AxonSeg: Axon Segmentation Toolbox

Segment axon and myelin from microscopy data. Written in Matlab.

Installation

1 - Download the latest release of Axon Segmentation Toolbox : https://github.com/neuropoly/axonseg/releases

2 - Add the folder code to your Matlab path

3 - Run the script SegmentationGUI

The main GUI is also available on Matlab File Exchange (https://www.mathworks.com/matlabcentral/fileexchange/53840-axonseg).

Tutorials

Link to video demo (SegmentationGUI.m): https://github.com/neuropoly/axonseg/releases/download/v2.1/Axon_Segmentation_GUI_Quick_Overview.mp4.

After installation, run the code/tutorial/as_tutorial.m script line by line to get a better understanding of AxonSeg.

Old tutorials:

• SegmentationGUI: Segment using Graphical interface --> https://drive.google.com/open?id=0B2Xe6kvfjHHnLVE1N2lMYktWMGM
• myelinInitialSegmention : Segment myelin using axon segmentation as input --> https://drive.google.com/open?id=0B2Xe6kvfjHHncWVRMG5mS3JZQUE

Segment any type of histology

Post-Processing tools

Reference: Zaimi A, Duval T, Gasecka A, Côté D, Stikov N and Cohen-Adad J (2016). AxonSeg: open source software for axon and myelin segmentation and morphometric analysis. Front. Neuroinform. 10:37. doi: 10.3389/fninf.2016.00037

Copyright (c) 2016 NeuroPoly (Polytechnique Montreal) and DCClab (Université Laval)