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

Estimated cost

Free

Progress

Python 3.0

MIT License

Resources

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

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