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

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arxiv 2306.01915 v2 pith:DKGKQNWO submitted 2023-06-02 q-bio.QM

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

Erin Weisbart , Callum Tromans-Coia , Barbara Diaz-Rohrer , David R Stirling , Fernanda Garcia-Fossa , Rebecca A Senft , Mark C Hiner , Marcelo B de Jesus
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Kevin W Eliceiri Beth A Cimini
This is my paper
classification q-bio.QM
keywords cellprofilertoolsmodulesanalysiscellprofiler-pluginscontainersimageplugins
verification ladder T0 review T1 audit T2 compute T3 formal T4 reserved
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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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