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* Add perimenter of axon and axonmyelin

* Update FSLeyes on_compute_morphometrics button

* Test: Add axon_perimeter

* Test: fix failing tests

* Fix typo

* Remove print statement for debuggin

* Elaborated comments on the axon and axonnyelin perimeter

* tests: Add axonmyelin_perimeter as an expected key

* Fix failing axonmyelin perimeter

* Remove extra space

* Tests: Clean the code

* Add axon + myelin perimeter to CLI

* Fix typo

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

* Fix typo

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

* Fix the ordering of CLI columns to that of FSLeyes

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>
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Segment axon and myelin from microscopy data using deep learning. Written in Python. Using the TensorFlow framework. Based on a convolutional neural network architecture. Pixels are classified as either axon, myelin or background.

For more information, see the documentation website.

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Help

Whether you are a newcomer or an experienced user, we will do our best to help and reply to you as soon as possible. Of course, please be considerate and respectful of all people participating in our community interactions.

  • If you encounter difficulties during installation and/or while using AxonDeepSeg, or have general questions about the project, you can start a new discussion on the AxonDeepSeg GitHub Discussions forum. We also encourage you, once you've familiarized yourself with the software, to continue participating in the forum by helping answer future questions from fellow users!
  • If you encounter bugs during installation and/or use of AxonDeepSeg, you can open a new issue ticket on the AxonDeepSeg GitHub issues webpage.

FSLeyes plugin

A tutorial demonstrating the installation procedure and basic usage of our FSLeyes plugin is available on YouTube, and can be viewed by clicking this link.

References

AxonDeepSeg

Applications

Reviews

Citation

If you use this work in your research, please cite it as follows:

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. Link to paper: https://doi.org/10.1038/s41598-018-22181-4.

Copyright (c) 2018 NeuroPoly (Polytechnique Montreal)

Licence

The MIT License (MIT)

Copyright (c) 2018 NeuroPoly, École Polytechnique, Université de Montréal

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Contributors

Pierre-Louis Antonsanti, Stoyan Asenov, Mathieu Boudreau, Oumayma Bounou, Marie-Hélène Bourget, Julien Cohen-Adad, Victor Herman, Melanie Lubrano, Antoine Moevus, Christian Perone, Vasudev Sharma, Thibault Tabarin, Maxime Wabartha, Aldo Zaimi.