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 convolutional neural networks. The package also includes a tool for automatic morphometrics computation.

• AxonDeepSeg pipeline:

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

• Segmentation of full slice histology and morphometrics extraction:

Contents:

• Introduction
• Testimonials
• Installation
  • Install AxonDeepSeg
  • Testing the installation
    • Quick test
    • Comprehensive test
  • Graphical User Interface (GUI)
  • Software Development with AxonDeepSeg
• Existing models
• Using AxonDeepSeg
  • Example dataset
  • Segmentation
    • Syntax
      • Segment a single image
      • Segment multiple images of the same resolution
      • Segment images from multiple folders
  • Morphometrics
    • Syntax
      • Morphometrics of a single image
      • Morphometrics of a specific image from multiple folders
      • Morphometrics of all the images present in folder(s)
    • Axon Shape: Circle vs Ellipse
      • Circle
      • Ellipse
    • Morphometrics file
    • Colorization
    • Implementation details
      • Diameter estimation
      • Eccentricity estimation
• Manual correction of segmentation masks
  • Napari plugin
    • Open image and mask
    • Modify the mask
    • Modify the mask
  • GIMP software
• Training Models
• Help
• Citation
• Changelog
  • v4.1.0 (2022-10-07)
  • Version 4.0.0 - 2022-02-03
  • Version 3.3.0 - 2022-01-14
  • Version 3.2.0 - 2020-10-16
  • 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