Federated nnU-Net for Privacy-Preserving Medical Image Segmentation
The nnU-Net framework has played a crucial role in medical image segmentation and has become the gold standard in multitudes of applications targeting different diseases, organs, and modalities. However, so far it has been used primarily in a centralized approach where the data collected from hospitals are stored in one center and used to train the nnU-Net. This centralized approach has various limitations, such as leakage of sensitive patient information and violation of patient privacy. Federated learning is one of the approaches to train a segmentation model in a decentralized manner that helps preserve patient privacy. In this paper, we propose FednnU-Net, a federated learning extension of nnU-Net. We introduce two novel federated learning methods to the nnU-Net framework - Federated Fingerprint Extraction (FFE) and Asymmetric Federated Averaging (AsymFedAvg) - and experimentally show their consistent performance for breast, cardiac and fetal segmentation using 6 datasets representing samples from 18 institutions. Additionally, to further promote research and deployment of decentralized training in privacy constrained institutions, we make our plug-n-play framework public. The source-code is available atthis https URL.
View on arXiv@article{skorupko2025_2503.02549, title={ Federated nnU-Net for Privacy-Preserving Medical Image Segmentation }, author={ Grzegorz Skorupko and Fotios Avgoustidis and Carlos Martín-Isla and Lidia Garrucho and Dimitri A. Kessler and Esmeralda Ruiz Pujadas and Oliver Díaz and Maciej Bobowicz and Katarzyna Gwoździewicz and Xavier Bargalló and Paulius Jaruševičius and Kaisar Kushibar and Karim Lekadir }, journal={arXiv preprint arXiv:2503.02549}, year={ 2025 } }