dumbest of questions,NEUBIAS,Teaching core computer vision and programming concepts and paradigm to facility staff how want to delve deep into Image Analysis,"Create more intuitive GUIs. For that, a very good QA is needed, which will most likely not happen because there's not enough money for it",Don't know.,"People will lose their interest in the field if the experts are not open to teach and help them. If topics are explained without deconstructing the logic behind them, new users will be scared away from them. This will ultimately mean that we'll develop tools to be used by experts who also prefer to develop their own tools, thus creating an unnecessary sea of software tools that are used by no one. It'll be a private club for a selected few with no interest in bridging the gap between users and developers. Which is not so different from the beginnings of scientific groups (case in point, the London royal society in 17th Century. Throughout history, Science has always been the hobby of the rich/privileged. A fact that does not seem likely to be changed anytime soon)",No
5/23/2022 19:39,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",North America,4,3,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Never,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D + time",,,,,,,,,segmentation,relationships between objects in 3D + time,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Website compiling this information,https://www.edx.org/course/image-processing-and-analysis-for-life-scientists ,,3D analysis,,,,Yes
5/23/2022 19:57,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,2,3,4,Sit down with a tool I know and start playing with the data,Never,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D + time,3D + time,3D + time,,,,,,,,,,,,,,,,,,,,,,,,Twitter,,None,My local microscopy facility,,,,,,,Yes
5/23/2022 20:14,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",North America,3,2,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Somewhat interested,Very interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)","2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,Not confident to answer,Not confident to answer,,,,,,,,,,,,,,My local microscopy facility,,None,Email list,No,Spatial/3D-oriented conferences in general - I think large spatial data is particularly challenging,"Comparisons between pieces of software and which is suitable for what data sets, how to use certain tools, explanations of automated aspects of specific tools (e.g. segmenting algorithms)",More software being open source would be great - so much of what is done in my field is so specific to individual experiments/to wet lab conditions that modularity and ability to mod are great.,,,Yes
5/23/2022 21:30,Yes,Clinician,Medicine,North America,4,4,5,Sit down with a tool I know and start playing with the data,Never,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,3D (<3000x3000x100),3D (<3000x3000x100),"2D, 3D (<3000x3000x100)",2D,,,,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,,,,No
5/23/2022 21:48,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Australia,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time",,,,,,,,Segmenting nuclei or other bright and spaced out samples,Segmenting low-fluorescent cell samples,,,,,,,,,,,,,,Twitter,,None,Twitter,,,How to take an image for image analysis. Most problems I've seen from end users are simply they do not understand what is needed for successful segmentation of their samples,,,Keep up the good work,Yes
5/23/2022 22:31,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Chemistry/Biochemistry",North America,3,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,3D large volume + time,,,,,,2D,2D + time,,,,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,Aqlm at mbl,,,,,,Yes
5/23/2022 23:13,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Cell/Molecular Biology, Developmental Biology",North America,3,4,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,Finding nuclei in monolayers,Finding nuclei in dense layers and correlating it with different channels,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,Comparisons between different segmentation tools and how to optimize them,Better documentation on the parameters that could be changed (vs what is ok to keep on default),Best practices on how to report usage of those tools. I've often had a hard time replicating image analysis results from papers,,Yes
5/23/2022 23:36,Yes,Research scientist,Physics/Biophysics,Asia,5,5,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Somewhat interested,Physical Sciences,,,,,,,,,,,,,,,,"Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,,,,,,,"2D + time, 3D large volume + time",,,segmentation and tracking,Twitter,Workshop/tutorial on imaging or image analysis,None,Twitter,,,,,,,Yes
5/23/2022 23:37,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all interested,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,None,Email list,,,,,,,Yes
5/23/2022 23:42,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Developmental Biology",North America,4,6,6,Look up solutions generally on the internet (Google),Often,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,3D + time,,,,,,,,,,"Cell tracking, PIV, strain measurment",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,Tutorials and documentation,,Yes
5/24/2022 1:19,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,3,4,2,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Not at all preferable,Not at all preferable,Not at all interested,Somewhat interested,Somewhat interested,Very interested,Not at all interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,2D,,,,,,Finding nuclei,Dealing with autofluorescence and background,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,,,Yes
5/24/2022 1:53,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",North America,4,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Somewhat interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",2D,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",3D large volume + time,2D,,,,,,,finding nuclei (unless they are too close together),"lineage analysis, finding cell boundaries of cells that are touching during embryo growth and development, correlating subcellular features (e.g., organelle movements; changes in pH/voltage/Ca+2 concentration) with larger scale cell and tissue behaviors (e.g., cell shape changes due to proliferation, differentiation, or tissue morphogenesis).",,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Email list","Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,"Hard to find generalizable solutions...since I'm not a programmer, it's hard to find someone interested in my specific problem (which is partly why we rely on imaris)",single file format that can be imported and analyzed across all platforms,,Yes
5/24/2022 2:09,Yes,Facility staff,Cell/Molecular Biology,Europe,5,3,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,2D,,,2D + time,,,,"Storm analysis, segmentation of some structures when signal is poor, image registration ",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Email list,"Neubias, variety of content and known image analists",,Practical examples are always very good for teaching purposes. ,Comunication with scientific community to create easy to follow pipelines or GUI,Best practices guidelines,,Yes
5/24/2022 2:14,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,3,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Sometimes,Not at all preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,3D (<3000x3000x100),,,"Nuclei segmentation, tracking","Automatic segmentation and guided proof-reading, finding structures in data",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,I2K,,,More interactive/easy to use manuals,Tighter interaction with professionals like imaging/data analysis facility ... Try to understand what is being done,,Yes
5/24/2022 3:27,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,3,4,4,"Ask a friend or colleague to help me, Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,3D + time,,,,,,,,,tracking segmented objects over time,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,Self paced learning mathworks tutorial image analysis. Hands on. Can structure learning time flexible. ,,Learning how to automate image analysis processes for big data using coding,,,,No
5/24/2022 4:43,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",Europe,4,3,5,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,2D,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,"Word of mouth, Email list",Workshop/tutorial on imaging or image analysis,None,Email list,,,,,,,No
5/24/2022 6:04,Yes,Postdoctoral fellow,Cell/Molecular Biology,Europe,3,2,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 3D (<3000x3000x100)",,2D,2D,,,,,,"Nuclei segmentation, semi automated user guided segmentation ","Accurate segmentation of non-round structures, denoising, data visualization ",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Email list,"Neubias tutorials, star dist présentation ","Imaging conferences not always accessible for scientists of all disciplines (funding reasons, unis unwilling to pay attendance if you’re project isn’t an imaging topic). Online retranscription or video repository would be nice ","Advanced tutorials, advanced macro scripting, focus on a specific image type or sample type ","Advertise beta versions so they can be user tested, facilitate communication between creators and users (helplines ?) ","Keep up to date with new options, adhere to best practice guidelines ",Open access and free softwares are crucial and we are thankful for them,Yes
5/24/2022 7:16,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",North America,4,5,1,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Not at all preferable,Somewhat preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,,"3D (<3000x3000x100), 3D (SPIM/large volume)",,3D (<3000x3000x100),,,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,Email list,,,,,,,Yes
5/24/2022 9:03,Yes,Principal investigator,Chemistry/Biochemistry,Asia,4,2,4,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D + time, 3D (<3000x3000x100)","2D + time, 3D (<3000x3000x100)","2D + time, 3D (<3000x3000x100)","2D + time, 3D (<3000x3000x100)",,,,,2D + time,2D + time,,Cell morphology analysis ,Super-resolution cluster/colocalization analysis ,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,None,Email list,No,No,Open-source and user-friendly options ,Very elaborate protocols including justifications for dummies. This is very useful for end-users with little to no coding knowledge. ,All users must know the limitations for the techniques that they use and figure out the best imaging techunique for the specific question they are addressing.,,Yes
5/24/2022 9:20,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,3,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D + time,,,,,,,,,,,,,,,,,,,,,,,,Twitter,,Some,Twitter,,,,,,,Yes
5/24/2022 10:25,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,5,5,5,Sit down with a tool I know and start playing with the data,Most of the time,Not at all preferable,Very preferable,Very preferable,Not at all preferable,Moderately preferable,Not at all preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D (SPIM/large volume)",,,,,,,,,,,,,,,,,,,,,,,,"Twitter, Email list",Workshop/tutorial on imaging or image analysis,Few,Email list,,,,"For Python tools specifically, I see a lot of YouTube videos showing the POWER of certain tools (e.g., look at all these cool things we can do in Napari), but very few videos showing step by step tutorials to access the power of these tools. Specifically, lets's download Anaconda, make an environment, install napari and plugin libraries, open a shared datasets, and apply these tools step by step (a channel producing content like this in the deep learning sphere is youtube.com/c/NicholasRenotte). 

IMO Robert Haase has by far the best step by step tutorials (notebooks) for new users, but if anybody is feeling outgoing, equivalent YouTube videos  would I think be quite popular in the imaging community. ",,,No
5/24/2022 10:51,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,4,5,4,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Email list,,,,,,,Yes
5/24/2022 12:24,Yes,Research scientist,"Developmental Biology, Statistics/Biostatistics, Computer science",North America,3,3,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Not at all preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,2D,,,,,,"roi for contrasting regions of an image, nuclei or whole cell counting if non-overlapping","distinguishing overlapping cells or nuclei for counts, selecting row that are not very fifferent in contrast",,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Many,Email list,free and online resources are always best for cost and convenience,,,menu driven scripting to overcome coding inability,a forum to enter requests or issues related to their analysis ,,Yes
5/24/2022 12:37,Yes,Facility staff,Cell/Molecular Biology,Europe,2,4,5,Look up solutions generally on the internet (Google),Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)",,,,,,"2D, 3D (<3000x3000x100), 3D large volume + time",,,,,,Denoising,Tem tomography segmentation ,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,Ors Dragonfly tutorials,,Low deep learning floor difficulty,Get far away from plugins that stop being supported like it happens a lot in fiji,Be less willing to use badly designed GUIs and half baked solutions,Web browser based solutions are nice,Yes
5/24/2022 12:45,Yes,Research scientist,Cell/Molecular Biology,North America,4,5,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Very interested,Somewhat interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D + time,3D + time,3D + time,3D + time,,,,,,,,"Segmenting nuclei, tracking blobs","Segmentation of single cell membranes in dense FOVs, particularly in phase imaging",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Postings on image.sc forum or microforum,,,"Building napari plugins for plug and play modules of numerous analysis tools with cooperating file formats (cellprofiler, cellpose, aics structure segmenter, tracking plugins)",Have dedicated personnel contributing to image.sc forums for active iteration and quick responses and discussions,Provide open datasets and descriptions of their metadata and analysis goals,,Yes
5/24/2022 17:13,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",South America,3,1,1,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",2D,,3D large volume + time,,2D,,,,,3D + time,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,My local microscopy facility,,,,,,,Yes
5/24/2022 17:14,Yes,Principal investigator,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,4,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 2D + time, 3D (<3000x3000x100)",,2D,2D,2D,,2D,,,"Counting particles, co-localization, measuring","super-resolution acquisition and processing, co-localization",,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter",Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
5/24/2022 18:30,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology",Australia,3,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D (SPIM/large volume)","2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,,,,,,,Locating sample,handling of large data files by imaging software,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Some,Email list,,,Automating image analysis using software,Ease of use for UI for better experience for all users of all levels,,,No
5/24/2022 18:40,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Somewhat preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,"2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time",,,,,,,,"nuclei segmentation, bandpass filtering for background/noise reduction, basic deconvolution","whole cell segmentation, object tracking in time, high content that still requires a manual threshold ",,,,,,,,,,,,,,new PI slack group,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,"Advanced Imaging Methods Workshop at UC Berkeley, for new tool and technique development",Large society conferences like ASM or ARVO could have an imaging workshop session to address challenges in specific biological systems,"Focus on open source options, not software where access is an issue. ",Make new FIJI plugins compatible with macros for batch processing.,"Publish any filtering or post processing done on images as a series of commands, instead of  excluding these steps from their methods. ",,No
5/24/2022 19:07,Yes,Undergraduate/Graduate student,Physics/Biophysics,North America,3,5,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D + time,,3D + time,,,,,,,,,,Automatic tissue segmentation of prokaryotic cells,,,,,,,,,,,,,,Twitter,,None,Twitter,,,Software ,,,,No
5/24/2022 19:35,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",North America,2,2,2,Ask a friend or colleague to help me,Never,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all interested,Moderately interested,Very interested,Not at all interested,Not at all interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,2D,,,,,,,,Cultured mammalian flat cell analysis as opposed to cells in embryos,Imaging embryos,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,Make analysis possible with 0 coding skills by users (point and click),,,No
5/24/2022 20:16,Yes,Postdoctoral fellow,Chemistry/Biochemistry,North America,4,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)",,,,2D,,,Segment and threshold images to identify objects ,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,Rob Philips python for biologists boot camp. Interactive and well documented ,,,,,,No
5/24/2022 22:22,Yes,Research scientist,Cell/Molecular Biology,North America,3,5,4,Sit down with a tool I know and start playing with the data,Sometimes,Moderately preferable,Very preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 3D + time",,"2D, 3D + time",,,2D,,,2D,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,None,A discipline-specific society or network,,,,,,,No
5/24/2022 22:29,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",South America,2,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Very interested,Moderately interested,Very interested,Somewhat interested,Not at all interested,Somewhat interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,2D,2D + time,2D,,,,,,,,,,,,,,,,,,,,,,Twitter,,Few,Twitter,,,,,,,Yes
5/25/2022 0:14,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",Asia,4,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Not at all preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat interested,Somewhat interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D + time, 3D + time",2D,,,,,,,,Finding and segmenting nuclei and cell boundaries and ,Segmenting structured with Low SNR,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list, ,,Image J macros / Python ,,,,Yes
5/25/2022 0:45,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Statistics/Biostatistics",North America,4,7,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Never,Not at all preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",,,,,,,,,Resolution,,,,,,,,,,,,,,Twitter,,None,Twitter,,,,,,,Yes
5/25/2022 4:01,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",Europe,3,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Moderately preferable,Moderately preferable,Very preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D + time, 3D + time",,3D + time,,,,,,,,,"Basic analysis of fluorescence intensity, simple segmentation ",3D segmentation (cell outlines/nuclei),,,,,,,,,,,,,,A discipline-specific society or network,Workshop/tutorial on imaging or image analysis,Few,Twitter,"I went to a Cell Profiler workshop which was interesting but as I didn't have immediate need, I never put it into practice.   Ability to ask questions (and listen into to other's questions) was great.  I'd encourage lab members to attend.",,,,,,Yes
5/25/2022 4:39,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology, Deep learning",Europe,3,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Moderately interested,Somewhat interested,Very interested,Not at all interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100)",,,,,,2D,2D,,"Within our scope (mostly rod shaped bacteria) there's some improvement possible for 2D segmentation, cell tracking, and 2D SMLM by simultaneously considering xyzt but pretty close to optimal.",Estimating and subtracting background from input of segmentation and fluorescence image trained by images with no signal where cell to cell background is sum of autofluorescence and unbound reporters at variable concentrations.,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,,,,"Underdocumentation is the norm and docs rarely keep pace with software versions. Text/video tutorials today are much better than what came before, though, and the trend is in the right direction. For ML approaches requiring sorting out GPU/driver/library cross compatibility, it would be amazing to adopt one cross platform standard to be stable for 2 years at a time. Colab notebooks are a good step in the right direction there but have their own drawbacks.","Take time to look at images first and phrase what they want to measure as a testable hypothesis, thinking about how intensities and other measurable relate to reality. Typically people are trying to put a number on what they see, they don't always start with the right number, and this leads to momentum not towards the ideal analysis that's hard to reverse.",,No
5/25/2022 4:57,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Africa,4,2,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D + time,3D + time,3D + time,3D + time,3D + time,,,2D,,,,,,,,,,,,,,,,,,,Twitter,,Few,Email list,,,,,,,Yes
5/25/2022 8:28,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology, Developmental Biology",North America,4,2,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Very interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D + time,,,2D,,,,,,,,,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,"Icy training (very hands on, small group, thorough workshop), FIJI macro workshop (hands on, practice writing macros and examples of what fiji can do with this tool)",,,,,,Yes
5/25/2022 9:33,Yes,Facility director,Chemistry/Biochemistry,North America,4,2,2,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Not at all preferable,Somewhat preferable,Moderately preferable,Not at all interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D,,2D,,2D,"2D, 3D (<3000x3000x100)",,,,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)","super-resolution, denoising",segmentation,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Word of mouth,ORS dragonfly and Rigaku monthly virtual workshops,,More Deep Learning,More online training and practical workshops such as what ORS has done over the past 2 years.,Suggest more sessions at national confeences and practical hands of workshops and training. MAybe even organization of soem of the series already out there so they are easier to find,,Yes
5/25/2022 9:43,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,3,3,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,2D,,,"Segmentation, object detection, particle tracking","Velocity and force measurements, analysis of 3D data",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
5/25/2022 9:48,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology",Europe,5,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Not at all interested,Not at all interested,Moderately interested,Very interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,,2D + time,,,3D (SPIM/large volume),,,,,,,,,,,,,,,,,,,,,Twitter,,None,Twitter,,,,,,,No
5/25/2022 11:22,Yes,Principal investigator,Cell/Molecular Biology,North America,2,3,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Not at all interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)",2D,2D,,,,,,,finding nuclei and watershed cells with very consistent cytosolic marker,"counting bacteria within cells, finding particles/vesicles, analyzing localization near objects of different sizes.",,,,,,,,,,,,,,"Word of mouth, Slack",,None,Twitter,,ASM Microbe,Training on open source tools for beginning undergraduate and early graduate students,,clearer best practices and staining + imaging guidelines ,,Yes
5/25/2022 11:39,Yes,Principal investigator,Cell/Molecular Biology,North America,3,2,5,Ask a friend or colleague to help me,Sometimes,Not at all preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Not at all interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D + time",2D + time,,,,2D,,,,"finding nuclei, counting spot and foci, colocalization","segmentation of intracellular organelles and characterization of paramenters (i.e. mitochondria tracks and lenght, diameter). Co-localization and counting of spots on subcellular organelles",,,,,,,,,,,,,,"Word of mouth, Twitter",,Few,Email list,,,Subcellular structures analysis and deep learning / training set ,"clearly define what biological questions can be answered from each tool. ImageJ contains hundreds of plugins and unless you know exactly what you find, you cannot just browse",preparing short video summing up what a tool do on an image,I would love to have access to a cost friendly imaging course. The only one I am aware is about 10K which is 1/5 of my startup package.,Yes
5/25/2022 13:27,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",Europe,3,1,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Not at all interested,Somewhat interested,Moderately interested,Very interested,Not at all interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,3D + time,,,,,,,,,NA,NA,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,NA,NA,NA,NA,NA,NA,No
5/25/2022 14:51,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",Europe,4,5,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D + time,,,,,,,3D (<3000x3000x100),,"Cell segmentation, particle tracking","Extracting forces, sptPALM (localization microscopy), deep learning",Twitter,,None,My local microscopy facility,,,,,,,No
5/25/2022 15:08,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",North America,1,2,6,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D large volume + time,3D large volume + time,3D large volume + time,3D large volume + time,2D + time,3D large volume + time,3D large volume + time,3D (<3000x3000x100),3D large volume + time,3D large volume + time,,,"deconvolution, noise removing",,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Postings on image.sc forum or microforum,,,,,,,Yes
5/25/2022 15:14,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Statistics/Biostatistics, Deep learning",North America,6,5,5,Look up solutions generally on the internet (Google),Often,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 3D (<3000x3000x100)",,,,,,,,,,Segmentation of nuclei (once found),,,,,,,,,,,,,,Word of mouth,,None,Word of mouth,,,"Segmentation of images, deep learning for image analysis","Consistently posting code with papers, making that a requirement for image analysis-based papers at journals",,,No
5/25/2022 15:39,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,2,3,4,Sit down with a tool I know and start playing with the data,Never,Somewhat preferable,Very preferable,Very preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time",,,,,,,,,Resolution,Chloroplast autofluorescence,,,,,,,,,,,,,,Twitter,Conference session on imaging or image analysis,Few,Twitter,No,Yes,Protocols for plant biology,Making it as user friendly as possible,Keep informed of new developments,,Yes
5/25/2022 15:50,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,5,6,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,,,,,,,Yes
5/25/2022 17:19,Yes,Image/data analyst,"Physics/Biophysics, Computer science",Asia,7,5,6,Sit down with a tool I know and start playing with the data,Often,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D + time",2D,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,,,,,"Finding round nuclei, sparse to dense (but not extremly dense)","Segment dense cells in 2d/3d tissues,  segment blood vesssels especially hollow,  smfish spots detection especially 3d, neuron tracing, registration/alignment, phenotype cells,  ...",,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,Email list,"Hands-on, networking, top quality teachers, presenting advanced tools and methods, presenting workflows, accompny material, pre-course learning requirments",,"Multiplex data, spatial analysis - whole worklows, spatial statistics theory, rna/fish analysis , building worklows for speciific problems,   data science from images,
 latest advanced tools and methods
How to use certain tools, advanced scriptimg/automation,    overviews and comparisons as well ","Open access, good documentation, webinars, training workshops, join and be active on image.sc !  Long-term Maintanance and bug fix , interact with users for usability and requested features ","Interact with the developers and community, Ask detailed questions , report bugs , ask for features.   Cite software !  Publish detailed description of worflows and make the scripts/macros available

Encourage by teaching, talks at comferences , guidelines by journals","Networking and community building is super importamt, image analysts have very important role in all the above, funding is needed for tools development and maintanance, and also for building the analysts community and support training by amalysts - NEUBIAS model should revive and get funded",Yes
5/25/2022 18:08,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,2,2,4,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Not at all preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",2D,"2D, 3D (<3000x3000x100)",,,"2D, 3D (<3000x3000x100)",,,,actyn fibers analysis ,,,,,,,,,,,,,,The Images2Knowledge(I2K) conference,Conference dedicated to imaging or image analysis,Few,Email list,I2K 2022,,"There might be example of several applications, solved by different software platforms ","I think there should a common and large platform, kind of database, where developers could post their software, tools, plugins, etc and put examples of how those could be applied to solve a specific problem. Probably an Imaging network, such as the GBI, BINA, COBA, etc, could create such database so that all of us, microscopists and software developers could have access to. I'm saying this because there are a lot of tools scattered elsewhere and at some point we don't even know they exist. However, even some FIJI plugins lack a better explanation of how they work. ","by creating a common and large platform where several distinct imaging topics or problems,  analyzed by any software, plugins, etc, could be posted as examples, so that they can be used as a guidance by us, the users, to solve our own imaging problems. ",,Yes
5/25/2022 18:52,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,1,3,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,3D (<3000x3000x100),3D (<3000x3000x100),,3D (<3000x3000x100),,,,,Finding nuclei ,Cell boundaries in tissue histology ,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,Cell profiler. Tutorial was very clear and TAs were really helpful,,"Colocalization, Cell morphology quantificarion",,,,Yes
5/25/2022 20:19,Yes,Postdoctoral fellow,Cell/Molecular Biology,North America,2,1,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Very interested,Not at all interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",3D + time,,3D large volume + time,3D large volume + time,2D,3D large volume + time,2D,,3D (<3000x3000x100),,,co localization,trafficking  ,,,,,,,,,,,,,,Twitter,,None,Twitter,,,,,,,Yes
5/26/2022 0:43,Yes,Principal investigator,Cell/Molecular Biology,Europe,4,3,5,Ask a friend or colleague to help me,Sometimes,Not at all preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D + time",2D,"2D + time, 3D large volume + time",2D,,,2D + time,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,,,Yes
5/26/2022 1:03,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology, Computer vision",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Not at all preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D + time,,"3D + time, 3D (SPIM/large volume)",,,,,,,,3D + time,Finding ultra high contrast nuclei in sparse images,Finding low contrast nuclei in dense samples in 3d,,,,,,,,,,,,,,"Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Email list,,,,,,,Yes
5/26/2022 4:35,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Australia,4,5,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,2D,,2D,,,2D,,,particle analysis,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,interactive seminars with question sessions ,,,,,,Yes
5/26/2022 7:07,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology, Computer vision",Europe,5,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 3D (<3000x3000x100)",,,,,,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",,Finding and analysing small spots,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,"Embl course in machine learning, set a good Basis of the Tonic and have confidence Go dich deeper",,,,,,No
5/26/2022 7:45,Yes,Facility staff,Physics/Biophysics,Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,,,,,,,No
5/26/2022 9:02,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,3,2,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Not at all interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (<3000x3000x100),3D (<3000x3000x100),,,,,,,,segmentation of nuclei and counting,segmentation of of non-circular objects,,,,,,,,,,,,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,My local microscopy facility,Step by step guide with examples,,,more automation and prepackaged programs,learning core concepts of image analysis and working through prepared tutorials,,Yes
5/26/2022 9:27,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,4,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,2D,,,,,,"finding nuclei, counting nuclei","I find it difficult to analyze images of my interest which is a parasite, mostly multinucleated. I often do not find tools for these images and would have to do it manually",,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
5/26/2022 9:31,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Developmental Biology",North America,3,3,5,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Somewhat preferable,Not at all preferable,Very preferable,Somewhat preferable,Not at all preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time",,,2D,,,,,,,,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
5/26/2022 9:34,Yes,Undergraduate/Graduate student,Developmental Biology,North America,2,3,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all interested,Very interested,Very interested,Very interested,Not at all interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D + time,,2D,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,,None,Email list,,,,,,,No
5/26/2022 10:28,Yes,Image/data analyst,"Developmental Biology, Medicine, Statistics/Biostatistics, Computer science",North America,4,4,6,"Ask on forum.image.sc, Look up solutions in the scientific literature",Often,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,2D,,2D,2D,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,,"Society of Toxicology Pathology, American College of Veterinary Pathology",,,,,No
5/26/2022 10:41,Yes,Postdoctoral fellow,"Cell/Molecular Biology, Medicine, Statistics/Biostatistics, Computer science",North America,4,6,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Very interested,Moderately interested,Not at all interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D,"2D, 2D + time, 3D (<3000x3000x100)",2D,,,,,,,,I think almost every step of image analysis still has plenty of improvement to be had.,"Stain free cell segmentation (i.e. using phase/DIC), dense cell image segmentation. large/stitched image segmentation (particularly for dim fluorophores that are heavily affected by illumination differences)",,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,Email list,"Actually, I attended a CellProfiler workshop at HMS. It was amazing. Every step was useful, from getting me used to building pipelines, to trying out different modules, to tying in ilastic. In one sense, that last step (ilastic tie-in) might have been the most valuable, just because it would have been hard for me to even consider trying to bridge two software together.
The workshop's material and test pipeline/images I've actually saved and use as training materials for my own students. I hope you guys don't mind!","Probably every conference, but it's a big investment for any lab to do it well.","I think 1) best practices in choosing FPs for specific applications - live cell, confocal, etc, and 2) a detailed breakdown of the ""IdentifyPrimaryObjects"" function of CellProfiler and how to compartmentalize it into its own modules (gaussian filter, threshold, fill holes, etc) would be super helpful.","Obviously, making their software free to use, but that's asking a lot. I think if there's a ""standard"" set of images for applications (like live cell image, fluorescent cell tracking, stain-free segmentation, etc), would be cool for different softwares to show their set-up time, runtime, and results. But obviously this is also from the perspective of an academic.",I guess to start with it's worth making clear to newer lab members that microscopy is hard and there is a lot to learn. Starting from that understanding rather than assuming that just sticking a poorly-prepped sample into an expensive microscopy system will yield easily quantifiable results sets people up for failure.,Thank you guys for your great work on CellProfiler!,Yes
5/26/2022 11:16,Yes,Facility staff,"Physics/Biophysics, Chemistry/Biochemistry, Statistics/Biostatistics, Deep learning",North America,4,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Not at all preferable,Not at all preferable,Not at all preferable,Very preferable,Very preferable,Very preferable,Not at all interested,Somewhat interested,Somewhat interested,Not at all interested,Not at all interested,Not at all interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","nucleus-based segmentation, STORM-PALM-SMLM, RICS","I think certain things just are not easy. period. The drive toward easier solutions is understandable, but some things just aren't. There is a broad palette of tools out there already, most of them purporting to be easy solutions, or automated (e.g. skeletonization and 3D filament trackers) they do work on very specific standard systems, but often fail when going into untapped new types of images. I guess what I am trying to say is, that instead of becoming easier, image analysis tools should focus on better, more broadly employable, robust and reproducible, That will be demanding on the user side and will require intensive care and meticulous data acquisition - it is not going to be easy, but better, in my opinion.",,,,,,,,,,,,,,i was cc-ed to an email,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Many,I don't think I need more reminders.,"Most LFD (University Irvine), fluorescence foundation etc. workshops were excellent because they have small-ish groups (of 50) and lots of one-on-one time.","no, I don't think there is a lack of awareness in any of the fields that already operate with image analysis methods",I think the key to success is education and training (thorough training) of users and a LOT of expectation management.,"Everything in this field is better and more successful if it is more broadly and universally applicable. Best encouragement (aside from money) to creators is to include them as co-authors, give kudos, generate awareness, applaud them openly, include them (and their salaries) in grant proposals, treat them not as providers of tools, but as high level partners at equal footing with the biological scientific side of the study.","Users such as microscopists must embrace the technology with all its complexity and stop looking for silver bullets and easy solutions. Encouragement is through recognition, too.","None of Image analysis is easy. Stop looking for silver-bullet easy solutions. Embrace the experts and give them money, kudos and applause.",No
5/26/2022 11:38,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,2D,,,,,2D,,,"Segmentation, intensity measurements",Maybe 3D imaging?,,,,,,,,,,,,,,Twitter,,None,Email list,,Pretty much any cell biology conference,"Machine learning, overview of which tools to use when, the theory or considerations of using different image analysis tools/algorithms ","Better explanations of the different tools and features, and improved computational efficiency ","Together with the creators, create guides for best practices in imaging and analysis methods, making publication of analysis workflows more common, encourage the use of open-source software   ",,Yes
5/26/2022 11:59,Yes,Research scientist,Cell/Molecular Biology,North America,4,3,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,,,,,,,,,,,,,,,,,,,,,,Email list,,None,My local microscopy facility,,,QuPath and basic ImageJ/FIJI analysis ,Have an open-source published website or document that contains the basic step-by-step analysis ,,,No
5/26/2022 13:20,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",North America,4,3,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,,,,,,,"3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,,My local microscopy facility,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",None,telegram channel,,,,,,,Yes
5/26/2022 13:46,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology, Developmental Biology",North America,1,5,1,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D + time,"2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",2D,,,"3D (<3000x3000x100), 3D + time",,,"I would argue no single problem has been, ""solved"". However, I think great progress has been made on non-purely threshold based analysis, nuclear identification, cell segmentation, and phase-contrast analysis. Great strides have also recently been made with respect to handling large data sets (though still a long way to go).","3D analysis in general. Segmenting individual cells that don't stain perfectly with membrane marker or don't overlap (e.g., cell types that grow on top/under each other). Deep/Machine learning that better recapitulates human eye. For example, StarDist is a great nuclear identification program, but often picks up micro-nuclei or clearly apoptotic nuclei. ",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,"In addition to twitter, notifications from major or society journals (e.g., MBoC) can help",Youtube series on FIJI/ImageJ by Robert Haase and ZeroCostDL4Mic by Henriques and collaborators. Both these resources provide narrated videos that are exceptionally well done and easy to follow along with (user walks viewer through software). ZeroCost also has a well annotated github/wiki page for topics not covered in videos. ,,"I think it is more beneficial to cover a topic (e.g., ""Cell Segmentation in 3D...""), introduce the problem and the best/current ways to analyze the data and future directions. ","Annotated Github pages! Biologists need help installing and running complex code, that is the reality. I can't tell how many times I've read a fascinating image analysis paper (for example the recent deep learning papers from Emma Lundberg and the human protein atlas), and been completely unable to run code due to lack of good annotation.  ","Plan experiments better to obtain data that can be analyzed. Have clear questions that need answers and clear reasons why existing tools are sufficient. Users also need to be more flexible (e.g., learning basic Python or Matlab and be able to run annotated code). ",,Yes
5/26/2022 14:05,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics, Computer science",North America,4,4,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Sometimes,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,None,Word of mouth,,,,,,,Yes
5/26/2022 14:11,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",North America,3,2,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D + time","2D, 2D + time, 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 3D (<3000x3000x100)",,,,,,,,Puncta analysis of very small ROI with very small puncta,,,,,,,,,,,,,,NewPI Slack,Conference session on imaging or image analysis,Few,Email list,,,,,,,Yes
5/26/2022 19:31,Yes,Principal investigator,Cell/Molecular Biology,North America,6,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Not at all preferable,Very preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Very interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,"2D, 3D (SPIM/large volume)",,,defining nuclei,image segment for things like time lapse imaging of growing filaments (actin and or MTs),,,,,,,,,,,,,,"Word of mouth, Twitter",Workshop/tutorial on imaging or image analysis,None,Twitter,none,,,,,,Yes
5/26/2022 20:55,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,3,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Very preferable,Very preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Not at all interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,3D (<3000x3000x100),,,2D,,,,,,,volumetric measurements,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,Hands-on examples to back up lectures,,,"Write clear, step-by-step guides",Better methods reporting,,Yes
5/26/2022 21:24,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,3,4,Look up solutions generally on the internet (Google),Never,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,2D,2D,,,2D,,,,,,,,,,,,,,,,,,,Twitter,,None,Twitter,,,,,,,Yes
5/27/2022 7:11,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Chemistry/Biochemistry, Statistics/Biostatistics, Computer science",Europe,4,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,2D,,2D,,,,,,,,Mononucleated cell detection,"Polynucleated cells, elongated cells, variable shapes and sizes",,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Postings on image.sc forum or microforum,,,,,,,No
5/27/2022 9:12,Yes,Principal investigator,"Physics/Biophysics, Chemistry/Biochemistry, Computer science",Europe,3,6,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,,,,,,,Yes
5/27/2022 11:24,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",Europe,4,4,4,Sit down with a tool I know and start playing with the data,Most of the time,Not at all preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,2D,,,,,,,Most 2D analysis is well solved. ,"Most 3D analysis is more taxing. Finding nuclei, cell boundaries.",,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,Twitter,Python course in Cambridge UK.  Great teachers. Lots of practice.,,"Getting to grips with Python. The absolute basics. How to install it, which instal method to use. Why there seem to be some many options.",Easier to install,Seek expert advice. Publicise image.sc as widely as possible.,,Yes
5/27/2022 12:54,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,3,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",2D + time,2D,"3D + time, 3D large volume + time",,2D,,,2D,,3D large volume + time,,Automated cell/organelle tracking in 4D in complex tissues/embryos,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,A discipline-specific society or network,AQLM,ASCB,,,,,Yes
5/27/2022 12:55,Yes,Principal investigator,"Cell/Molecular Biology, Statistics/Biostatistics",North America,4,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all preferable,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,2D,2D,,,,,,,fluoresence for cells,tissues,,,,,,,,,,,,,,newPI slack,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,UCLA QCBio workshop. interactive,,,alternative to 75K MBF system for stereology,,,Yes
5/27/2022 13:47,Yes,Facility director,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,5,6,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 3D (<3000x3000x100)",2D,2D,2D,,,,2D,,finding nuclei,tissue analysis,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,,,,,,,Yes
5/27/2022 15:39,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology",North America,4,5,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Often,Not at all preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Not at all interested,Somewhat interested,Somewhat interested,Very interested,Moderately interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",3D large volume + time,3D large volume + time,3D large volume + time,3D large volume + time,,,,,,,,Segmenting cells using fluorescent imaging.,Segmenting cells using brightfield/DIC/PC.,,,,,,,,,,,,,,Word of mouth,,None,Email list,,,,,,"I am not sure if this already exists, but I would love to be in some kind of Boston-based slack group or discord server or forum of some kind that consists of people knowledgeable about image analysis.",Yes
5/29/2022 12:10,Yes,Research scientist,Chemistry/Biochemistry,Europe,4,4,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions on a particular website (please list below)",Often,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",2D + time,2D + time,2D,,,2D + time,,2D + time,,Segmentation mostly.,Extraction of 3D properties of objects in volume.,Postings on image.sc forum or microforum,,Few,Postings on image.sc forum or microforum,Not been to any.,MMC,NA,Sometimes difficult to get certain (Python) packages working - more instructions here would help.,"Clearly state their needs on the imagse.sc forum, with images and examples. Share their experience with colleagues inside and outside their scientific field.",NA,Yes
5/30/2022 6:02,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",Europe,4,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me",Never,Not at all preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100), 3D (SPIM/large volume)",,2D,,,,,,,None,Cell segmentation in dense tissue,,,,,,,,,,,,,,Email list,Workshop/tutorial on imaging or image analysis,Few,Email list,,British Society for Developmental Biology Annual Spring Conference,Cell segmentation,Enable better comparison between the numerous tools,,,Yes
5/30/2022 7:12,Yes,Clinician,"Cell/Molecular Biology, Statistics/Biostatistics",Europe,7,2,2,"Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,,,,,2D,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Conference session on imaging or image analysis,Few,Postings on image.sc forum or microforum,,,,,,,Yes
5/30/2022 12:25,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,3,3,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",3D (<3000x3000x100),2D,,,,,,,finding nuclei,finding and qunatifying particles (e.g. FISH signals),,,,,,,,,,,,,,Twitter,,None,Email list,,,,,,,Yes
5/31/2022 12:55,Yes,Facility staff,"Cell/Molecular Biology, Developmental Biology",Europe,2,4,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100), 3D large volume + time",,,,,,"tracking cells, segmentation of fluorescent data","automatic EM image segmentation, large scale EM data alignment (automatic)",,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,A discipline-specific society or network,Zeiss CLEM workshop,,comparison between software possibilities and intro to solving a particular kind of experiment,good tutorials for using their software (explanation of parameters plus examples which normally work...),"provide ""bad"" images for software testing, not only the images we are proud of",,Yes
5/31/2022 17:33,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology, Computer science",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Often,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,,"3D (<3000x3000x100), 3D (SPIM/large volume)",2D,2D,3D (<3000x3000x100),,,3D (<3000x3000x100),,,classic or AI segmentation of stereotyped cells/subcellular compartments in images with high S:N,"1) 3D neuronal reconstruction with non-optimal datasets (i.e., high SNR, highly variable cell morphologies, sparse datasets) ; 2) super-resolution for distribution of synaptic vesicles and synaptic vesicle proteins",,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,A discipline-specific society or network,,,,"spend time looking at real-world data, collected using the techniques researchers have to use (e.g., genetic cell fills can create images with beautifully high SNR, but depending on biological organism, age, target, or other esoteric challenges, not all researchers can use this technique); as a user of existing tools and a developer (when I have to), I like to see open formats and transparency vis a vis algorithms
ideally, have the developers spend some time in the lab!","oohh... I run a lab full of biologists... #1 is to get them to understand the basics of image formation, digital image acquisition, and what a digital image is. I'm still trying to figure out the best way to train everyone to the level they need. We have mandatory readings, and we have a gatekeeper system, whereby students have to 'pass' an oral test before they can advance to being taught to use a new microscope, but at the end of the day, we still have one group (usually those who had some interest in physics/compsci) who've caught on and can think for themselves at the scope, and another group who can use the various imaging setups that they've been taught with preparations they know well, but who struggle with anything new. For trainees, a combination of readings, videos, required workshops, and interactions with more knowledgeable peers is I think optimal.",,Yes
6/1/2022 6:41,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",Europe,6,3,6,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,3D (SPIM/large volume),,,,,,,,finding nuclei in a cleared brain,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Email list,,,,coat their tools with a user-friendly GUI and expansive documentation,,,Yes
6/1/2022 9:54,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Medicine, Statistics/Biostatistics, Computer science",Asia,4,6,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D + time,,3D (<3000x3000x100),,,,,,,,"Noise removal, ways to extract certain quantifiable parameters, image segmentation",,,,,,,,,,,,,,"Postings on image.sc forum or microforum, Twitter",Workshop/tutorial on imaging or image analysis,Few,Email list,Hands on practice,,Image segmentation and how to extract biological information from your data.,Make easy manual for people who don't understand math behind an algorithm. Talk with people who are not proficient in developing.,They should learn some basic principles behind how software functions are made. Give them easy video tutorials/ manuals.,,Yes
6/1/2022 10:29,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology",North America,2,2,6,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,,,,,,,,,,,,,,"Word of mouth, Twitter",,None,Twitter,,,I wish there were more videos of people explaining how to use my specific software (CellSens),,,,No
6/1/2022 10:56,Yes,Facility director,"Cell/Molecular Biology, Computer vision, Deep learning",North America,6,5,7,Look up solutions in the scientific literature,Most of the time,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time","2D, 3D (<3000x3000x100), 3D large volume + time",,,,,,,,Easier reliable 3D neuron tracing that integrates with other plugins / modules in Python or Fiji,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Neubias - fantastic European effort - meetings with high density of highly skilled people open to sharing ideas and tools. Would be great to have a similar active network in USA,,Full Python walkthroughs for biological questions aimed at beginners (with Jupyter notebooks and good documentation and reasoning for tool/module/filter use),Clear documentation. Ensure working solutions are uploaded to github with clear requirements and small example dataset for troubleshooting.,"Be mindful of minimum image resolution and SNR required for successful use of a tool. Understand how to read documentation, and issues open/closed on github to troubleshoot first.",,Yes
6/1/2022 11:17,Yes,Image/data analyst,"Physics/Biophysics, Cell/Molecular Biology, Statistics/Biostatistics, Computer science, Deep learning",North America,7,6,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Not at all interested,Not at all interested,Not at all interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,2D,,,,,,,finding nuclei,better 3D visualization (similar to Imaris) in open-source softwares such as Napari,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,interactive workshops,,"comparisons between pieces of software, 3D visualization and segmentation using deep learning, big data processing",Provide an example dataset and step-by-step instructions for getting the results,Attend image analysis seminars/tutorials/workshops,,No
6/1/2022 20:32,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,1,2,2,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D (<3000x3000x100),,3D (<3000x3000x100),,3D (<3000x3000x100),,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
6/2/2022 17:02,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",North America,5,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately interested,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 3D (<3000x3000x100), 3D + time, 3D large volume + time","2D, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,Cell Counting,Blood Vessel Skeletonization,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,Few,Postings on image.sc forum or microforum,The videos by Johanna M. Dela Cruz have been useful,,,"Standardize processes, datatypes and plugin function across the same image analysis platform.",,,No
6/2/2022 17:59,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science, Computer vision",North America,7,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Not at all preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,2D,,2D,2D,,2D,,,,,Nucleus detection and stain deconvolution,pathologist-driven multiplexed analysis workflows,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,2022 I2K conference,,,,,,No
6/3/2022 3:07,Yes,Research scientist,Physics/Biophysics,Asia,7,4,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",2D + time,,,,,,,2D + time,,"Reconstruction of images in optical super resolution microscopy, thunderstorm",NA,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Image analysis part helps me a lot. Reconstruction of images in STORM microscopy.,Yes,Reconstruction of images in Optical Super-Resolution Microscopy such as STORM. Autofocusing techniques in Microscopy. Image analysis of HYPERSPECTRAL IMAGING. ,"Every software developer should mail the users asking about the kind of development they want after every period of 4 months. Also, the developers should remain active to answer all the questions of the customers at any time. Of possible the developers of a particular software should held workshops twice a year to let people know how their software works or how we can do different different image analysis with their softwares.",Workshops probably 3-4 times a year reared to image analysis relevant to different fields.,,Yes
6/3/2022 3:52,Yes,Image/data analyst,"Cell/Molecular Biology, Medicine, Computer vision, Deep learning",Europe,6,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","2D, 2D + time",2D,,,,,,,Nuclei with Stardist,"modelling vascular structures in large 3-D confocal volumes (capillaries vs large vessels, branching, merging, etc etc...)",,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,"Meeting other people with similar issues, step by step tutorials, help from the software developers themselves (QuPath, CellProfiler, ...)","MMC in Manchester, maybe?",Use of deep learning for solving complex segmentation problems,"Solving API / UX / UI issues pointed out by users. Users have expectation of how the tools *should* behave, and unresolved issues can lead to a lot of frustration and absolute dread towards using the  tools (e.g. Visiopharm)","Read the manual, learn how to search for information, don't put oil on dry objectives :-(",,No
6/3/2022 8:51,Yes,Facility director,Cell/Molecular Biology,North America,3,2,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)",,2D + time,"2D, 2D + time","2D, 2D + time",2D,,,,,"2D, 2D + time",,"basic thresholding, counting, intensity measures, machine learning approaches","identification of positive signals from background, handling large data sets from light sheet systems",,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,"Watched QuPath workshop on YouTube and it was helpful although I still am a complete novice at using that program. The ability to watch, and re-watch, segments is very useful.",N/A,"Overview of software that can be used for whole slide analysis and step-by-step description of HOW to use it to batch process samples. Software used for multiplexed immunofluorescence, how to register images, etc.",Make the software as easy to use as possible - clear pipelines or 'recipe' setup for processing. Make it easier for us to send them $ to help fund their efforts and keep the software open and ideally out of the hands of corporations that want to make everything 'software-as-a-service' with a yearly subscription.,Make more tutorials (written and video) demonstrating things we can do well and sharing those with everyone. ,,Yes
6/3/2022 17:50,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Cell/Molecular Biology, Statistics/Biostatistics, Computer vision, Deep learning",North America,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,2D + time,,,,,,,,particle counting,"Robust segmentation, object tracking through cell division ",,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Few,Postings on image.sc forum or microforum,,,"Walking through a workflow from raw image to visualization, while explaining the thinking behind tool selection and parameter choice",Better documentation and example usecases,"Standardize formats, better metadata annotation",,Yes
6/5/2022 3:15,Yes,Undergraduate/Graduate student,Developmental Biology,Europe,6,4,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,,2D nuclear segmentation ,3D nuclear segmentation ,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,I2K but wasn't really useful. ,,General good practices and specialized analysis tool in terms of quantification of images,Simplify their tools and make video tutorials. ,Video recordings of their successful analysis.,,Yes
6/6/2022 16:53,Yes,Facility staff,Cell/Molecular Biology,Europe,4,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Moderately preferable,Moderately preferable,Not at all preferable,Very preferable,Somewhat preferable,Not at all preferable,Moderately interested,Very interested,Very interested,Moderately interested,Not at all interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","3D (<3000x3000x100), 3D + time",,"3D (<3000x3000x100), 3D + time",,,,,,,,,,"3D visualisation of fluorescence data is either expensive and good, or free but clunky. Better open source visualisation software would help in choosing the correct down-stream analysis for a given sample",,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,My local microscopy facility,,,,"Be realistic about how generalised their software is. Often tools are talked about as general purpose, but don't perform well outside of the biological field (or sub-field) they were created in.",,,Yes
6/6/2022 17:56,Yes,Undergraduate/Graduate student,Developmental Biology,Europe,4,3,1,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Never,Very preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D + time,3D + time,3D + time,3D + time,3D + time,3D + time,3D + time,3D + time,3D + time,3D + time,3D + time,,tracing cells and mitochondria quantitative analysis ,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Email list,,,,,,,Yes
6/7/2022 16:25,Yes,Facility staff,Cell/Molecular Biology,North America,3,4,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time, 3D (<3000x3000x100)",,2D,2D,,,,,,segmenting large and bright objects,segmenting small and heterogeneous signal (such as bacteria),,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,It's helpful when they use real images which are more difficult to analyze,ABRF,,"Make pipelines easy to use, but also transparent so we know exactly what is done to analyze the images.",Write very clear and detailed imaging and analysis methods.,,No
6/7/2022 16:27,Yes,Principal investigator,"Physics/Biophysics, Cell/Molecular Biology",Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Not at all preferable,Moderately preferable,Not at all preferable,Not at all preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,Need for denoising and segmentation tools.,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,Twitter,,,,,,,Yes
6/7/2022 16:33,Yes,Principal investigator,"Cell/Molecular Biology, Developmental Biology",North America,4,5,5,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,"2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,Finding nuclei is getting better but not in tissue or cleared brains,Segmentation of cells with complex morphologies and determining the spatial relationships between signals in our image (especially correlative images).,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,There have been a lot of virtual resources in the pandemic that were useful.,ASCB and SFN,Spatial relationships ,Generalizable tools are needed,"Users need to think of analysis before doing a single experiment.  Unfortunately, they still think about it after data is collected and worse when they are trying to publish a paper.",,No
6/7/2022 16:44,Yes,Research scientist,"Physics/Biophysics, Cell/Molecular Biology",Europe,3,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Moderately interested,Moderately interested,Not at all interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D + time, 3D (<3000x3000x100)",,,,,,,,,"registration, segmentation",,,,,,,,,,,,,,,Twitter,,None,Twitter,,,,,,,No
6/7/2022 16:50,Yes,Undergraduate/Graduate student,"Medicine, Statistics/Biostatistics, Computer vision",Europe,6,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,2D,2D,2D,,,,,,,,finding nuclei for common stain types,quantifying fibers (e.g. collagen),,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,,,,find out and play with varied use cases aside from maybe typical ones such as DAPI staining quantification or something that's relatively common; expand the toolbox of functions your tool may have,,,Yes
6/7/2022 17:17,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D (<3000x3000x100)",,"2D, 3D (<3000x3000x100)",,,,,,,,"3D registration, non rigid registration, denoising, ML-based segmentation, deconvolution microscopy",,,,,,,,,,,,,,Twitter,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,"Write extensive documentation, provide tutorials",Scripting workflows for better reproducibility,,Yes
6/7/2022 17:27,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology, Statistics/Biostatistics",Europe,3,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Not at all preferable,Moderately preferable,Moderately preferable,Not at all preferable,Moderately interested,Somewhat interested,Very interested,Moderately interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,"2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D + time",2D,,,,,,,"identifying objects/nuclei in static cell culture micrographs, large batch analysis","coherent feature extraction/object recognition in tissues, extracting non-linear spatial relationships between many objects (e.g., defining polygonal fields based on cell clusters) ",,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,An accessible (= easy to follow for non-specialists) intro to the theory underpinning the method combined with walkthroughs/use case scenarios that clearly articulate benefits and limitations,,Goal-focussed tutorials that explore how to address a specific problem (e.g. classifying cells in tissues based on morphology) rather than what a particular tool can do. A good tutorial suggests a pipeline and introduces the required tools but also explains where one could deviate and what the limitations of the particular approach would be.,"Provide realistic use case scenarios (r.g., based on beta-tester feedback from field experts/potential users) and use those as backbone for manuals/vignettes. Focus on doing a few tasks well rather than trying to cover too many and facilitate modularity (compatibility with other formats/tools) for easy integration into pipelines. Then relentlessly promote that the tool excels at those tasks by getting users involved as advocates.",Provide detailed methods/reproducible pipelines (as part of a publication) on how a tool was used rather than just stating that a tool was used. Cite tool developers and maintainers generously. Advocate for funding to support (in house) tool development and more crucially maintenance/updating e.g. by allocating a bigger share of departmental budget to imaging facilities.,,Yes
6/7/2022 20:49,Yes,Research scientist,Cell/Molecular Biology,Asia,3,3,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Sometimes,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,3D + time,3D + time,2D,2D,2D,2D,3D (<3000x3000x100),2D,2D,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,,,No
6/7/2022 23:56,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Cell/Molecular Biology, Computer science, Computer vision",North America,4,7,7,Sit down with a tool I know and start playing with the data,Most of the time,Not at all preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,"2D, 2D + time",,"2D, 2D + time",,,,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,,,,,,,,,Twitter,,Few,Email list,,,,,,,Yes
6/8/2022 2:31,Yes,Facility staff,Developmental Biology,Asia,5,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D large volume + time",,,,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Some,Postings on image.sc forum or microforum,"Robert Haase's website, clear explanation, video recordings, and PowerPoint are available.",,Image Analysis Workflow and strategy (especially by using open source software).,,,,Yes
6/8/2022 2:49,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Asia,3,6,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,2D + time,2D + time,2D + time,,,,,,2D + time,,"Finding nuclei, image registration, segmentation",Particle tracking,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Twitter,I2k conference. Really detailed view on multiple tools,,Comparison between different softwares.,,,,Yes
6/8/2022 4:13,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Asia,4,3,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D + time, 3D (<3000x3000x100)","3D (<3000x3000x100), 3D + time",3D + time,,,,,,,Localisation of proteins,"Colocalisation, Intensity analysis, Background subtraction",,,,,,,,,,,,,,Word of mouth,Workshop/tutorial on imaging or image analysis,Some,Email list,,"I had attended a 10-day workshop called Image2Numbers by JNCASR. Even though the techniques taught were useful, the codes associated with it were a little difficult to understand.",I would like to see better ways to customise background subtraction techniques. Intensity analysis of images where the SNR is not as good is something I'd like to learn.,I think a more user friendly way of explaining the codes that are scripted or a tutorial attached with the instructions to personalise some plugins or scripts for image analysis would be helpful.,,,Yes
6/8/2022 4:15,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Asia,4,2,6,Look up solutions generally on the internet (Google),Never,Somewhat preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Moderately preferable,Somewhat preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D large volume + time,,,,,,,,,Nuclei,Super resolution,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,"Yes, Image2Numbers workshop organized by JNCASR. It was not very helpful. Too much specific information instead of the fundamental basics.",No,"Co transport analysis. Cell body imaging of small cell body such as that of
C.elegans.",By organizing more free seminars where the understanding of the basics is stressed upon and not something specific.,By attending more workshops related to microscopy.,,Yes
6/8/2022 4:43,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Asia,2,2,3,"Ask a friend or colleague to help me, Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D + time, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,Any cell biology conference would,Colocalization analysis - software and methods,Websites can have video tutorials? Or maybe encourage experienced users to submit video tutorials.,Experiences users can share their expertise at conferences/workshops. Students perhaps can compete for best tutorial?,,Yes
6/8/2022 5:46,Yes,Facility staff,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,3,5,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Somewhat interested,Somewhat interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,,"2D, 2D + time, 3D (<3000x3000x100)",,,"2D, 3D (SPIM/large volume)",,,,,,"2D segmentation of nuclei and other ""solid"" organelles. Cell counting.","3D segmentation and measurments - volume and surface area etc. More well defined rationale for quantification of intensity, particularly in 3D data. Alignment and segmentation of volumeEM data",,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Few,Postings on image.sc forum or microforum,,,"Setting a benchmark of best practice, guidelines of how to approach common problems.",,"Consider analysis before beginning experiments. Best achieved through comprehensive training at facilities, as well as full-pipeline assistance. Better training in image analysis/emphasis on employing specialists at imaging facilities.",,Yes
6/8/2022 7:56,Yes,Facility staff,Physics/Biophysics,Europe,5,6,6,Sit down with a tool I know and start playing with the data,Most of the time,Not at all preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat interested,Not at all interested,Moderately interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time",2D,,,,,2D,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Twitter,Hackathon,,,Make things compatible between each others and easy to install,,,No
6/8/2022 15:45,Yes,Research scientist,Physics/Biophysics,Europe,7,7,7,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Most of the time,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Very preferable,Somewhat preferable,Not at all preferable,Very interested,Very interested,Very interested,Very interested,Not at all interested,Somewhat interested,Not at all interested,Physical Sciences,,,,,,,,,,,,,,,,"Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 3D (<3000x3000x100), 3D (large volume)",,,,,,,,Ptychography :-),"Word of mouth, Twitter, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Hyperspy workshop (by ePSIC staff at EMAG),"M&M, MRS","I'd really like a broad overview of 4D-STEM tools (ie, ptych vs NBED etc)",Commenting code properly so others can understand accurately how it works. ,Accurately understand the tool they're using rather than applying it blindly...,Maybe a session/workshop at MMC/similar on an intro to github would be useful?,Yes
6/9/2022 5:26,Yes,Principal investigator,"Developmental Biology, Computer science",Europe,7,6,7,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Very preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Moderately interested,Not at all interested,Not at all interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"3D (SPIM/large volume), 3D large volume + time","3D (SPIM/large volume), 3D large volume + time",,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,Yes
6/9/2022 7:53,Yes,Image/data analyst,"Physics/Biophysics, Chemistry/Biochemistry, Deep learning",Europe,7,5,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Very interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,2D,,,,"2D, 3D (<3000x3000x100)",,,"Counting well separated yeast cells. Otherwise, users keep wanting more and more, so we have to push it futher",An open-source file format and solution set for super-res like STORM,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum, Twitter","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,"Neubias, was well presented and had a lot of different ideas/technologies",American Biophysical Society,I think a workshop on how to acquire images and do labelling for machine learning would be useful.,"Try to make more things interoperable, as opposed to reinventing the wheel to get a paper out","Realize that it's an iterative process, not unlike any other experiment.  Many users think there is going to be a solution out of the box, and they'll never have to optimize their image acquisition",,No
6/9/2022 14:36,Yes,Principal investigator,"Cell/Molecular Biology, Medicine, Statistics/Biostatistics",North America,3,4,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,"2D, 2D + time, 3D + time","2D + time, 3D (<3000x3000x100), 3D + time","2D + time, 3D (<3000x3000x100), 3D + time",2D,2D,2D,2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,Image analysis as I understand it is all a work in progress.,All image analysis has the potential for better solutions.,,,,,,,,,,,,,,"Postings on image.sc forum or microforum, from google search linking to image.sc forum post",,None,A discipline-specific society or network,participated in none,NA,super resolution applications and immunofluorescent image analysis,make it more entry level friendly with simple tutorials,easier to post questions with the USERS images,My lab is in desperate need of image analysis assistance.,Yes
6/9/2022 15:02,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology",North America,4,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D,,,,,,,,,"I have an easy time with: finding nuclei, counting segmented cells, background correction, measuring fluorescence intensity within a selection.","I have a difficult time with: segmenting cells that are not round (for instance, highly branched cells such as astrocytes), analyzing the morphology of cells (i.e. ""count the number of branches""), segmenting overlapping cells (I don't have experience with creating z-stacks)",,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Few,Email list,"I've only been to one, which was a Fiji workshop offered by my university's microscopy core facility. It was relatively helpful, but I found making an appointment with the analysis specialist who gave it to talk about my data one-on-one was more helpful for my project. It did give me a lot of background knowledge about image analysis and image data in general though which was nice.",,"I can only speak to my experience using ImageJ, but an issue I have is that tutorials all seem to be with older versions of the software than I have and sometimes there are discrepancies. I guess it's hard to make video tutorials for a software that updates so frequently. But that might be something to try to address. Other than that, a lot of my issues come from working with images of cells with a non-round/branched morphology, so tutorials addressing analyzing structures with different morphologies from round particles could be helpful.",This is vague but I feel like when I read the instruction manual for ImageJ it doesn't really give me a very good sense of what each command actually does. Maybe more detailed instructions?,"Before I started trying to teach myself image analysis, I was relying on protocols given to me by other wetlab biologists and a lot of them were honestly really terrible. People just don't really know basic things like what gamma correction is and how unreliable manual counting is. I think it would be helpful if there were more accessible primers on image analysis that people read as part of learning microscopy.",I'm someone who came to image analysis (with ImageJ) with very little guidance or relevant background. I wouldn't say I have a great grasp of it but I'm able to do some basics now. It's been a real uphill battle teaching myself!,Yes
6/10/2022 11:21,Yes,Facility staff,Developmental Biology,Europe,5,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions in the scientific literature",Often,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,,2D,2D,,2D,,,,,nuclei segmentation in 2D,nuclei segmentation 3D,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,NeuBias 2019 training school,,,,,,Yes
6/10/2022 11:29,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Developmental Biology, Medicine, Statistics/Biostatistics, Computer science",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Not at all preferable,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Not at all preferable,Not at all preferable,Not at all interested,Moderately interested,Very interested,Very interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Other commercial software (Imaris, Volocity, etc)","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)",,,,,,,,,,,,,,,,,,,,,,,My local microscopy facility,Workshop/tutorial on imaging or image analysis,Many,My local microscopy facility,,,,,,,No
6/10/2022 11:38,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,North America,6,2,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,,,2D,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Postings on image.sc forum or microforum,,,,,,,No
6/10/2022 16:51,Yes,Postdoctoral fellow,"Physics/Biophysics, Cell/Molecular Biology, Developmental Biology",Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Most of the time,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume)","3D (<3000x3000x100), 3D + time",,,,,,,,finding nuclei (thanks to cellpose/stardist),"3D morphological analysis (beyond visualization), 3D mesh-based analysis, 3D+high content imager, integrating spatial transcriptomics with 2d/3d morphological information",,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Some,Twitter,,,,,,"I am power user of many open source packages, but we should advocate for more funding of image analysis software development and engineering positions. CZI is a doing a great job.",No
6/11/2022 9:24,Yes,Research scientist,"Physics/Biophysics, Chemistry/Biochemistry",North America,4,3,4,Sit down with a tool I know and start playing with the data,Sometimes,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Other commercial software (Avizo, Imaris, Volocity, etc)",,,,,,"3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time",,,,Difficult to answer due to the highly varying nature of 3D tomography,"3D reconstructions, automated advanced segmentation methods",Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"M&M conference, CLIJ workshops",Workshops at M&M,Advanced scripting languages and methods!,Listen to customers! Each problem is unique. Don't question why we want to do something but to accept our feedback as strong suggestions for improving software!,"Accurately and thoroughly report image analysis methods! Just because a method may be demonstrated on a specific material system or in a specific discipline doesn't mean that other disciplines know what you are doing! Make it reproducible! If I have the tools and data available, I should be able to read your article or report and reproduce the same results. Work with publishers to encourage accurate methods reporting. It is so frustrating to read an article that uses a new image processing or analysis method only to find out that I can't understand it or there is too little information to reproduce it or that it isn't even reported (ie, proprietary methods...). ",,Yes
6/12/2022 17:23,Yes,Undergraduate/Graduate student,"Developmental Biology, Medicine",North America,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Somewhat interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (<3000x3000x100),,2D,,,,,,,For all of them I had to rely on some extent of human intervention in the analysis.,Cell segmentation in a noisy background.,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,None,A discipline-specific society or network,,,,,,,Yes
6/14/2022 5:18,Yes,Facility staff,Cell/Molecular Biology,Europe,2,5,5,Sit down with a tool I know and start playing with the data,Sometimes,Not at all preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D + time,3D + time,3D + time,3D + time,2D + time,,,,3D + time,3D + time,,finding nuclei,tissue analysis and analysis of super resolution data,,,,,,,,,,,,,,Word of mouth,Workshop/tutorial on imaging or image analysis,Few,My local microscopy facility,Expand processing knowledge,Yes,Processing pipeline generation,Simpler explains of processing functions and variables,Pilot test an imaging protocol can be used to confirm the desired information can be extracted.,,Yes
6/15/2022 4:54,Yes,Principal investigator,Physics/Biophysics,Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Other commercial software (Avizo, Imaris, Volocity, etc)",,2D,,,,"3D + time, 3D (large volume), 3D large volume + time",2D,,,Segmenting,Easier software front end,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,TOSCA,Needs something new,Various,Work more closely with the applications,Work more closely with creators,N/A,No
6/15/2022 5:07,Yes,Image/data analyst,"Cell/Molecular Biology, Statistics/Biostatistics, Computer science",Europe,6,6,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",2D,"2D, 2D + time",2D,2D,,,,,,,,segmentation,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,,,,No
6/15/2022 7:57,Yes,Facility staff,Cell/Molecular Biology,Europe,2,2,3,Ask on forum.image.sc,Never,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all interested,Somewhat interested,Somewhat interested,Very interested,Somewhat interested,Not at all interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,3D (<3000x3000x100),,2D,"2D, 3D (<3000x3000x100)",,,"2D, 3D (<3000x3000x100)",,,Almost anythng for mammalian cells,"Tools for microbiology, like parasites, normally do not work as well as for mammalian cells",,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Ones from Neubias,Microscience Microscopy Congress (MMC run by RMS),"How-to use particular plugins or tools from software, with people bringing their data",Better graphic interfaces and how-to sessions in the Help area,Start thinking on image acquisition if aiming for image analysis or just a nice image. Set ups are quite different and sometimes you acquire a data set that is not fir for purpose for image analysis,,Yes
6/15/2022 19:07,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,7,2,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Never,Not at all preferable,Very preferable,Very preferable,Not at all preferable,Very preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,,,,,,,,Spatial analysis ,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,None,Email list,Working in small groups with experts ,,Spatial analysis ,,,,Yes
6/16/2022 0:45,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",Asia,3,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Often,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,3D (SPIM/large volume),,3D (SPIM/large volume),,,,,,,,,Segmentation and deconvolution,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Conference session on imaging or image analysis,Few,,,,,,,,Yes
6/16/2022 10:15,Yes,Image/data analyst,"Statistics/Biostatistics, Computer science, Computer vision",North America,7,6,7,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,,,,,,,,,,,,,,,,,,,,,,,Email list,,Some,Email list,,,,,,,Yes
6/16/2022 10:20,Yes,Facility staff,Cell/Molecular Biology,North America,2,3,4,Look up solutions generally on the internet (Google),Never,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Not at all interested,Very interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",None,,,"2D, 3D (<3000x3000x100)","2D, 3D (<3000x3000x100)",,,,,,,,,,,,,,,,,,,,,,,BINA email,Workshop/tutorial on imaging or image analysis,None,BINA,"QFM at MDIBL, good introduction on image analysis",,,,,,No
6/16/2022 10:39,Yes,Research scientist,Physics/Biophysics,North America,4,4,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,3D (<3000x3000x100),2D,2D,,2D,,,,,,Annotations,,,,,,,,,,,,,,A discipline-specific society or network,,None,Email list,,,Analysis provenance,A tighter feedback loop between developers and users,Explicitly define constraints and non-constraints,,Yes
6/17/2022 9:47,Yes,Facility director,Cell/Molecular Biology,Europe,2,2,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 3D (<3000x3000x100)",2D,,,,"2D, 3D (<3000x3000x100)",,,"Separation of signal from autofluorescence in plants, detecting faint objects against background",,,,,,,,,,,,,,"My local microscopy facility, Postings on image.sc forum or microforum, Email list","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,RMS facility managers forum; like-minded people with similar issues.,,Comparison of deconvolution outputs and the artefacts they can create.,,,,No
6/17/2022 11:57,Yes,Research scientist,Cell/Molecular Biology,North America,3,2,4,"Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,"2D, 2D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,2D,,,2D,2D,,Cell segmentation on well labeled items. Quantification of cells. Rendering of 3D data. ,Rapid processing of STORM/PALM data for groups of experiments. 3D tracking and extraction of motion metrics. ,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Email list,"Huygens put on a good workshop with their deconvolution package. They provided a walk through with example data, PDFs and offered the whole thing downloadable after. Imaris has offered a similar in person experience without the recording. ",NA,Any discussion of imageJ and how to utilize the vast tools in there is always great because it is an accessible platform for the most imaging scientists.  ,"I love a tool that has a PDF guide or youtube walk through. It is important that non-developers help generate these because not all of us have the same though process. Additionally, explaining how to NOT use said tools to prevent the misinterpretation of data. Also,  getting varied data from other similar users to make sure the tool is robust. ","My main concern with a lot of these image analysis tools are having them extract information with PERFECT data, or at least optimizing the tool around these data. Not all microscopes are setup or used by equally skilled people, so having illustrations/explanations showing what the best data for said analysis pipeline are. IE: for this pipeline, you need to do X control and it should give you Y result with minimal variation. Deviation from that will alter the power of said method. ",NA,Yes
6/18/2022 5:15,Yes,Postdoctoral fellow,"Chemistry/Biochemistry, Cell/Molecular Biology",Europe,3,5,7,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 3D (<3000x3000x100)",,"2D, 2D + time",,,,,,,,,Cell morphology,Focal adhesion analysis,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Few,Postings on image.sc forum or microforum,,,"Overview of particular tools, ML/AI approaches mostly",Moving away from scripting to GUI tools,"Intuitive, easy to use software",,Yes
6/18/2022 20:08,Yes,Postdoctoral fellow,"Computer science, Computer vision, Deep learning",South America,7,6,7,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Not at all preferable,Very preferable,Very preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time, 3D (<3000x3000x100)",3D + time,"2D, 3D + time",2D,2D,,,,,,,nuclei segmentation,3d cell tracking ,,,,,,,,,,,,,,BINA newsletter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"I2K, presented several interesting softwares",,Deep learning applications,Graphical User Interface for software,,,No
6/19/2022 18:55,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,4,1,1,Sit down with a tool I know and start playing with the data,Sometimes,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Not at all interested,Not at all interested,Somewhat interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (<3000x3000x100),,,,,,,,,,3d segmentation for quantifying multiple channels. Deconvolution with multiple cores,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Postings on image.sc forum or microforum,,,,pay attention to usability,learn programming,,No
6/20/2022 8:47,Yes,Image/data analyst,"Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics, Computer science",Europe,7,6,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time","2D, 2D + time","3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",3D (<3000x3000x100),,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Postings on image.sc forum or microforum,,,,,,,No
6/21/2022 5:17,Yes,Image/data analyst,Computer vision,South America,7,5,7,"Sit down with a tool I know and start playing with the data, Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Somewhat interested,Very interested,Very interested,Somewhat interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,,,,,,,,"2D, 2D + time","In principle, the program causes admiration and gratitude.","With a terrible contrast, it is bad to look for a contour. What can be done here? Think more about the illumination in the visual experiment =)))",This poll found me :)   (It appeared when visiting the page),Conference dedicated to imaging or image analysis,Few,Email list,"Started learning on the Coursera platform. However, due to the war, it was not possible to start practical tasks (sanctions). At the present time we have left Russia, tk. we are against war. looking for a job, trying to find a job in America.","At any scientific conference, if you listen to reports, you can learn something new.","It may seem elementary to you, but I would note clustering","Direct communication with experimenters. It is necessary to create common teams: at least one programmer must always be on the team, in any research.","You can try to add a new tool-button ""problem"". Its function is to send all actions that were made by the user in the session to programmers. You can add a pop-up dialog box ""what is not working? What did you want to get?"" . It is possible to limit the effect of this function: the session is recorded only after it is pressed.",Still missing is a tool that allows you to equalize the brightness of the image with a gradient in any direction. What we have does not work as we would like,Yes
6/21/2022 8:39,Yes,Research scientist,Cell/Molecular Biology,North America,4,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Very interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,3D (SPIM/large volume),3D (SPIM/large volume),3D (SPIM/large volume),,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,None,Postings on image.sc forum or microforum,,,,,,,Yes
6/21/2022 9:53,Yes,Principal investigator,"Cell/Molecular Biology, Medicine",Europe,4,5,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,2D + time,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,"nuclear segmentation, simple cell segmentation",segmentation of neurons in 2D / 3D; segmentation of fluorescently stained tissue sections,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Email list,SBI2,,data mining strategies,,,,Yes
6/21/2022 12:54,Yes,Research scientist,"Physics/Biophysics, Cell/Molecular Biology, Deep learning",North America,2,2,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,"2D, 2D + time, 3D (<3000x3000x100)",,2D,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,"2D, 2D + time, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100)",,denoising,2D automated segmentation of EM images,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,"not really. most are over my head. there needs to be a ""basics"" class for people not specifically trained in computer science",Microscopy and Microanalysis,how to import and use scripts in common software packages,"make it more user friendly. if it's not easy to use for non-coders, it won't be broadly used","understand basic coding tasks, educated developers on the limitations of the imaging technique",,Yes
6/21/2022 14:46,Yes,Facility staff,Cell/Molecular Biology,North America,6,4,5,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Very preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,3D (<3000x3000x100),2D,,,,,,,,,,,,,,,,,,,,,,A discipline-specific society or network,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,I2k conference and Robert Haas youtude tutorial series,Expansion of image analysis offerings at ABRF,,,,,Yes
6/22/2022 10:02,Yes,Facility staff,Developmental Biology,North America,2,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Moderately interested,Not at all interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,2D,,2D,2D,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Postings on image.sc forum or microforum,,,,,,,Yes
6/22/2022 12:28,Yes,Research scientist,"Physics/Biophysics, Computer vision",North America,5,5,6,"Ask a friend or colleague to help me, Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100)",3D (<3000x3000x100),3D (<3000x3000x100),,,,Atom identification from HAADF-STEM images,"Inverse problems, and specifically phase imaging",Twitter,Conference session on imaging or image analysis,Few,Twitter,"ORNL had a deep learning for electron microscopy workshop in Dec 2020. It was very helpful, as the morning sessions were dedicated to research talks, and the afternoon sessions were dedicated to tutorials.","M&M already has, but APS annual meetings, MRS meetings would highly benefit.","Open source scriptable software. People need to learn them rather than sticking to point and click tools. Point and click is fine for initial exploration and that's it. The reason is scripts, which are based on open source tools, are reproducible and contribute to open science. Other methods do not.","Make it scriptable and make it open source. Do not reinvent the wheel - use Python. Look at NION Swift for example (written by Chris Meyer, who also wrote Digital Micrograph) as best practices. ",Again. Learn how to use open source scriptable tools.,"Image analysis, scripting and data visualization must be a core part of graduate curriculum at almost STEM department. This is 2022, not having such courses is not training graduate students at this point.",Yes
6/23/2022 3:58,Yes,Image/data analyst,"Computer science, Computer vision, Deep learning",Asia,7,7,7,Sit down with a tool I know and start playing with the data,Sometimes,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Very interested,Moderately interested,Moderately interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,HCS Data Analysis,HCS Data Analysis,,,,,,,,,,,,,,google,,Few,Email list,None,None,Image-based profiling ,image normalization or standardization (like a  DICOM standard),-,-,Yes
6/23/2022 4:28,Yes,Facility staff,Cell/Molecular Biology,Europe,2,4,4,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",,,,2D,"2D, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,Standardised nuclear/cell segmentation ,,,,,,,,,,,,,,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,,,Comparison of single cell segmentation scripts,User friendly GUIs,Interact with creators to better inform on analysis outputs ,,Yes
6/23/2022 5:51,Yes,Research scientist,"Computer science, Computer vision, Deep learning",Europe,7,6,7,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Somewhat interested,Somewhat interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)","2D, 2D + time",,"2D, 2D + time",,2D,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,,,,,,,No
6/23/2022 10:08,Yes,Research scientist,"Physics/Biophysics, Chemistry/Biochemistry",North America,4,4,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)","2D + time, 3D (<3000x3000x100)",,2D,2D,,,2D + time,"2D + time, 3D (<3000x3000x100)","2D + time, 3D (<3000x3000x100)",,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Email list,,,,,,,No
6/23/2022 13:14,Yes,Principal investigator,Statistics/Biostatistics,South America,5,3,2,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Never,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very preferable,Very preferable,Very preferable,Somewhat interested,Moderately interested,Very interested,Somewhat interested,Moderately interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",3D (<3000x3000x100),3D (<3000x3000x100),3D (<3000x3000x100),,,,,,,,,,pollen morphology,,,,,,,,,,,,,,A discipline-specific society or network,,None,Email list,,,,,,"I have been analyzing pollen in the microscope >30 years and now I want to use digital images to analyze the pollen, much to learn ",Yes
6/23/2022 14:12,Yes,Facility director,Physics/Biophysics,North America,2,4,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below)",Sometimes,Moderately preferable,Moderately preferable,Very preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Moderately interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,2D + time,,,,,,,2D,,,,,,,,,,,,,,,,,A discipline-specific society or network,Workshop/tutorial on imaging or image analysis,Some,A discipline-specific society or network,,,,,,,Yes
6/27/2022 15:31,Yes,Facility staff,Cell/Molecular Biology,South America,2,4,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Moderately preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,"2D, 2D + time","2D, 3D (<3000x3000x100)","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,,2D + time,,"finding nuclei, cell count","membrane identification and analysis, non-stained segmentation, ",,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Some,Postings on image.sc forum or microforum,,,,,,,No
6/28/2022 7:24,Yes,Principal investigator,"Computer science, Computer vision, Deep learning",Europe,7,7,5,Sit down with a tool I know and start playing with the data,Most of the time,Somewhat preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Moderately interested,Moderately interested,Life Sciences,"Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",2D,2D + time,2D + time,2D + time,2D,3D (<3000x3000x100),,,,,,,,,,,,,,,,,,,,,Word of mouth,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Postings on image.sc forum or microforum,,,,,,,No
6/28/2022 7:36,Yes,Research scientist,Physics/Biophysics,Europe,5,5,5,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Very preferable,Moderately preferable,Somewhat preferable,Moderately interested,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,2D,,"2D + time, 3D (<3000x3000x100), 3D + time",,,,,,,,A discipline-specific society or network,,Few,A discipline-specific society or network,,,An expansion of the HyperSpy workshops to applications beyond the TEM focus.,Better commenting of Source code + including examples on how to contribute to Code development. Making sure everything is Open Source or able to export into non-proprietory/open source formats (i.e. hdf5),"Acknowledge open source libraries on publications. Contribute where possible, clearly describe analysis gaps.",,No
6/28/2022 11:02,Yes,Postdoctoral fellow,Physics/Biophysics,Europe,4,5,4,Sit down with a tool I know and start playing with the data,Sometimes,Somewhat preferable,Moderately preferable,Somewhat preferable,Not at all preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Somewhat interested,Moderately interested,Somewhat interested,Not at all interested,Somewhat interested,Somewhat interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,"2D, 3D (large volume)","2D, 2D + time","2D, 2D + time, 3D (large volume)",,,,,,"Segmenting separate round particles, tomography that follows the projection rule",Segmenting non-round particles that have some overlap,Word of mouth,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,A discipline-specific society or network,EMAG Hyperspy workshop,EMAG & Microscience,Dream3D for large and/or complex datasets e.g. strained material,Beta-test their user guides to make sure they haven't missed things that seem obvious to an expert but not to a beginner.,"Ask for help more, but I don't know how to encourage. Maybe a forum for ""no stupid questions""?",,No
6/29/2022 7:29,Yes,Facility staff,"Cell/Molecular Biology, Medicine",Asia,1,3,4,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions in the scientific literature",Never,Very preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Moderately preferable,Somewhat preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc)",None,,,2D,,2D,,,,,,,"cellcounting, cell measurements",staining intensity,,,,,,,,,,,,,,A discipline-specific society or network,,None,Email list,none attended,none attended,,,,,No
6/29/2022 8:31,Yes,Undergraduate/Graduate student,"Physics/Biophysics, Chemistry/Biochemistry, Cell/Molecular Biology",North America,6,6,6,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google)",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Somewhat interested,Moderately interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,2D,2D,2D,2D,2D,2D,2D,2D,3D (<3000x3000x100),,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Email list,,,,,,,Yes
6/29/2022 13:04,Yes,Research scientist,"Physics/Biophysics, Cell/Molecular Biology, Statistics/Biostatistics, Computer science, Computer vision, Deep learning",North America,7,7,7,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Somewhat interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",,"2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,"2D, 3D (<3000x3000x100)",,,,,nuc finding in boring cell types,human in the loop model assisted annotation,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,Postings on image.sc forum or microforum,,,,make everything pip installable,,,Yes
6/29/2022 14:10,Yes,Research scientist,"Cell/Molecular Biology, Developmental Biology",North America,2,3,4,Look up solutions generally on the internet (Google),Never,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Somewhat interested,Very interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Moderately interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"3D (<3000x3000x100), 3D + time","3D (<3000x3000x100), 3D + time",,,,2D,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,A discipline-specific society or network,,,,,,,No
6/29/2022 18:43,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,1,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Sometimes,Very preferable,Very preferable,Very preferable,Somewhat preferable,Moderately preferable,Moderately preferable,Somewhat preferable,Somewhat interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 3D (<3000x3000x100)",,2D,2D,,,"2D, 3D (<3000x3000x100)",,,,"Analyzing images where the focal plane is not flat. i.e. Fundus images and fluorescein angiograms from murine eyes, where the entire image is not in focus and the background is more intense in the middle and where large vessels are very bright and small vessels are dim, and the retina is curved/spherical.",,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Email list,,,,,,,Yes
6/30/2022 0:56,Yes,Undergraduate/Graduate student,Physics/Biophysics,Europe,3,3,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Very preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Somewhat interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Moderately interested,Physical Sciences,,,,,,,,,,,,,,,,"Commercial software that comes with my microscope (AutoMET, Gatan Digital Micrograph. Aztec, etc), Other commercial software (Avizo, Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",,"2D, 3D (<3000x3000x100), 3D (large volume)",,,,,,,,,"Tomographic reconstruction, 2D image analysis in terms of producing statistics from your intensity map in a standard SEM image ",Word of mouth,"Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",None,Email list,,,,,,,Yes
6/30/2022 4:17,Yes,Undergraduate/Graduate student,Chemistry/Biochemistry,Europe,4,1,2,Look up solutions generally on the internet (Google),Never,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Not at all preferable,Not at all preferable,Not at all preferable,Not at all interested,Moderately interested,Not at all interested,Somewhat interested,Not at all interested,Moderately interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,,,,,,,2D,Don't know,overall basic best practices using light microscopy + stereo microscopes esp. how to ge most out of digital cameras etc. ,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,Few,Postings on image.sc forum or microforum,,,Workshops on microscopy related to food analysis would be great! ,,,,No
6/30/2022 11:29,Yes,Facility staff,Cell/Molecular Biology,North America,3,5,4,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Moderately interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Commercial software that comes with my microscope (ie Columbus, Elements, Softworx, etc)",2D + time,2D + time,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",2D,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time",,finding nuclei,cell/particle tracking,,,,,,,,,,,,,,Email list,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"AIM at UC Berkeley, ABRF Image Analysis Workshop",-,How to use a certain tool for a certain kind of experiment,A good documentation about the tool ,The users would need to be informed and understand what kind of image data needs to be generated for the analysis,-,Yes
6/30/2022 17:36,Yes,Undergraduate/Graduate student,"Chemistry/Biochemistry, Cell/Molecular Biology",North America,4,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Moderately preferable,Very preferable,Somewhat preferable,Somewhat preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Moderately interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,2D,,"2D, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,2D,,,3D (SPIM/large volume),,,When cell around 10 um and above and do not overlap.,Cells that cluster together and are very small like cerebellar granule cells. The cells are not clearly visible because they are layered on top of each other. Programs are good at segmenting clearly definable cells but not clusters. Cellpose has been my best solution yet. I also think tools to create a 3D volume out of histology serial sections needs further work.,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, Postings on image.sc forum or microforum","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,"I watched Robert Hansens YouTube class, that was super informative and helpful. About the conference, when the designers of the tool were able to explain their tool to the person without a lot of computational background, this was helpful. The I2K conference stated that it was open for amateurs but much of the content was unreachable for those of us without substantial background in programming. There were many tools that I could not get installed because of my lack of knowledge and experience, let alone understand the tool well enough to perform the tutorials suggested before I EVER even attended the conference. I found the workshops of little worth because I couldn't follow along with the program. I was frustrated that the seminars were question and answer periods about how to use the software and not introductions on explaining what the software does. The Q&A has its uses but for true BEGINNERS, we needed explanation for what we can do. We don't know what is out there and often don't understand the documentation well enough to know if it will work for us.",,"What do I need to know about setting up anaconda? I have broken it twice now and have found help to get it working, but I broke it because I didn't (and still don't really)know how the foundation (supporting software packages) needed to be set up.","GUI interfaces are much easier for the uninitiated to use. Many low budget Research labs do not have access to an imaging analysis core, don't know they exist, and don't know they need one. They may get sold a high dollar software to do something very specific that can be done for free with know how. If you want your tools to really be used by experts and amateurs make your program easy to install and give it a GUI interface.","We need to understand how to set up an experiment for analysis. Amateur users do not understand the limitations or capabilities of image analysis. If there were workshops teaching us how to set up a research station, software installation, how to keep it running, how to install packages, and then finally how to use some of the packages. That would be awesome. There is such a huge gap in communication between the computer world and research biologists needing image analysis.","I apologize if I am coming across harsh about the conference. I'm sure it was hugely successful and helpful for most of your attendees. However, there is a segment of your attendees that probably felt left out because they didn't understand the jargon or because of the enormous effort it was to prepare for the workshops that then didn't even do the thing they thought the software package was designed to do. Yes, some of this is on the amateur user but beyond hours of reading how are we supposed to bridge that gap? I watched 15 hours of Robert Hansen teaching image analysis class on YouTube and while that was hugely helpful. It wasn't enough to get me up to speed for the conference. ",Yes
7/5/2022 23:16,Yes,Undergraduate/Graduate student,Physics/Biophysics,Asia,6,5,5,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions on a particular website (please list below), Look up solutions in the scientific literature",Sometimes,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Physical Sciences,,,,,,,,,,,,,,,,"Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc), Computational libraries and scripts (python (scikit-image), MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Gwyddion, etc)",2D,,,,,,,2D,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",None,Email list,,,,,,,Yes
7/6/2022 4:29,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Never,Not at all preferable,Very preferable,Very preferable,Moderately preferable,Very preferable,Somewhat preferable,Not at all preferable,Moderately interested,Moderately interested,Not at all interested,Very interested,Not at all interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time",2D,,,,,,,,Finding nuclei,Segmentation of objects that are not round,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,A discipline-specific society or network,No,No,How to use certain softwares for certain kinds of experiments.,"Write tutorials and help pages in a more accessible way. The jargon currently used is very hard to understand, especially for beginners. ",,,Yes
7/6/2022 5:05,Yes,Undergraduate/Graduate student,Cell/Molecular Biology,Europe,4,3,3,"Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very interested,Very interested,Very interested,Very interested,Moderately interested,Somewhat interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,,,2D,,2D,,,,,Finding nuclei,Segmenting extracellular matrix I.e not cell associated things ,,,,,,,,,,,,,,Twitter,Workshop/tutorial on imaging or image analysis,Few,Twitter,,,,,,,Yes
7/6/2022 14:25,Yes,Facility director,Cell/Molecular Biology,North America,6,5,6,"Sit down with a tool I know and start playing with the data, Ask on forum.image.sc, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D (<3000x3000x100), 3D (SPIM/large volume)",2D,2D,,,,,"2D, 2D + time",,finding nuclei,"easy multiplex analysis. Intuitive, simplified colocalization, simplified 3D visualization",,,,,,,,,,,,,,Postings on image.sc forum or microforum,,Some,Postings on image.sc forum or microforum,,,Comparisons of popular image analysis software: CellProfiler vs Cellpose vs QuPath vs others.,"Make good videos demonstrating actual use. Videos with careful demonstrations of the programming setups required - for those of us that can code, but are not great at it. Well organized FAQs-like web pages for ""I have this problem, I would like to do this"" with some kind of breakdown of coding that is required.",Users should also make how to videos. It's difficult from the creator side to see how the users might struggle. Users could post to more general sites like reddit or youtube. Legitimate Awards for users that distribute / post content that they could include on CVs.   ,,Yes
7/7/2022 7:32,Yes,Postdoctoral fellow,Developmental Biology,Europe,4,1,3,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,2D,"2D, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D + time, 3D + time",,,,,,,,"2D segmentation for fluorescence images, specially nuclei that display an homogeneous label",DIC image segmentation; 3D nuclei segmentation not based on intensity thresholding nor convex shapes (nuclei that are not round); 3D cell segmentation.,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,ELMI page,"NEUBIAS Academy, gives a good overview of current open source tools developed; tutorials are also helpful to get started although there should be more for people with no programming experience. ",FOM _ offering hands on tutorials; QBI offers tutorials but they are at the end of the day of a very packed schedule thus not very useful as our brains are already overwhelmed. Would be useful to actually offer more dedicated sessions in the mornings.,"Definitely deeplearning for biologists... How to use DeepImageJ, CSBDeep, UNet, etc; BigData processing, analysis, visualization and management.","They develop so many tools, but it is easy to get lost as a user, and takes a huge amount of time to navigate all those tools, understand how they work, test them and successfuly apply them to our own image data. Perhaps is good to have video tutorials that also explain for which type of data the tool is most adequate. Even having a summary table with that would be usefull. Although the ZeroCost4Mic for example is a great initiative, written tutorials are hard to navigate through for non computational biologists. Having more videos like for example the ones that Robert Haase or that Craig Daly has on youtube would be very useful.","Really keeping an open channel of communication between users and developers. The image.sc forum is a very useful way of communication but sometimes a more direct channel would perhaps be faster. Also would be good that more users themselves participate in the teaching of tutorials as we speak a different ""language"" as the developers. I think this would make a lot of the tools easier to understand and implement.",,Yes
7/7/2022 11:08,Yes,Facility director,"Cell/Molecular Biology, Developmental Biology",North America,2,2,1,"Sit down with a tool I know and start playing with the data, Ask a friend or colleague to help me, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Never,Moderately preferable,Very preferable,Moderately preferable,Moderately preferable,Moderately preferable,Very preferable,Moderately preferable,Moderately interested,Very interested,Very interested,Moderately interested,Moderately interested,Moderately interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time","2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,"2D, 2D + time, 3D (<3000x3000x100), 3D + time, 3D (SPIM/large volume), 3D large volume + time",,,,,,,,,,,,,,,,,,Twitter,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis",Few,Twitter,,,,,,,Yes
7/7/2022 15:45,Yes,Principal investigator,"Chemistry/Biochemistry, Cell/Molecular Biology, Computer science",North America,5,4,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Somewhat preferable,Moderately preferable,Very preferable,Very preferable,Very preferable,Moderately preferable,Moderately preferable,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)",2D,,"2D, 2D + time, 3D + time","2D, 2D + time, 3D + time",2D,,,,,,,Finding nuclei stained with DAPI and then quantify Cytoplasm/Nucleus,Spot detection; Single particle tracking; 3D volumetric measurements; classification of cancer vs. normal tissue in histology images etc. ,,,,,,,,,,,,,,"The Images2Knowledge(I2K) conference, A discipline-specific society or network, Twitter, BINA","Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Some,A discipline-specific society or network,I2K,ASCB,Unification of image data management and processing pipelines (enough of having to piece together different tools and moving disconnection datasets around),"Work together to unify image data management and processing pipelines (enough of having to piece together different tools and moving disconnection datasets around). 
Reward structure 
More funding for maintenance of software tools
More funding for documentation
More funding for serious image analysis remote-access help desks","Make their voice heard with institutions, journals, funders that we need more high-quality, professionally developed, unified OPEN SOURCE tools that expedite the process and facilitate integrated image data management","Again we need to improve the environment for software developers that want to work in image data analysis:
More (serious) Funding capable of attracting excellent Sofware developers to the exciting field of open BioImage informatics
",Yes
7/9/2022 9:19,Yes,Postdoctoral fellow,"Statistics/Biostatistics, Computer science",Europe,5,7,7,"Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Most of the time,Somewhat preferable,Very preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Very interested,Very interested,Very interested,Somewhat interested,Very interested,Very interested,Very interested,Life Sciences,"Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Computational libraries and scripts (python (scikit-image), MATLAB, etc)",,,,,2D,,,,,,,finding nuclei,tissue analysis,,,,,,,,,,,,,,Postings on image.sc forum or microforum,"Workshop/tutorial on imaging or image analysis, Conference session on imaging or image analysis, Conference dedicated to imaging or image analysis",Few,Email list,Medical Image Computing and Computer Assisted Interventions (MICCAI)- ISMRM annual meeting,MICCAI,Quality assurance of images,,,,Yes
7/10/2022 2:19,Yes,Research scientist,"Chemistry/Biochemistry, Cell/Molecular Biology, Developmental Biology, Statistics/Biostatistics",Asia,2,4,3,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google), Look up solutions in the scientific literature",Sometimes,Moderately preferable,Very preferable,Moderately preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Somewhat preferable,Moderately interested,Moderately interested,Very interested,Very interested,Very interested,Very interested,Very interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Other commercial software (Imaris, Volocity, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc), Computational libraries and scripts (scikit-image, MATLAB, etc)","Other commercial software (Imaris, Volocity, etc)",2D,"2D + time, 3D + time",2D + time,,,,,,,,3D (<3000x3000x100),finding nuclei,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,Workshop/tutorial on imaging or image analysis,Few,Email list,,,,,,,Yes
7/11/2022 9:33,Yes,Undergraduate/Graduate student,"Cell/Molecular Biology, Statistics/Biostatistics",Europe,4,5,6,"Sit down with a tool I know and start playing with the data, Look up solutions generally on the internet (Google)",Often,Very preferable,Very preferable,Not at all preferable,Moderately preferable,Not at all preferable,Somewhat preferable,Somewhat preferable,Somewhat interested,Moderately interested,Very interested,Moderately interested,Somewhat interested,Somewhat interested,Somewhat interested,Life Sciences,"Commercial software that comes with my microscope (Columbus, Nikon Elements, Softworx, etc), Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","Open source point-and-click software (ImageJ, FIJI, Icy, CellProfiler, etc)","2D, 2D + time",,"2D, 2D + time",,,,,,,,,,,,,,,,,,,,,,,,Postings on image.sc forum or microforum,,None,Email list,,,,,,,Yes