Welcome to polarityjam’s documentation!
The Polarity-JaM suite is a software package that lets you study cell polarity, junctions and morphology.
Explore the software suite here!

Contents:
- What is PolarityJaM?
- Installation
- Usage
- Features
- Visualizations
- Web-App
- Python API
- Python Extended API
- Python Segmentation API
- OMERO and Polarity-JaM
- Methods
- Frequently Asked Questions
- I have problems during installation with imagecodecs, what can i do?
- How to bring your own segmentation?
- Can I bring my own nuclei segmentation?
- How can I correct my segmentation?
- How does such a segmentation file look?
- How to bring your own model?
- What is a parameter file?
- The definitions in my parameter file are ignored
- How does a parameter file look?
- What is a key file?
- How does a key file look?
- Why are my paths in the key file not recognized?
- Contribute
- Citation