CellProfiler plugins - An easy image analysis platform integration for containers and Python tools
Erin Weisbart1, Callum Tromans-Coia1, Barbara Diaz-Rohrer1
1Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Journal of Microscopy
|September 10, 2023
Summary
CellProfiler plugins enhance image analysis workflows with new modules and containerized tools. This upgraded repository improves usability and community contributions for reproducible scientific imaging.
Area of Science:
- Bioimage analysis
- Computational biology
- Scientific software development
Background:
- CellProfiler is a popular open-source software for reproducible biological image analysis.
- Its plugin system enables integration with external Python tools and containerized applications.
- The CellProfiler-plugins repository hosts experimental and dependency-heavy modules.
Purpose of the Study:
- To present an upgraded CellProfiler-plugins repository.
- To demonstrate accessing containerized tools within CellProfiler.
- To improve documentation and add citation/reference functionalities.
Main Methods:
- Developed and integrated new modules into the CellProfiler-plugins repository.
- Implemented examples for accessing containerized tools.
- Enhanced existing documentation and added citation management features.
Main Results:
- An upgraded CellProfiler-plugins repository is now available.
- Users can access containerized tools for expanded image analysis capabilities.
- Improved documentation and citation tools facilitate easier use and contribution.
Conclusions:
- The enhanced CellProfiler-plugins repository lowers barriers for advanced image analysis.
- It promotes reproducibility and community engagement in scientific software.
- Facilitates integration of diverse computational tools into bioimage analysis workflows.
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