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:2608. 08135v1 Announce Type: cross Abstract: Cross-modality medical image translation can reduce the burden of multi-modal acquisitions, yet the field remains constrained by two coupled limitations: methods operate on 2D slices or 3D patches rather than whole volumes, and train a separate model for each translation task.
By Daniele Molino, Alessio Zoboli, Camillo Maria Caruso, Valerio Guarrasi, Paolo Soda
arXiv:2603. 13377v2 Announce Type: replace-cross Abstract: Representation learning has driven major advances in natural image analysis by enabling models to acquire high-level semantic features.
By Ivan Svatko, Maxime Sanchez, Ihab Bendidi, Gilles Cottrell, Auguste Genovesio
arXiv:2404. 06294v2 Announce Type: replace-cross Abstract: Super-Resolution (SR) is a time-hallowed image processing problem that aims to improve the quality of a Low-Resolution (LR) sample up to the standard of its High-Resolution (HR) counterpart.
By Arkaprabha Basu, Kushal Bose, Sankha Subhra Mullick, Anish Chakrabarty, Swagatam Das
arXiv:2607. 22712v1 Announce Type: cross Abstract: Single-cell light microscopy images have become an important data source for characterizing cell phenotypes, but their complexity and heterogeneity pose challenges to high-throughput automated analysis.
By Yifan Shang (Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China, College of Computer Science and Electronic Engineering, Hunan University, Changsha, China), Jiahui Tan (College of Computer Science and Electronic Engineering, Hunan University, Changsha, China), Xiangxiang Zeng (College of Computer Science and Electronic Engineering, Hunan University, Changsha, China), Renjie Zhou (Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China)
arXiv:2508. 05321v4 Announce Type: replace-cross Abstract: Assume you encounter an inverse problem that shall be solved for a large number of data, but no ground-truth data is available.
By Laura Hellwege, Johann Christopher Engster, Moritz Schaar, Thorsten M. Buzug, Maik Stille
arXiv:2609.09863v1 Announce Type: new
Abstract: Choosing a deep learning architecture for label-free single-cell classification remains an open question, with microscopy benchmarks reporting conflict...
By Philip Graemer, Giuseppe Di Caprio
arXiv:2607. 14703v1 Announce Type: cross Abstract: Multiple instance learning (MIL) has become the main paradigm for whole-slide image (WSI) analysis in computational pathology.
By Mingxi Fu, Jiawen Li, Renao Yan, Jiali Hu, Qiehe Sun, Tian Guan, Yonghong He
SlowFast‑SCI introduces a dual‑speed deep‑unfolding framework for spectral compressive imaging that combines a slow, pre‑trained backbone with a fast, test‑time adaptation stage. The slow phase distills a priors‑based model into a compact fast‑unfolding network, while the fast phase embeds lightweight modules that self‑supervise at test time without retraining the backbone. This design yields significant reductions in parameters and FLOPs, improves out‑of‑distribution PSNR by up to 5.79 dB, and accelerates adaptation four‑fold, all while remaining modular enough to integrate with any existing deep‑unfolding system.
By Haijin Zeng, Xuan Lu, Jiezhang Cao, Kai Zhang, Yurong Zhang, Qiangqiang Shen, Guoqing Chao, Li Jiang, Yongyong Chen, Jingyong Su, Jie Liu
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:2507. 06764v5 Announce Type: replace-cross Abstract: In this work, we propose Fast Equivariant Imaging (FEI), a novel unsupervised learning framework to rapidly and efficiently train deep imaging networks without ground-truth data.
By Guixian Xu, Jinglai Li, Junqi Tang
The paper introduces StyleGANCA, a lightweight neural cellular automata (NCA) based generative adversarial network designed for medical image synthesis. By combining a StyleGAN-inspired mapping network with adaptive style modulation in a multi-scale NCA framework, the model achieves high-quality image generation with far fewer parameters than existing adversarial, variational, diffusion, and NCA baselines. Experiments on BloodMNIST and PathMNIST show competitive FID and KID scores, and the synthetic images preserve class-specific information, effectively supporting downstream multi-class classifier training.
By Anh Thi Luu, Nick Lemke, Anirban Mukhopadhyay