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

J Microsc. 2023 Sep 10. doi: 10.1111/jmi.13223. Online ahead of print.


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 containerised tools, improved documentation and added citation/reference tools to facilitate the use and contribution of the community.

Keywords: CellProfiler; Python; image analysis; plugin; software; software container; workflow.