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Open Source Science

https://github.com/brainlesion/stroke_segmentor

stroke segmentation in MRI data

https://github.com/brainlesion/stroke_segmentor

Science Score: 26.0%

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

mri segmentation stroke
Last synced: 6 months ago · JSON representation

Repository

stroke segmentation in MRI data

Basic Info
  • Host: GitHub
  • Owner: BrainLesion
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 131 KB
Statistics
  • Stars: 1
  • Watchers: 0
  • Forks: 0
  • Open Issues: 3
  • Releases: 0
Topics
mri segmentation stroke
Created 7 months ago · Last pushed 6 months ago
Metadata Files
Readme Contributing

README.md

Stroke Segmentor

Python Versions Stable Version Documentation Status tests License <!-- codecov -->

State-of-the-art ischemic stroke lesion segmentation in MRI

Installation

With a Python 3.9+ environment, you can install stroke_segmentor directly from PyPI:

bash pip install stroke_segmentor

Use Cases and Tutorials

A minimal example to create a segmentation could look like this:

```python from stroke_segmentor.inferer import Inferer

inferer = Inferer() pred = inferer.infer( adcpath="path/to/adc.nii.gz", dwipath="path/to/dwi.nii.gz", segmentation_path="seg.nii.gz", # optional. the numpy array is always returned for direct usage ) ```

Logging

By default our package is silent, although we do use logging under the hood.
If you want, you can enable it like this: ```py from loguru import logger

logger.enable("stroke_segmentor") ```

Citation

[!IMPORTANT] stroke_segmentor is based on DeepISLES and offers its NVAUTO algorithm as part of the BrainLesion suite.
Please cite all relevant manuscripts!

DeepISLES

de la Rosa, Ezequiel, et al. "DeepISLES: a clinically validated ischemic stroke segmentation model from the ISLES'22 challenge." Nature Communications 16.1 (2025): 7357. ```

@article{de2025deepisles, title={DeepISLES: a clinically validated ischemic stroke segmentation model from the ISLES'22 challenge}, author={de la Rosa, Ezequiel and Reyes, Mauricio and Liew, Sook-Lei and Hutton, Alexandre and Wiest, Roland and Kaesmacher, Johannes and Hanning, Uta and Hakim, Arsany and Zubal, Richard and Valenzuela, Waldo and others}, journal={Nature Communications}, volume={16}, number={1}, pages={7357}, year={2025}, publisher={Nature Publishing Group UK London} } ```

BrainLesion Suite

Kofler, F., Rosier, M., Astaraki, M., Möller, H., Mekki, I. I., Buchner, J. A., ... & Menze, B. (2025). BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis. arXiv preprint arXiv:2507.09036. ```

@article{kofler2025brainlesion, title={BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis}, author={Kofler, Florian and Rosier, Marcel and Astaraki, Mehdi and M{\"o}ller, Hendrik and Mekki, Ilhem Isra and Buchner, Josef A and Schmick, Anton and Pfiffer, Arianna and Oswald, Eva and Zimmer, Lucas and others}, journal={arXiv preprint arXiv:2507.09036}, year={2025} } ```

NVAUTO Algorithm

Siddique, M. M. R., Yang, D., He, Y., Xu, D., & Myronenko, A. (2022). Automated ischemic stroke lesion segmentation from 3D MRI. arXiv preprint arXiv:2209.09546. @article{siddique2022automated, title={Automated ischemic stroke lesion segmentation from 3D MRI}, author={Siddique, Md Mahfuzur Rahman and Yang, Dong and He, Yufan and Xu, Daguang and Myronenko, Andriy}, journal={arXiv preprint arXiv:2209.09546}, year={2022} }

Contributing

We welcome all kinds of contributions from the community!

Reporting Bugs, Feature Requests and Questions

Please open a new issue here.

Code contributions

Nice to have you on board! Please have a look at our CONTRIBUTING.md file.

Owner

  • Name: BrainLesion
  • Login: BrainLesion
  • Kind: organization

GitHub Events

Total
  • Create event: 6
  • Issues event: 4
  • Release event: 2
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 1
  • Member event: 1
  • Push event: 8
  • Pull request review event: 9
  • Pull request event: 4
  • Pull request review comment event: 7
Last Year
  • Create event: 6
  • Issues event: 4
  • Release event: 2
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 1
  • Member event: 1
  • Push event: 8
  • Pull request review event: 9
  • Pull request event: 4
  • Pull request review comment event: 7

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 6
  • Average time to close issues: 6 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 6
  • Average time to close issues: 6 days
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • MarcelRosier (3)
  • neuronflow (1)
Pull Request Authors
  • MarcelRosier (6)
Top Labels
Issue Labels
enhancement (4)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 234 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
pypi.org: stroke-segmentor
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 234 Last month
Rankings
Dependent packages count: 8.7%
Average: 28.7%
Dependent repos count: 48.7%
Maintainers (1)
neuronflow
Last synced: 6 months ago

Dependencies

.github/workflows/autoformat.yml actions
.github/workflows/pr-lint.yml actions
.github/workflows/release.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/tests.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
poetry.lock pypi
  • alabaster 0.7.16
  • babel 2.16.0
  • beautifulsoup4 4.12.3
  • certifi 2024.8.30
  • charset-normalizer 3.3.2
  • colorama 0.4.6
  • coverage 7.6.1
  • docutils 0.21.2
  • exceptiongroup 1.2.2
  • flake8 7.1.2
  • furo 2024.8.6
  • idna 3.10
  • imagesize 1.4.1
  • iniconfig 2.0.0
  • jinja2 3.1.4
  • markdown-it-py 3.0.0
  • markupsafe 2.1.5
  • mccabe 0.7.0
  • mdit-py-plugins 0.4.2
  • mdurl 0.1.2
  • myst-parser 3.0.1
  • packaging 24.1
  • pluggy 1.5.0
  • pycodestyle 2.12.1
  • pyflakes 3.2.0
  • pygments 2.18.0
  • pytest 8.3.3
  • pytest-cov 5.0.0
  • pyyaml 6.0.2
  • requests 2.32.3
  • snowballstemmer 2.2.0
  • soupsieve 2.6
  • sphinx 7.4.7
  • sphinx-basic-ng 1.0.0b2
  • sphinx-copybutton 0.5.2
  • sphinxcontrib-applehelp 2.0.0
  • sphinxcontrib-devhelp 2.0.0
  • sphinxcontrib-htmlhelp 2.1.0
  • sphinxcontrib-jsmath 1.0.1
  • sphinxcontrib-qthelp 2.0.0
  • sphinxcontrib-serializinghtml 2.0.0
  • tomli 2.0.1
  • urllib3 2.2.3
pyproject.toml pypi
  • flake8 >=5.0.1 develop
  • pytest >=8.0.0 develop
  • pytest-cov >=5.0.0 develop
  • Sphinx >=7.0.0 docs
  • furo >=2024.8.6 docs
  • myst-parser >=2.0.0 docs
  • sphinx-copybutton >=0.5.2 docs
  • python >=3.10