DeepISLES: a clinically validated ischemic stroke segmentation model from the ISLES'22 challenge

Ezequiel Rosa (), Mauricio Reyes, Sook-Lei Liew, Alexandre Hutton, Roland Wiest, Johannes Kaesmacher, Uta Hanning, Arsany Hakim, Richard Zubal, Waldo Valenzuela, David Robben, Diana M. Sima, Vincenzo Anania, Arne Brys, James A. Meakin, Anne Mickan, Gabriel Broocks, Christian Heitkamp, Shengbo Gao, Kongming Liang, Ziji Zhang, Md Mahfuzur Rahman Siddiquee, Andriy Myronenko, Pooya Ashtari, Sabine Huffel, Hyunsu Jeong, Chiho Yoon, Chulhong Kim, Jiayu Huo, Sebastien Ourselin, Rachel Sparks, Albert Clèrigues, Arnau Oliver, Xavier Lladó, Liam Chalcroft, Ioannis Pappas, Jeroen Bertels, Ewout Heylen, Juliette Moreau, Nima Hatami, Carole Frindel, Abdul Qayyum, Moona Mazher, Domenec Puig, Shao-Chieh Lin, Chun-Jung Juan, Tianxi Hu, Lyndon Boone, Maged Goubran, Yi-Jui Liu, Susanne Wegener, Florian Kofler, Ivan Ezhov, Suprosanna Shit, Moritz R. Hernandez Petzsche, Michael Müller, Bjoern Menze, Jan S. Kirschke and Benedikt Wiestler ()
Additional contact information
Ezequiel Rosa: University of Zurich
Mauricio Reyes: University of Bern
Sook-Lei Liew: University of Southern California
Alexandre Hutton: University of Southern California
Roland Wiest: University Institute of Diagnostic and Interventional Neuroradiology
Johannes Kaesmacher: University Institute of Diagnostic and Interventional Neuroradiology
Uta Hanning: University Medical Center Hamburg-Eppendorf
Arsany Hakim: University Institute of Diagnostic and Interventional Neuroradiology
Richard Zubal: University Institute of Diagnostic and Interventional Neuroradiology
Waldo Valenzuela: University Institute of Diagnostic and Interventional Neuroradiology
David Robben: icometrix
Diana M. Sima: icometrix
Vincenzo Anania: icometrix
Arne Brys: icometrix
James A. Meakin: Radboud University Medical Center, Institute for Health Sciences
Anne Mickan: Radboud University Medical Center, Institute for Health Sciences
Gabriel Broocks: University Medical Center Hamburg-Eppendorf
Christian Heitkamp: University Medical Center Hamburg-Eppendorf
Shengbo Gao: Deepwise AI Lab
Kongming Liang: Beijing University of Posts and Telecommunications
Ziji Zhang: Beijing University of Posts and Telecommunications
Md Mahfuzur Rahman Siddiquee: Arizona State University
Andriy Myronenko: NVIDIA
Pooya Ashtari: STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics
Sabine Huffel: STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics
Hyunsu Jeong: Pohang University of Science and Technology (POSTECH)
Chiho Yoon: Pohang University of Science and Technology (POSTECH)
Chulhong Kim: Pohang University of Science and Technology (POSTECH)
Jiayu Huo: King’s College London
Sebastien Ourselin: King’s College London
Rachel Sparks: King’s College London
Albert Clèrigues: University of Girona
Arnau Oliver: University of Girona
Xavier Lladó: University of Girona
Liam Chalcroft: University College London
Ioannis Pappas: University of Southern California
Jeroen Bertels: Processing Speech and Images (PSI), KU Leuven
Ewout Heylen: Processing Speech and Images (PSI), KU Leuven
Juliette Moreau: Université Lyon1, CNRS UMR5220, INSERM U1206, INSA-Lyon
Nima Hatami: Université Lyon1, CNRS UMR5220, INSERM U1206, INSA-Lyon
Carole Frindel: Université Lyon1, CNRS UMR5220, INSERM U1206, INSA-Lyon
Abdul Qayyum: Imperial College London
Moona Mazher: University College London
Domenec Puig: University Rovira I Virgili
Shao-Chieh Lin: China Medical University Hsinchu Hospital
Chun-Jung Juan: China Medical University Hsinchu Hospital
Tianxi Hu: University of Toronto
Lyndon Boone: University of Toronto
Maged Goubran: University of Toronto
Yi-Jui Liu: Feng Chia University
Susanne Wegener: University Hospital of Zurich
Florian Kofler: Technical University of Munich
Ivan Ezhov: Technical University of Munich
Suprosanna Shit: Technical University of Munich
Moritz R. Hernandez Petzsche: Technical University of Munich
Michael Müller: University of Bern
Bjoern Menze: University of Zurich
Jan S. Kirschke: Technical University of Munich
Benedikt Wiestler: Technical University of Munich

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Diffusion-weighted MRI is critical for diagnosing and managing ischemic stroke, but variability in images and disease presentation limits the generalizability of AI algorithms. We present DeepISLES, a robust ensemble algorithm developed from top submissions to the 2022 Ischemic Stroke Lesion Segmentation challenge we organized. By combining the strengths of best-performing methods from leading research groups, DeepISLES achieves superior accuracy in detecting and segmenting ischemic lesions, generalizing well across diverse axes. Validation on a large external dataset (N = 1685) confirms its robustness, outperforming previous state-of-the-art models by 7.4% in Dice score and 12.6% in F1 score. It also excels at extracting clinical biomarkers and correlates strongly with clinical stroke scores, closely matching expert performance. Neuroradiologists prefer DeepISLES’ segmentations over manual annotations in a Turing-like test. Our work demonstrates DeepISLES’ clinical relevance and highlights the value of biomedical challenges in developing real-world, generalizable AI tools. DeepISLES is freely available at https://github.com/ezequieldlrosa/DeepIsles .

Date: 2025
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DOI: 10.1038/s41467-025-62373-x

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