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?
  • PolarityJaM suite
  • Feature Extraction Pipeline
  • Online Service
  • Security
• Installation
  • Polarity-JaM - Feature Extraction Pipeline
  • Polarity-JaM - Web App
• Usage
  • Run options
  • Parameter file
  • Key file
  • Napari Plugin
  • Web app
  • Testing
• Features
  • Feature types
  • Type: Identification & Localization
  • Type: Morphology
  • Type: Polarity
  • Type: Intensity
  • Type: Topology
  • Targets
  • Target: Single cell
  • Target: Nucleus
  • Target: Organelle
  • Target: Marker
  • Target: Junction
  • Target: Topology - neighborhood
  • Target: Topology - group
• Visualizations
  • Segmentation
  • Elongation
  • Organelle polarity
  • Cue intensity ratios
  • Cell shape and nuclei shape orientation
  • Marker expression
  • Marker polarity
  • Marker nucleus orientation
  • Junction features
  • Junction polarity
  • Nucleus displacement orientation
  • Cell Corners
  • Feature of interest
• Web-App
  • Circular statistics
  • Panel: Data preparation
  • Panel: Plot data
  • Panel: Correlation analysis
  • Panel: Compare
  • Further literature
• Python API
  • Parameter
  • Segmentation
  • Change segmentation parameters
  • Change segmentation algorithm
  • Feature extraction
  • Visualization
• Python Extended API
  • Setup data
  • Segmentation & Feature Extraction
  • Working with the pyplot visualization
  • Working with a BioMedicalImage, Channels and simple Masks
  • Working with instance and semantic masks
  • Working with the extracted features
  • Working with the feature objects
• Python Segmentation API
  • Setup your data
  • Several segmentation algorithms in parallel
  • Segmentation Mode “Nuclei”
  • Segmentation Mode “Organelle”
• Methods
  • Segmentation
  • Cell properties
  • Region adjacency graph (neighborhood statistics)
  • Other
• Frequently Asked Questions
  • How to bring your own 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
  • How can I become a contributor?
  • Contributing to PolarityJaM
• Citation