Software Image processing/visualization

AxonDeepSeg: Axon Segmentation Toolbox

Application

Segment axon and myelin from microscopy data

Contributors

Aldo Zaimi1, Tanguy Duval1, Alicja Gasecka2,3, Daniel Cote1, Mathieu Boudreau1, Christian Perone1, Oumayma Bounou1, Victor Herman1, Melanie Lubrano1, Maxime Wabartha1, Nikola Stikov1,4, Julien Cohen-Adad1,5

Contact

jcohen@polymtl.ca

Estimated cost

Free

Progress

Python 3.0

MIT License

Resources

https://axondeepseg.readthedocs.io

 

Older AxonSeg (Matlab based) version:

https://github.com/neuropoly/axonseg

AxonDeepSeg is an open-source software using deep learning and aiming at automatically segmenting axons and myelin sheaths from microscopy images. It performs 3-class semantic segmentation using a convolutional neural network.

  • Segment axons and myelin sheaths from various imaging modalities
  • Extract statistics from segmented histology
  • Compare histology with MRI

AxonDeepSeg was developed by NeuroPoly, the neuroimagery laboratory of Polytechnique Montréal.

Publications

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

Zaimi, A., Wabartha, M., Herman, V., Antonsanti, P.-L., Perone, C. S., & Cohen-Adad, J. (2018). AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks. Scientific Reports, 8(1), 3816.

Affiliations

Figures

1Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada

2Institut Universitaire en Santé Mentale de Québec, Quebec, QC, Canada

3Centre d’Optique, Photonique et Laser, Université Laval, Quebec, QC, Canada

4Montreal Heart Institute, Montreal, QC, Canada

5Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada

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