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Segment axon and myelin from microscopy data. Written in Matlab.
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AxonSeg: Axon Segmentation Toolbox

Segment axon and myelin from microscopy data. Written in Matlab (R2014a).

ANNOUNCEMENT: AxonSeg software now has a little brother: AxonDeepSeg, which is based on deep-learning and provides better performance. We encourage you to switch to AxonDeepSeg



Please refer to issue #51 to solve installation error on MAC OS Sierra and later


1 - Download the latest release of Axon Segmentation Toolbox :

2 - Add the folder code to your Matlab path

3 - Run the script AxonSeg

Help & Support

For help or support related to AxonSeg (bugs, trouble with installation, feedback), please add an issue at


Link to video demo (note: SegmentationGUI.m was renamed AxonSeg.m):

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

Segment any type of histology

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Post-Processing tools

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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) 2017 NeuroPoly (Polytechnique Montreal) and DCClab (Université Laval)

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