The study evaluates self‑supervised learning (SSL) models pretrained on ImageNet‑1k and the Human Protein Atlas (HPA) Field‑of‑View (FOV) for protein localization in microscopy images. DINO‑based Vision Transformer backbones pretrained on either dataset transfer well to the OpenCell dataset, achieving strong performance even without fine‑tuning and improving further when fine‑tuned (0.704 ± 0.027 macro F1 on 17 classes). At the single‑cell level, the HPA‑pretrained model outperforms others in k‑nearest‑neighbor classification across all neighborhood sizes (macro F1 ≥ 0.515).
By Ben Isselmann, Dilara G\"oksu, Heinz Neumann, Andreas Weinmann
arXiv:2605. 23995v2 Announce Type: replace-cross Abstract: Self-supervised learning (SSL) has emerged as a promising paradigm for addressing the annotation bottleneck in medical imaging by learning representations from unlabeled data.
By Chathura Wimalasiri
Pix2Rep-v2 is a self‑supervised learning framework that learns pixel‑ and voxel‑level representations for dense medical imaging tasks, using a redundancy‑reduction objective and equivariance principles to scale to 3D and wide field‑of‑view data. The method is evaluated on four datasets across multiple modalities, tasks, and backbones, demonstrating higher data‑efficiency in few‑shot scenarios and competitive performance, such as a +9.3 Dice point improvement in one‑shot segmentation on the M&Ms‑2 dataset. An in‑context dense prototype approach is also proposed, eliminating the need for downstream training.
By S. Sifaoui, E. Angelini, S. Toupin, T. Pezel, L. Le Folgoc
arXiv:2608. 10657v1 Announce Type: cross Abstract: Leukemia cell image classification is challenged by real-world domain shifts from acquisition, staining, illumination, and site protocols, causing single-dataset models to generalize poorly in real clinical scenarios.
By Carlos Zamora, Hiram Zuniga, Ulises Orozco-Rosas, Kenia Picos
arXiv:2605. 23995v4 Announce Type: replace-cross Abstract: Self-supervised learning (SSL) is increasingly used in medical image analysis to reduce dependence on costly expert annotations by learning transferable representations from unlabeled data.
By Chathura Wimalasiri, Kishor Nandakishor, Marimuthu Palaniswami
arXiv:2603. 18846v3 Announce Type: replace-cross Abstract: Foundation models are used to extract transferable representations from large amounts of unlabeled data, typically via self-supervised learning (SSL).
By Samuel Ofosu Mensah, Camila Roa, Kerol Djoumessi, Philipp Berens
arXiv:2606. 07633v1 Announce Type: cross Abstract: Accurate classification of nuclei subtypes in histopathology images is critical for downstream tasks including tumor grading, immune infiltrate quantification, and prognosis prediction.
By Spoorthi M, Suja Palaniswamy
arXiv:2606. 06983v1 Announce Type: cross Abstract: Computational pathology requires visual representations that transfer across diverse clinical endpoints and remain robust to variation in magnification, staining, scanner type, slide preparation, and input resolution.
By Bokai Zhao, Yiyang Zhang, Long Bai, Tai Ma, Hanqing Chao, Minfeng Xu
arXiv:2407.03463v2 Announce Type: replace-cross
Abstract: In the realm of self-supervised learning (SSL), conventional wisdom has gravitated towards the utility of massive, general domain datasets fo...
By Jes\'us M Rodr\'iguez-de-Vera, Imanol G Estepa, Ignacio Saras\'ua, Bhalaji Nagarajan, Petia Radeva
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:2609.25850v1 Announce Type: new
Abstract: Deep learning performance generally improves with increasing training data, yet this scaling is fundamentally constrained by annotation cost in large-s...
By Xiaofei Du, Lei Zhang, Shuyu Yan, Manning Wang, Zhijian Song
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