All Competitors

Every biological foundation model, evaluated and ranked by the bio.rodeo team

Showing 124 of 31 filtered models

  • Vermeer

    2
    Microsoft Research +2 othersJune 1, 2026autoregressivecell_biologyfluorescence_microscopy+7

    Channel-adaptive autoregressive generative model that synthesizes in-silico fluorescence microscopy of protein subcellular localization from amino-acid sequence and cellular landmark stains.

    ImagingProtein
    17Openness
  • mnDINO

    Morgridge Institute for ResearchMarch 12, 2026cell_biologyfluorescence_microscopyfoundation_model+4

    A DINO-pretrained vision transformer for accurate, robust segmentation of micronuclei in DNA-stained fluorescence microscopy across cell lines and instruments.

    Imaging
    32Openness
  • PerturbGen

    21
    Wellcome Sanger InstituteMarch 5, 2026cell_biologyfoundation_modelgene_expression+6

    Generative single-cell foundation model trained on 100M+ transcriptomes that predicts how genetic perturbations reshape cellular trajectories over time.

    Single-cell
    72Openness
  • CellPace

    McGill UniversityFebruary 26, 2026cell_biologydiffusiongene_expression+5

    A temporal diffusion-forcing generative framework for simulating, interpolating, and forecasting single-cell developmental dynamics from irregularly sampled time-series data.

    Single-cell
    9Openness
  • CLM-X

    Hangzhou Institute of Medicine, CASFebruary 18, 2026batch_correctioncell_biologycell_type_annotation+6

    A multimodal single-cell foundation model with a multiway Transformer that jointly models scRNA-seq and scATAC-seq, including RNA-only, ATAC-only, and paired inputs.

    Single-cell
    4Openness
  • Tsinghua UniversityFebruary 14, 2026autoregressivecell_biologyde_novo_design+8

    A hierarchical sequence-based protein representation that encodes proteins as discrete 'words' for zero-shot functional discovery and generative design.

    Protein
    24Openness
  • COSMIC

    EPFLJanuary 24, 2026autoencodercell_biologycell_type_annotation+7

    Bidirectional generative framework linking single-cell nuclear morphology and gene expression, built on a morphology foundation model trained on 21M+ segmented nuclei.

    ImagingSingle-cellSpatial omics
    4Openness
  • OKR-CELL

    BGI ResearchJanuary 9, 2026batch_effect_correctioncell_biologycell_clustering+7

    Cross-modal cell-language foundation model that aligns single-cell expression with LLM-enriched textual descriptions using a noise-robust contrastive objective.

    Single-cellLanguage model
    23Openness
  • Nobuyuki OtaJanuary 3, 2026cell_biologygene_expressiongenomics+4

    A multimodal architecture that couples pretrained DNA, RNA, and protein language models via directional cross-attention following the central dogma to form a unified Virtual Cell Embedding.

    DNA & GeneRNAProtein
    22Openness
  • Harvard Medical SchoolDecember 31, 2025cell_biologycell_trackingfoundation_model+6

    A native 3D vision transformer self-supervised on unlabeled fluorescence microscopy volumes that generalizes to unseen object classes without retraining or voxel annotations.

    Imaging
    8Openness
  • scMOBA

    Chinese Academy of Sciences +1 otherDecember 2, 2025cell_biologycell_type_annotationdata_integration+6

    A conversational single-cell and spatial multi-omics brain agent pretrained on 130 million cells across species for zero-shot cell annotation and disease prediction.

    Single-cellLanguage model
    5Openness
  • Micellangelo

    Eindhoven University of TechnologyNovember 24, 2025cell_biologycell_morphology_simulationconditional_generation+5

    Flow-matching generative model that simulates high-resolution fluorescence images of human fibroblasts conditioned on surface micro-topographies, a digital twin of cell-material interactions.

    Imaging
    5Openness
  • scLDM

    525
    Chan Zuckerberg InitiativeNovember 4, 2025autoencodercell_biologydata_augmentation+8

    A scalable latent diffusion model for generating realistic single-cell gene expression profiles, using a permutation-invariant VAE and flow-matching diffusion transformer.

    Single-cell
    75Openness
  • Chan Zuckerberg InitiativeNovember 4, 2025autoencodercell_biologydiffusion+8

    A fine-tuned scLDM variant trained on 14.5 million CD4+ T cells for counterfactual prediction of single-gene perturbation effects in immune cells.

    Single-cell
    75Openness
  • rBio

    14213
    Chan Zuckerberg InitiativeAugust 18, 2025biological_question_answeringcell_biologyfoundation_model+4

    A reasoning language model post-trained on virtual cell simulations to answer complex biological questions about gene perturbations in natural language.

    Language model
    60Openness
  • Cellpose-SAM

    2.2K152
    HHMI Janelia Research CampusMay 1, 2025cell_biologyfoundation_modelgeneralist_model+4

    Generalist cell segmentation model combining SAM's ViT-L backbone with Cellpose flow fields. First model to surpass average human annotators on the Cellpose benchmark.

    Imaging
    50Openness
  • Cellpose 3

    2.2K322
    HHMI Janelia Research CampusFebruary 1, 2025cell_biologygeneralist_modelimage_restoration+2

    Generalist cell segmentation framework with a super-generalist cyto3 model and one-click image restoration networks optimized for downstream segmentation quality.

    Imaging
    65Openness
  • SubCell

    610
    Chan Zuckerberg Initiative +2 othersDecember 8, 2024cell_biologyfluorescence_microscopyfoundation_model+4

    Self-supervised Vision Transformer models trained on proteome-wide fluorescence microscopy images from the Human Protein Atlas for subcellular protein localization.

    Imaging
    84Openness
  • AIDO.Cell

    1631778
    genbio.aiNovember 28, 2024bertcell_biologycell_type_annotation+7

    Single-cell RNA-seq foundation model series pretrained on 50 million human cells with full transcriptome-scale context for cell clustering and perturbation modeling.

    Single-cell
    29Openness
  • CELL-Diff

    5
    Chan Zuckerberg InitiativeOctober 18, 2024cell_biologyde_novo_designdiffusion+7

    A unified diffusion model enabling bidirectional transformation between protein amino acid sequences and fluorescence microscopy images for subcellular localization prediction.

    Imaging
    87Openness
  • DynaCLR

    972
    Chan Zuckerberg InitiativeOctober 15, 2024cell_biologycell_state_classificationcnn+5

    A self-supervised contrastive learning method for embedding cell and organelle dynamics from time-lapse microscopy using temporal regularization and single-cell tracking.

    Imaging
    71Openness
  • CellFM

    10864
    Sun Yat-sen UniversityJune 6, 2024cell_biologyfoundation_modeltranscriptomics+1

    An 800M-parameter single-cell foundation model pre-trained on 100 million human cells via a RetNet architecture for cell annotation, perturbation prediction, and gene analysis.

    Single-cell
    26Openness
  • Cytoland

    979
    Chan Zuckerberg Biohub +1 otherJune 3, 2024cell_biologyimage_translationmicroscopy+3

    A suite of virtual staining models that translate label-free microscopy images into fluorescent-equivalent staining of nuclei and plasma membranes.

    Imaging
    99Openness
  • CellPLM

    10382
    OmicsMLMay 1, 2024cell_biologyfoundation_modellanguage_model+1

    Single-cell transformer that treats cells as tokens and tissues as sentences, encoding cell-cell relationships with 100x faster inference than prior pre-trained models.

    Single-cell
    50Openness