State-of-the-art ischemic stroke lesion segmentation in MRI
With a Python 3.9+ environment, you can install stroke_segmentor directly from PyPI:
pip install stroke_segmentorA 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
)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")Important
stroke_segmentor is based on DeepISLES and offers its NVAUTO algorithm
as part of the BrainLesion suite.
Please cite all relevant manuscripts!
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}
}
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}
}
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}
}
We welcome all kinds of contributions from the community!
Please open a new issue here.
Nice to have you on board! Please have a look at our CONTRIBUTING.md file.
