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

TL;DR

This paper introduces an upgraded CellProfiler plugins repository that enhances integration with containerized tools and Python, improving usability, reproducibility, and community contribution in image analysis workflows.

Contribution

It presents an improved plugins repository with better documentation, container access, and citation tools, facilitating easier integration of external tools into CellProfiler.

Findings

Enhanced plugin repository with container support

Improved documentation and citation tools

Facilitates community contributions and reproducibility

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.