Stroke Segmentor

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:

pip install stroke_segmentor

Use Cases and Tutorials

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

from stroke_segmentor.inferer import Inferer

inferer = Inferer()
pred = inferer.infer(
    adc_path="path/to/adc.nii.gz",
    dwi_path="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:

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.