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arXiv · 2306.01915

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·Kevin W Eliceiri·Beth A Cimini
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Abstract

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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Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer, David R Stirling, Fernanda Garcia-Fossa, Rebecca A Senft, Mark C Hiner, Marcelo B de Jesus, Kevin W Eliceiri, Beth A Cimini. 2023-06-02. CellProfiler plugins -- an easy image analysis platform integration for containers and Python tools. https://doi.org/10.1111/jmi.13223

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