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arXiv · 2507.09036

BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis

Florian Kofler·Marcel Rosier·Mehdi Astaraki·Hendrik Möller·Ilhem Isra Mekki·Josef A. Buchner·Anton Schmick·Arianna Pfiffer·Eva Oswald·Lucas Zimmer·Ezequiel de la Rosa·Sarthak Pati·Julian Canisius·Arianna Piffer·Ujjwal Baid·Mahyar Valizadeh·Akis Linardos·Jan C. Peeken·Surprosanna Shit·Felix Steinbauer·Daniel Rueckert·Rolf Heckemann·Spyridon Bakas·Jan Kirschke·Constantin von See·Ivan Ezhov·Marie Piraud·Benedikt Wiestler·Bjoern Menze
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Abstract

BrainLesion Suite is a versatile toolkit for building modular brain lesion image analysis pipelines in Python. Following Pythonic principles, BrainLesion Suite is designed to provide a 'brainless' development experience, minimizing cognitive effort and streamlining the creation of complex workflows for clinical and scientific practice. At its core is an adaptable preprocessing module that performs co-registration, atlas registration, and optional skull-stripping and defacing on arbitrary multi-modal input images. BrainLesion Suite leverages algorithms from the BraTS challenge to synthesize missing modalities, inpaint lesions, and generate pathology-specific tumor segmentations. BrainLesion Suite also enables quantifying segmentation model performance, with tools such as panoptica to compute lesion-wise metrics. Although BrainLesion Suite was originally developed for image analysis pipelines of brain lesions such as glioma, metastasis, and multiple sclerosis, it can be adapted for other biomedical image analysis applications. The individual BrainLesion Suite packages and tutorials are accessible on GitHub.

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Florian Kofler, Marcel Rosier, Mehdi Astaraki, Hendrik Möller, Ilhem Isra Mekki, Josef A. Buchner, Anton Schmick, Arianna Pfiffer, Eva Oswald, Lucas Zimmer, Ezequiel de la Rosa, Sarthak Pati, Julian Canisius, Arianna Piffer, Ujjwal Baid, Mahyar Valizadeh, Akis Linardos, Jan C. Peeken, Surprosanna Shit, Felix Steinbauer, Daniel Rueckert, Rolf Heckemann, Spyridon Bakas, Jan Kirschke, Constantin von See, Ivan Ezhov, Marie Piraud, Benedikt Wiestler, Bjoern Menze. 2025-07-11. BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis. https://arxiv.org/abs/2507.09036

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