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Volumetric cell segmentation for 3D fluorescence microscopy, pretrained on 5.1 TB of unlabeled volumes and generalizing across species and imaging.
Predicts protein complex stoichiometry from amino acid sequence alone, ranking copy numbers in seconds and exporting AlphaFold3-ready JSON files.
Biozentrum / University of Basel / SIB Swiss Institute of Bioinformatics
Released November 27, 2025
Protein sequence encoder that maps ESM2 embeddings to a learned 20-letter alphabet for structure-quality remote homology detection at MMseqs2 speed.
ETH Zurich / EPFL / University of Basel / University Hospital Basel / Idiap Research Institute / Icahn School of Medicine at Mount Sinai
Released March 24, 2025
Histopathology foundation model pretrained with DINOv2 on tiles chosen by unsupervised hierarchical clustering over 350 million whole-slide tiles.
ETH Zurich / University Hospital Zurich / University of Zurich / University of Basel / SIB Swiss Institute of Bioinformatics / Tumor Profiler Consortium
Released January 26, 2024
Virtual staining model that generates 11-marker spatially resolved protein multiplexes from routine H&E histopathology whole-slide images.
Helmholtz Munich / University of Basel / Technical University of Munich / ETH Zurich / SIB Swiss Institute of Bioinformatics / MRC Laboratory of Molecular Biology / Genentech / University of Murcia / German Cancer Research Center (DKFZ) / Helmholtz Imaging / King's College London
Released January 5, 2024
Cryo-electron tomography membrane analysis pipeline pairing generalizable U-Net membrane segmentation with mesh-based particle localization.