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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
---
cff-version: 1.2.0
title: CytoTable
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: David
family-names: Bunten
orcid: 'https://orcid.org/0000-0001-6041-3665'
- given-names: Faisal
family-names: Alquaddoomi
orcid: 'https://orcid.org/0000-0003-4297-8747'
- given-names: Erik
family-names: Serrano
orcid: 'https://orcid.org/0000-0003-4188-9080'
- given-names: Gregory
family-names: Way
orcid: 'https://orcid.org/0000-0002-0503-9348'
repository-code: 'https://github.com/cytomining/CytoTable'
url: 'https://cytomining.github.io/CytoTable/'
abstract: >-
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
keywords:
- python
- cellprofiler
- single-cell-analysis
- microscopy
- profiling
- data
- data-engineering
- pycytominer
- way-lab
license: BSD-3-Clause
references:
- authors:
- name: "cytominer-database Development Team"
date-accessed: "2022-10-27"
title: cytominer-database
type: software
repository-code: "https://github.com/cytomining/cytominer-database"
scope: "tests/"
notes: >-
cytominer-database testing data is used to help validate expected results
identifiers:
- description: "CITATION.cff"
type: url
value: "https://github.com/cytomining/cytominer-database/blob/master/CITATION.cff"
- authors:
- name: "ExampleHuman CellProfiler Data Team"
date-accessed: "2022-09-01"
title: ExampleHuman CellProfiler Data
type: data
repository-code: "https://github.com/CellProfiler/examples/tree/master/ExampleHuman"
url: "https://cellprofiler.org/examples"
scope: "ExampleHuman"
notes: >-
ExampleHuman CellProfiler data is used to help validate expected results
for CytoTable.
identifiers:
- description: "README.md with Citation Information"
type: url
value: "https://github.com/CellProfiler/examples/blob/master/ExampleHuman/README.md"
- authors:
- name: "Way Lab NF1_SchwannCell_data Team"
date-accessed: "2022-09-01"
title: Way Lab NF1_SchwannCell_data CellProfiler Data
type: data
repository-code: "https://github.com/WayScience/NF1_SchwannCell_data"
url: "https://github.com/WayScience/NF1_SchwannCell_data/blob/7b0f5a232ddaf87a92d93bc3a7d23be666cd3627/CellProfiler_pipelines/Analysis_Output/Plate1_Output/all_cellprofiler.sqlite"
scope: "all_cellprofiler.sqlite"
notes: >-
CellProfiler generated data from NF1_SchwannCell_data project is used to help validate
expected results for CytoTable.
identifiers:
- description: "Github Link with Contributors"
type: url
value: "https://github.com/WayScience/NF1_SchwannCell_data/graphs/contributors"
- authors:
- family-names: "Way"
given-names: " Gregory P."
- family-names: "Kost-Alimova"
given-names: " Maria"
- family-names: "Shibue"
given-names: " Tsukasa"
- family-names: "Harrington"
given-names: " William F."
- family-names: "Gill"
given-names: " Stanley"
- family-names: "Piccioni"
given-names: " Federica"
- family-names: "Becker"
given-names: " Tim"
- family-names: "Shafqat-Abbasi"
given-names: " Hamdah"
- family-names: "Hahn"
given-names: " William C."
- family-names: "Carpenter"
given-names: " Anne E."
- family-names: "Vazquez"
given-names: " Francisca"
- family-names: "Singh"
given-names: " Shantanu"
date-accessed: "2023-04-18"
title: "Predicting cell health phenotypes using image-based morphology profiling"
type: "article"
repository-code: "https://github.com/broadinstitute/cell-health"
doi: "10.1091/mbc.E20-12-0784"
url: "https://doi.org/10.1091/mbc.E20-12-0784"
notes: >-
Cell Health datasets used as a reference for building CytoTable.
Data located at: https://nih.figshare.com/articles/dataset/Cell_Health_-_Cell_Painting_Single_Cell_Profiles/9995672/5
- title: >-
Parsl: Pervasive Parallel Programming in Python
type: software
url: https://dl.acm.org/doi/10.1145/3307681.3325400
authors:
- family-names: Babuji
given-names: Yadu
- family-names: Woodard
given-names: Anna
- family-names: Li
given-names: Zhuozhao
- family-names: Katz
given-names: Daniel S.
- family-names: Clifford
given-names: Ben
- family-names: Kumar
given-names: Rohan
- family-names: Lacinski
given-names: Lukasz
- family-names: Chard
given-names: Ryan
- family-names: Wozniak
given-names: Justin M.
- family-names: Foster
given-names: Ian
- family-names: Wilde
given-names: Michael
- family-names: Chard
given-names: Kyle
date-released: 2019-06-17
identifiers:
- type: doi
value: 10.1145/3307681.3325400
notes: >-
Parsl is used to help enable parallel task completion for scalable data engineering.
- title: >-
DuckDB: an Embeddable Analytical Database
type: software
url: https://dl.acm.org/doi/10.1145/3299869.3320212
authors:
- family-names: Raasveldt
given-names: Mark
- family-names: Mühleisen
given-names: Hannes
date-released: 2019-06-25
identifiers:
- type: doi
value: 10.1145/3299869.3320212
notes: >-
DuckDB is used throughout many data operations within CytoTable.
- title: >-
MapReduce: simplified data processing on large clusters
type: software
url: https://dl.acm.org/doi/10.1145/1327452.1327492
authors:
- family-names: Dean
given-names: Jeffrey
- family-names: Ghemawat
given-names: Sanjay
identifiers:
- type: doi
value: 10.1145/1327452.1327492
notes: >-
MapReduce techniques are used via Parsl apps and workflow configuration
to help achieve scalable data engineering for CytoTable.
- authors:
- family-names: Lamba
given-names: Aashna
- family-names: Colas
given-names: Alexandre
date-accessed: "2024-01-09"
title: Colas Lab Example IN Carta Dataset
type: data
notes: >-
The Colas Lab provided access to a single-cell dataset exported from
IN Carta Image Analysis Software (Molecular Devices) for
use within CytoTable tests for furthering development efforts.
A modified testing dataset appears within this project
under `tests/data/in-carta/colas-lab`.
See:
- https://sbpdiscovery.org/our-scientists/alexandre-colas-phd
- https://www.moleculardevices.com/products/cellular-imaging-systems/acquisition-and-analysis-software/in-carta-image-analysis-software
- authors:
- name: "Way Lab nf1_cellpainting_data Team"
date-accessed: "2024-04-03"
title: Way Lab nf1_cellpainting_data CellProfiler Data
type: data
repository-code: "https://github.com/WayScience/nf1_cellpainting_data"
url: "https://github.com/WayScience/nf1_cellpainting_data/raw/main/2.cellprofiler_analysis/analysis_output/Plate_3/Plate_3_nf1_analysis.sqlite"
scope: "Plate_3_nf1_analysis.sqlite"
notes: >-
CellProfiler generated data from nf1_cellpainting_data project is used to help validate
expected results for CytoTable.
identifiers:
- description: "Github Link with Contributors"
type: url
value: "https://github.com/WayScience/nf1_cellpainting_data/graphs/contributors"