Welcome to AxonDeepSeg !

Welcome to the AxonDeepSeg framework. In this site you will find the documentation on how to install and how to use AxonDeepSeg to obtain segmentations of your own microscopy data.

AxonDeepSeg is a segmentation software for microscopy data of nerve fibers. It is based on a convolutional neural network.

• AxonDeepSeg pipeline:

• Segmentation of axon/myelin from various species/contrasts:

• Segmentation of full slice histology and morphometrics extraction:

Contents:

• Introduction
• Installation
  • Miniconda
    • Linux
    • macOS
    • Windows
  • Git (optional)
  • Virtual Environment
  • AxonDeepSeg
    • Stable release
    • Development version
  • Testing the installation
    • Quick test
    • Comprehensive test
  • Graphical User Interface (GUI) (optional)
    • macOS
    • Linux (tested on ubuntu)
    • Known issues
  • GPU-compatible installation
• Existing models
• Getting started
  • Example dataset
  • Syntax
    • Segment a single image
    • Segment multiple images of the same resolution
    • Segment images from multiple folders
  • Jupyter notebooks
• Guide for manual labelling
  • Manual masks for training your own model
  • Manual correction of segmentation masks
• Help
• Citation
• Changelog
  • Version [3.0] - 2020-03-13
  • Version [2.1] - 2018-09-25
  • Version [2.0] - 2018-09-11
  • Version [1.1] - 2018-08-02
  • Version [1.0] - 2018-08-02
  • Version [0.6] - 2018-08-01
  • Version [0.4.1] - 2018-05-16
  • Version [0.3] - 2018-02-22
• Licensing
• Contributors

Indices and tables

• Index
• Module Index
• Search Page