nnFoundation introduces complementary convolutional and transformer-based 3D foundation models for radiology, trained on 2.1 million CT, MRI, and PET volumes from 125 datasets. The models are evaluated on 108 tasks—including segmentation, detection, classification, report generation, and image retrieval—under domain shift, low-data, and low-compute scenarios, consistently outperforming prior 3D foundation models and training from scratch. Performance varies by task type, with convolutional models excelling at spatially localized tasks and transformer models at global semantic reasoning, and dynamic alignment with dataset characteristics further enhances transferability.
By Constantin Ulrich Harsy, Tassilo Wald, Karol Gotkowski, Yannick Kirchhoff, Marcel Knopp, Maximilian Rokuss, Elisa Stegmeier, Philipp Schader, Dasha Trofimova, Raphael Stock, Kim-Celine Kahl, Stephen Schaumann, Selen Erkan, David Zimmerer, Stefan Denner, Moritz Langenberg, Sebastian Ziegler, Katharina Eckstein, Maximilian Fischer, Jonathan Suprijadi, B\'alint Kov\'acs, Benjamin Hamm, Anand Deshpande, Dimitrios Bounias, Nico Disch, Shuhan Xiao, Jessica K\"achele, Jan Sellner, Rajesh Baidya, Jeremias Traub, Lars Kr\"amer, Maximilian Zenk, Tim R\"adsch, Stefan Dvoretskii, Robin Peretzke, Jonathan Deissler, Alexandra Ertl, Partha Ghosh, Kris Dreher, Stefan Dinkelacker, Annika Reinke, Evangelia Christodoulou, Numan Saeed, Yoland Savriama, Santiago Estrada, David K\"ugler, Laura Alexandra Daza Barragan, Cristina Isabel Gonzalez Osorio, Jan Peeken, Michael Baumgartner, Marvin Teichmann, Guillaume Chabin, Matthias Kirchler, Valentin Koch, for the ALFA study, Markus Hohenhaus, Dimitri Koslov, Nina Decker, Mohammad Yaqub, Arnd Heuser, Martin Reuter, Julia A. Schnabel, Tobias Heimann, Florin Ghesu, Paul Brachmann, Claus P. Heu{\ss}el, Alexander Radbruch, Gianluca Brugnara, Aditya Rastogi, Martha Foltyn-Dumitru, Heinz-Peter Schlemmer, Ignaz Reicht, Julius C. Holzschuh, Michael Bach, Bram Stieltjes, Kai Schlamp, Lena Maier-Hein, Marco Nolden, Ralf Floca, Paul F. J\"ager, Philipp Vollmuth, Fabian Isensee, Klaus H. Maier-Hein
arXiv:2511.05782v3 Announce Type: replace
Abstract: Unsupervised domain adaptation (UDA) for medical image segmentation remains challenging due to substantial domain shifts across imaging modalities,...
By Lalit Maurya, Honghai Liu, Reyer Zwiggelaar
Generating CT volumes from MRI and CBCT can improve treatment planning in adaptive radiotherapy while avoiding additional radiation exposure. However, direct regression of CT intensities is challenged by the inherently high dynamic range and long-tailed distributions, thereby averaging out sparse yet clinically important structures.
The paper presents the first systematic evaluation of out‑of‑distribution generalization for congenital heart disease (CHD) segmentation, using the ImageCHD cohort as a held‑out target. It compares several segmentation architectures under different training regimes, showing that in‑distribution performance is a poor predictor of cross‑cohort robustness: nnU‑Net drops from 0.77 to 0.51 Dice, while SwinUNETR maintains higher performance at 0.67 Dice. Limited target‑domain adaptation with only 11 labeled ImageCHD cases boosts all SwinUNETR variants above 0.76 Dice, highlighting the importance of explicit cross‑dataset testing.
By Aniketh Vijesh, Shrisharanyan Vasu, Abhijit Ramesh, Clare Pomeroy-Ward, Harikrishnan Anil Maya, Sarin Xavier, Mahesh Kappanayil, Gilad Gressel
Congenital heart disease (CHD) diagnosis and surgical planning often require patient-specific 3D anatomical models, but manual segmentation is labor-intensive, particularly in complex anatomies. Altho...
arXiv:2607. 23343v1 Announce Type: cross Abstract: Intraoperative 2D/3D registration aligns preoperative CT volumes with intraoperative X-ray or fluoroscopic images and is essential for image-guided interventions.
By Minheng Chen, Youyong Kong
The paper presents a 3D foundation model for light sheet fluorescence microscopy (LSM) that is pretrained on a large curated set of 3D images from various organisms, stains, and imaging protocols. By jointly optimizing for masked reconstruction and image‑text alignment, the model learns transferable volumetric representations that dramatically reduce the need for annotated data. The pretrained backbone enables efficient few‑shot adaptation to downstream tasks such as segmentation, classification, and deblurring, consistently outperforming baselines according to standard metrics and expert evaluation.
By Adina Scheinfeld, Haotan Zhang, Shang Mu, Rudolf L. M. van Herten, Lucas Stoffl, Ali Erturk, Zhuhao Wu, Johannes C. Paetzold
arXiv:2510. 15042v3 Announce Type: replace-cross Abstract: In the 3D medical image domain, vision-language pre-training is used to create vision-language encoders (VLEs) that can support radiologists by retrieving patients with similar abnormalities, predicting likelihoods of abnormality, or, with downstream adaptation, generating radiological reports.
By Tassilo Wald, Ibrahim Ethem Hamamci, Yuan Gao, Sam Bond-Taylor, Harshita Sharma, Maximilian Ilse, Cynthia Lo, Olesya Melnichenko, Anton Schwaighofer, Noel C. F. Codella, Maria Teodora Wetscherek, Klaus H. Maier-Hein, Panagiotis Korfiatis, Valentina Salvatelli, Javier Alvarez-Valle, Fernando P\'erez-Garc\'ia
arXiv:2602.20773v2 Announce Type: replace
Abstract: Purpose: Developing generalizable medical image segmentation models is challenging because imaging data are distributed across institutions and dif...
By Sachin Dudda Nagaraju, Ashkan Moradi, Bendik Skarre Abrahamsen, Mattijs Elschot
arXiv:2608. 05960v1 Announce Type: cross Abstract: Routine CT interpretation is inherently comprehensive, capturing incidental findings across the entire scan volume.
By Maulik Chevli, Johannes Brandt, Rickmer Braren, Daniel Rueckert, Philip M\"uller
arXiv:2609.26756v1 Announce Type: new
Abstract: X-ray is medicine's most widely used imaging modality, yet remains among its least quantitative. Unlike volumetric modalities like CT or MRI, X-ray col...
By Victor Ion Butoi, Vivek Gopalakrishnan, John V. Guttag, Adrian V. Dalca, Neel Dey
arXiv:2608. 19965v1 Announce Type: cross Abstract: Segmentation of curvilinear anatomical structures in 3D medical images remains challenging due to complex topology, severe class imbalance, weak contrast, and large variations in structure morphology.
By Sidi Mohamed Sid'El Moctar, Nicolas Vitry, H\'el\`ene Bouvrais