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Open Source Science

axondeepseg

Axon/Myelin segmentation using Deep Learning

https://github.com/axondeepseg/axondeepseg

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, sciencedirect.com, nature.com
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary

Keywords

axon convolutional-neural-networks deep-learning electron-microscopy histology machine-learning microscopy myelin neuropoly segmentation spinalcord

Keywords from Contributors

magnetization mri interactive standardization serializer packaging network-simulation hacking autograding observability
Last synced: 6 months ago · JSON representation

Repository

Axon/Myelin segmentation using Deep Learning

Basic Info
Statistics
  • Stars: 122
  • Watchers: 11
  • Forks: 31
  • Open Issues: 40
  • Releases: 19
Topics
axon convolutional-neural-networks deep-learning electron-microscopy histology machine-learning microscopy myelin neuropoly segmentation spinalcord
Created over 9 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

ADS logo (simplified image of segmented axons/myelin in blue and red beside the text 'AxonDeepSeg')

Binder Build Status Documentation Status Coverage Status Twitter Follow

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.

alt tag

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.

Napari plugin

A tutorial demonstrating the basic features of our plugin for Napari is hosted 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.

Owner

  • Name: AxonDeepSeg
  • Login: axondeepseg
  • Kind: organization
  • Location: Canada

Segmentation software for microscopy data of nerve fibers based on deep learning.

GitHub Events

Total
  • Create event: 45
  • Release event: 4
  • Issues event: 171
  • Watch event: 9
  • Delete event: 60
  • Issue comment event: 436
  • Push event: 420
  • Pull request review event: 188
  • Pull request review comment event: 140
  • Pull request event: 89
Last Year
  • Create event: 45
  • Release event: 4
  • Issues event: 171
  • Watch event: 9
  • Delete event: 60
  • Issue comment event: 436
  • Push event: 420
  • Pull request review event: 188
  • Pull request review comment event: 140
  • Pull request event: 89

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 679
  • Total Committers: 23
  • Avg Commits per committer: 29.522
  • Development Distribution Score (DDS): 0.741
Past Year
  • Commits: 17
  • Committers: 3
  • Avg Commits per committer: 5.667
  • Development Distribution Score (DDS): 0.353
Top Committers
Name Email Commits
Aldo Zaimi a****i@p****a 176
MaxWab m****a@g****m 116
Mathieu Boudreau e****0@g****m 95
Victor Herman v****3@g****m 69
Julien Cohen-Adad j****n@p****a 40
Pierre-Louis p****8@g****m 33
Vasudev Sharma v****4@y****m 31
Stoyan I. Asenov 4****A 28
mariehbourget 5****t 23
Christian S. Perone c****e@g****m 13
Armand 8****n 12
maxwab m****l@r****a 10
alzaia z****o@g****m 9
Maxime Wabartha m****b@m****a 6
Jean-François Fortin Tam n****o@g****m 4
Antoine Moevus m****8 4
oumayb b****a@g****m 3
Alexandru Foias a****s 2
Joshua Newton j****n@g****m 1
Nick n****r@p****a 1
dependabot[bot] 4****] 1
Michael Rizvi-Martel 5****i 1
Yang Ding d****1@g****m 1
Committer Domains (Top 20 + Academic)
polymtl.ca: 3 marsalis.neuro.polymtl.ca: 1 rosenberg.neuro.polymtl.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 223
  • Total pull requests: 196
  • Average time to close issues: about 3 years
  • Average time to close pull requests: about 1 month
  • Total issue authors: 29
  • Total pull request authors: 8
  • Average comments per issue: 2.77
  • Average comments per pull request: 5.86
  • Merged pull requests: 150
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 39
  • Pull requests: 97
  • Average time to close issues: 7 days
  • Average time to close pull requests: 11 days
  • Issue authors: 6
  • Pull request authors: 4
  • Average comments per issue: 1.85
  • Average comments per pull request: 3.77
  • Merged pull requests: 80
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mathieuboudreau (61)
  • hermancollin (47)
  • jcohenadad (29)
  • mariehbourget (17)
  • vasudev-sharma (13)
  • Stoyan-I-A (12)
  • alzaia (11)
  • antmoev (5)
  • maxwab (4)
  • GrimmSnark (3)
  • perone (2)
  • tanguyduval (2)
  • dccote (1)
  • Paasu (1)
  • joshuacwnewton (1)
Pull Request Authors
  • mathieuboudreau (123)
  • hermancollin (36)
  • Stoyan-I-A (20)
  • mariehbourget (7)
  • joshuacwnewton (5)
  • vasudev-sharma (2)
  • michaelrizvi (2)
  • kousu (1)
Top Labels
Issue Labels
enhancement (29) feature (24) priority:LOW (20) refactoring (19) documentation (16) priority:MEDIUM (14) good first issue (14) priority:HIGH (13) good internship project (12) training (11) fsleyes (11) installation (10) GUI (9) models (8) patching (7) processing (7) testing (6) bug (6) morphometrics (6) discussion (5) augmentation (4) nnunetv2 (3) ci (3) dependencies (2) readme (2) cli (2) question (1) windows (1) quality assurance (1) duplicate (1)
Pull Request Labels
bug (33) installation (29) documentation (28) morphometrics (23) feature (19) cli (19) enhancement (16) testing (16) dependencies (15) refactoring (14) GUI (10) processing (8) release (7) fsleyes (5) unmyelinated axon (4) ci (3) priority:HIGH (3) priority:MEDIUM (2) readme (2) models (2) nnunetv2 (2) patching (1) exceptions (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 841 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 49
  • Total maintainers: 3
proxy.golang.org: github.com/axondeepseg/axondeepseg
  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 6 months ago
pypi.org: axondeepseg

Axon/Myelin segmentation using AI

  • Versions: 40
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 841 Last month
Rankings
Stargazers count: 6.8%
Forks count: 7.3%
Dependent packages count: 10.0%
Average: 23.2%
Downloads: 24.4%
Dependent repos count: 67.6%
Maintainers (3)
mathieuboudreau alzaia mariehbourget
Last synced: 6 months ago

Dependencies

docs/environment.yml conda
  • recommonmark
  • sphinx 4.2.0
  • sphinx_rtd_theme >=0.2.4
.github/workflows/run_tests.yaml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
Dockerfile docker
  • jupyter/datascience-notebook python-3.7.6 build
environment.yml conda
  • h5py 2.10.0.*
  • imageio <2.28.0
  • jupyter
  • matplotlib
  • mpld3
  • nibabel 3.2.*
  • numpy
  • openpyxl
  • pandas
  • pillow !=9.0.0
  • pip
  • prettytable
  • pytest
  • pytest-cov
  • python 3.8.*
  • qtconsole <5.4.2
  • raven
  • requests
  • scikit-image 0.19.3.*
  • scikit-learn 1.1.1.*
  • scipy
  • tabulate
  • tqdm