Welcome to PyFibre documentation!

PyFibre (Python Fibrous Image Analysis Toolkit) is an open source, extensible image analysis toolkit for fibrous tissue that can be run either in a terminal or GUI. It is designed to be as automated as possible so that it can easily be applied to multiple image sets in order to generate databases of properties for further large-scale analysis.

PyFibre has been designed to work with the Tagged Image File Format (TIFF), and is shipped with a plugin that provides automated analysis routines for a multi-channel image format containing Second Harmonic Generation (SHG) and Phospholuminescene (PL) signals.

User Manual

• Installation instructions
• Running PyFibre
  • PyFibre CLI
  • PyFibre GUI
• Core Features
  • PyFibre Segments
  • FIRE Algorithm
  • Network Segmentation
  • Colour Segmentation
• Extending PyFibre
  • PyFibre Factories
  • Creating a Plugin
  • Install the Plugin
• SHG-PL Analysis
  • File Reader
  • Segmentation Algorithms
  • Metrics
  • Output Files
  • Databases

API Reference

• pyfibre
  • pyfibre package

Indices and tables

• Index

• Module Index

• Search Page