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Bioptimus builds foundation models that learn the dynamics of human biology across scales — from cell to tissue to organ. This documentation covers how to access, deploy, and build with our models on AWS and on-premise.

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How it works

Bioptimus models are pretrained on large, diverse histology data, so their representations transfer to many tasks without training from scratch. Point the SDK at a slide and a model, and it tiles the slide, masks out background, runs the model, and writes results to disk. For precise definitions, see the Glossary.
A scanned H&E slide can be billions of pixels — too large to process at once — so the pipeline starts from the slide and splits it into small tiles, each processed independently.
H&E whole-slide image thumbnail

H&E whole-slide image (TCGA-LUAD TCGA-75-7027). Representative example.

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The models

H-Optimus

A vision foundation model for histology. Extracts tile-level features from H&E whole slide images.

M-Optimus

A multimodal, multi-scale model (M-Optimus-1) that predicts spatial gene expression from routine H&E, refined with bulk RNA.
Both models are trained on data from STELA, our data engine:

STELA — data engine

A multi-institutional data engine generating the deeply profiled, clinically linked patient data our models train on.

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Where to get each model

A quick map of which model is available on which channel, and where to start.

AWS SageMaker

Managed endpoints from AWS Marketplace.

On-premise

Self-hosted container for full data control.

Hugging Face

H-Optimus weights for non-commercial academic use.

Proscia

H-Optimus embeddings for slides in Concentriq® LS.

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Where to start

Run your first inference

Deploy a model and get embeddings back in minutes. For ML engineers and data scientists.

Explore use cases

See how teams use our models for biomarker discovery, indication expansion, and trial design.

Security & compliance

Data handling, residency, and deployment options for regulated environments.
Bioptimus models are for research use and are not approved medical devices. See Responsible use for intended use and your responsibilities.