Create Dataset Browser for the OMERO Server

[gab1one]

We need a minimal browser that visualizes the OMERO server file structure and allows the user to select a dataset that will be read by the node.

Needs to work on desktop and webportal!

[ctrueden]

Everyone wants this, and there has been quite a bit of past discussion about having a shared browser component, and where it should live. Obviously, OMERO.insight has such things, but it is monolithic and unusable downstream.

Here is one such effort by @imunro: the OMEROImageChooser, part of the ome-ui-utils project.

There are also some UI components in the Omega project by @Akramhar, although I think they are less oriented toward general-purpose downstream consumption.

I would vote for this shared component to live in the ImageJ-OMERO project. See imagej/imagej-omero#53, which is the corresponding issue there.

[gab1one]

We probably want both a file chooser for single images, i.e on that shows thumbnails etc. and one that reads whole folders. For the later we will probably need to build a custom component that is webtech based.

For the thumbnail browser we would love to contribute to ImageJ-OMERO.

[imunro]

My effort doesn't currently display thumbnails. See http://blog.openmicroscopy.org/community/tools/2016/08/23/image-chooser/ for screenshots. Feel free to add that. I have no strong feelings on where this lives however.

[Akramhar]

Hello :)
As @ctrueden said, I have a imagej op/plugin that is able to read images from OMERO, using swing GUI components.
It is still very raw but I'm planning to spend time on it in the next weeks to finally refine it.
Here some screenshots:
https://www.dropbox.com/s/5npfskx4o5ed80f/OmeroPlugin_screen2.png?dl=0
https://www.dropbox.com/s/shg2oexapvuyd2c/OmeroPlugin_screen3.png?dl=0

[gab1one]

Hi @Akramhar, that looks cool, is the code anywhere I could see it?
NVM @dietzc found it: https://github.com/OmegaProject/ImageJPlugins

[imunro]

Hi @akramar I was looking at https://github.com/OmegaProject/ImageJPlugins but I couldn't see much code there. Am I missing something? In particular I was thinking about "borrowing " your thumbnail approach for my code if that's ok?

[gab1one]

Hi @Akramhar
Currently there is no LICENSE file or any copyright/license information in any of the omega repositories. The http://omega.umassmed.edu/ website says it is an open source project though. I think http://choosealicense.com/ gives a good overview over practical open source licenses.

I think it would be helpful if we could bundle our efforts into an unified solution in imagej-omero!

[dietzc]

Maybe we could start with either the version of @imunro or @Akramhar as an initial commit in e.g. imagej-omero-browser world and then subsequently make the component better together, such that it can be reused by ImageJ, KNIME and of course your own software. If you don't like this idea, it would be great if you guys could share your code somewhere with a license statement attached. Then, we would either fork your code or open PRs on your repository. It's up to you 👍 Thanks for the great work in either case!

My very personal (and of course very, very biased) opinion:
The advantage of having the code in one place is that we could join efforts on the same repository and we would benefit from the imagej-x universe infrastructure (maven deployment via jenkins, version management in pom-imagej etc) and also it maybe attractive for others to contribute as the visibility is much higher in a centralized repository.

Maybe @ctrueden can comment on this, too.

[imunro]

Happy to do that guys. My code is at https://github.com/imperial-photonics/omeUiUtils.
Please let me know what you need added & where in the way of licenses?

Also A ready-to-use .jar file compatible with OMERO 5.2.x can be also downloaded from https://bintray.com/imperial-photonics/omeUiUtils/omeUiUtils/.
For instructions on how to integrate with Maven/Gradle, refer to the Bintray user documentation.
If you want to have a look.

[gab1one]

@imunro regarding the license, usually there is a file called LICENSE or similar in the root directory of a repository. http://stackoverflow.com/questions/31639059/how-to-add-license-to-a-existing-github-project/37895659#37895659 shows how to add one on Github.

I think any GPL compatible license should work out fine.

[imunro]

@gab1one Thanks. Hope that helps.

[Akramhar]

@imunro @gab1one most of the code sits in 2 different common project because I use it in my software too.
You can look here:
omega.omero.commons
some common GUI components maybe here:
omega.commons

@gab1one as I said to @ctrueden in imagej/imagej-omero#53 I'm going to refine it in these days and move it to imagej-omero.

@gab1one thanks, I forgot to add license there :)

[ctrueden]

In particular I was thinking about "borrowing " your thumbnail approach for my code if that's ok?

@imunro Can we please just create a shared Swing component that everyone depends on?

Edit: Sorry, I did not initially see the later posts after this.

Please let me know what you need added & where in the way of licenses?

License should be permissive. Either BSD-2, ISC, MIT, or Apache 2.

As for where: probably it should not depend on ImageJ, but rather extend the pom-omero-client parent? Ideally it should live in the ome org on GitHub, if the main OME team is OK with that.

[imunro]

@ctrueden I can't speak for the OME team but they asked me to move it into it's current repo before publishing the blog. I went for GPL. Should I change?

[ctrueden]

I went for GPL. Should I change?

Oh, I forgot one thing: OMERO is built on Ice, and both OMERO and Ice are GPL. So I fear everything we do built on them will need to be GPL too. So no need to change it!

[imunro]

Cool! Just to be clear I was wondering about implementing the thumbnail functionality, as people seem to want it, as a possible stop-gap measure until something else comes on-line.

[jburel]

@ctrueden: that was/is the plan to have a "utils" (name to be decided) repo under the omeorganisation for some of the components discussed here i.e. common login etc. We could not dedicate resources before publishing @imunro post

[imunro]

As I haven't heard much and in an attempt to get the ball rolling here I've attempted to add thumbnail functionality to my existing code. See the "thumb" branch. https://github.com/imperial-photonics/omeUiUtils/tree/thumb
Could somebody who needs this functionality possibly have a look and see if this is of use please?
Please note However!! This is not fully tested yet! I am currently testing against a VM. Please be cautious about testing against an OMERO server that others use.

[Akramhar]

As I said I'm working on and off to integrate my GUI in a imagej2 command / op.
I found some problems that I'm trying to solve.
I'm going to update you guys as soon as I have a working version of it.

[Akramhar]

Updates here

[Akramhar]

hi @gab1one,
I just completed the update/overhaul of my OmeroBrowser.
You can find it here .
Keep in mind it requires an update of the imagej-omero component of imagej so it cannot work outside debug mode (see here).
I would like to understand if this satisfies your needs and if not what additional feature else would you need.
Ciao