CellProfiler plugins - an easy image analysis platform integration for containers and Python tools

CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate wit...

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Autores principales: Weisbart, Erin, Tromans-Coia, Callum, Diaz-Rohrer, Barbara, Stirling, David R, Garcia-Fossa, Fernanda, Senft, Rebecca A, Hiner, Mark C, de Jesus, Marcelo B, Eliceiri, Kevin W, Cimini, Beth A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cornell University 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462170/
https://www.ncbi.nlm.nih.gov/pubmed/37645041
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author Weisbart, Erin
Tromans-Coia, Callum
Diaz-Rohrer, Barbara
Stirling, David R
Garcia-Fossa, Fernanda
Senft, Rebecca A
Hiner, Mark C
de Jesus, Marcelo B
Eliceiri, Kevin W
Cimini, Beth A
author_facet Weisbart, Erin
Tromans-Coia, Callum
Diaz-Rohrer, Barbara
Stirling, David R
Garcia-Fossa, Fernanda
Senft, Rebecca A
Hiner, Mark C
de Jesus, Marcelo B
Eliceiri, Kevin W
Cimini, Beth A
author_sort Weisbart, Erin
collection PubMed
description CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or tools that are packaged in software containers. The CellProfiler-plugins repository contains a number of these CellProfiler modules, especially modules that are experimental and/or dependency-heavy. Here, we present an upgraded CellProfiler-plugins repository, an example of accessing containerized tools, improved documentation, and added citation/reference tools to facilitate the use and contribution of the community.
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spelling pubmed-104621702023-08-29 CellProfiler plugins - an easy image analysis platform integration for containers and Python tools Weisbart, Erin Tromans-Coia, Callum Diaz-Rohrer, Barbara Stirling, David R Garcia-Fossa, Fernanda Senft, Rebecca A Hiner, Mark C de Jesus, Marcelo B Eliceiri, Kevin W Cimini, Beth A ArXiv Article CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main CellProfiler program, CellProfiler has a plugins system that allows for the creation of new modules which integrate with other Python tools or tools that are packaged in software containers. The CellProfiler-plugins repository contains a number of these CellProfiler modules, especially modules that are experimental and/or dependency-heavy. Here, we present an upgraded CellProfiler-plugins repository, an example of accessing containerized tools, improved documentation, and added citation/reference tools to facilitate the use and contribution of the community. Cornell University 2023-08-15 /pmc/articles/PMC10462170/ /pubmed/37645041 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Weisbart, Erin
Tromans-Coia, Callum
Diaz-Rohrer, Barbara
Stirling, David R
Garcia-Fossa, Fernanda
Senft, Rebecca A
Hiner, Mark C
de Jesus, Marcelo B
Eliceiri, Kevin W
Cimini, Beth A
CellProfiler plugins - an easy image analysis platform integration for containers and Python tools
title CellProfiler plugins - an easy image analysis platform integration for containers and Python tools
title_full CellProfiler plugins - an easy image analysis platform integration for containers and Python tools
title_fullStr CellProfiler plugins - an easy image analysis platform integration for containers and Python tools
title_full_unstemmed CellProfiler plugins - an easy image analysis platform integration for containers and Python tools
title_short CellProfiler plugins - an easy image analysis platform integration for containers and Python tools
title_sort cellprofiler plugins - an easy image analysis platform integration for containers and python tools
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10462170/
https://www.ncbi.nlm.nih.gov/pubmed/37645041
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