Welcome to polarityjam’s documentation!

The PolarityJaM 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
  • Feature Extraction Pipeline
  • Web App
• Usage
  • Run options
  • Parameter file
  • Key file
  • Web app
  • Testing
• Features
  • Single cell features
  • Nucleus features
  • Organelle features
  • Marker features
  • Junction features
  • Neighborhood features
  • Group features
• Visualizations
  • Segmentation
  • Elongation
  • Organelle polarity
  • Cue intensity ratios
  • Cell shape and nuclei shape orientation
  • Marker expression
  • Marker polarity
  • Marker nucleus orientation
  • 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
• Python API
  • Setup your image
  • Segmentation
  • 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
• Methods
  • Segmentation
  • Cell properties
  • Region adjacency graph (neighborhood statistics)
  • Other
• Contribute
  • How can I become a contributor?
  • Contributing to PolarityJaM
• Citation