# Bioptimus Documentation

- [Welcome](https://docs.bioptimus.com/documentation/introduction.md): Deploy and build with foundation models for biology — across histology, transcriptomics, and genomics.
- [Quickstart](https://docs.bioptimus.com/documentation/quickstart.md): Pick your model and platform, then run your first inference.
- [H-Optimus](https://docs.bioptimus.com/documentation/models/h-optimus.md): A vision foundation model for histology feature extraction.
- [M-Optimus](https://docs.bioptimus.com/documentation/models/m-optimus.md): A multimodal, multi-scale foundation model that predicts spatial gene expression from histology.
- [Tissue segmentation](https://docs.bioptimus.com/documentation/models/tissue-segmentation.md): Separate tissue from background before feature extraction.
- [Benchmarks](https://docs.bioptimus.com/documentation/models/benchmarks.md): Independent benchmark results for Bioptimus pathology models.
- [Drug target & biomarker discovery](https://docs.bioptimus.com/documentation/use-cases/biomarker-discovery.md): Predict drug target distribution, immune microenvironment, and stromal architecture from routine histology slides.
- [Indication expansion](https://docs.bioptimus.com/documentation/use-cases/indication-expansion.md): Identify the patient subsets and indications where a therapeutic is most likely to succeed.
- [Diagnostics & spatial biology](https://docs.bioptimus.com/documentation/use-cases/diagnostics-spatial-biology.md): Integrate histology, spatial transcriptomics, and genomics in a single pipeline.
- [Treatment response & trial design](https://docs.bioptimus.com/documentation/use-cases/treatment-response.md): Discover multimodal biomarker signatures that distinguish responders from non-responders.
- [FAQ](https://docs.bioptimus.com/documentation/resources/faq.md): Common questions about deploying and using Bioptimus models.
- [Glossary](https://docs.bioptimus.com/documentation/resources/glossary.md): Key terms used across Bioptimus documentation.
- [Responsible use](https://docs.bioptimus.com/documentation/resources/responsible-use.md): Intended use, regulatory status, license terms, responsibilities, and disclaimer.
- [License](https://docs.bioptimus.com/license.md)
- [Deployment overview](https://docs.bioptimus.com/deployment/overview.md): Choose the right way to access Bioptimus models.
- [Requirements](https://docs.bioptimus.com/deployment/requirements.md): Prerequisites for each deployment option.
- [Validation & acceptance testing](https://docs.bioptimus.com/deployment/validation.md): Verify a deployment produces correct, expected outputs.
- [AWS SageMaker](https://docs.bioptimus.com/deployment/platforms/aws-sagemaker.md): Deploy a Bioptimus model from AWS Marketplace to a SageMaker endpoint.
- [On-premise](https://docs.bioptimus.com/deployment/platforms/on-premise.md): Load, run, and verify the Bioptimus Model Server container in your own environment.
- [Hugging Face](https://docs.bioptimus.com/deployment/platforms/hugging-face.md): Load H-Optimus-1 weights directly for non-commercial academic research.
- [Proscia](https://docs.bioptimus.com/deployment/platforms/proscia.md): Generate H-Optimus embeddings from slides in your Concentriq® LS workspace with Proscia's Concentriq® Embeddings service.
- [Bioptimus SDK](https://docs.bioptimus.com/guides/get-started/sdk.md): The Bioptimus Python SDK — installation and the two ways to use it.
- [Inference pipeline](https://docs.bioptimus.com/guides/get-started/inference-pipeline.md): Configure the whole pipeline with one object — tissue masking, embeddings, predictions, and reproducible workspaces.
- [Visualizing results](https://docs.bioptimus.com/guides/get-started/visualizing-results.md): Load Zarr/HDF5/NPZ outputs and overlay gene expression or tissue masks.
- [Performance tuning](https://docs.bioptimus.com/guides/get-started/performance-tuning.md): What to change to get more embedding/prediction throughput, and what to expect from each change.
- [WSI processing](https://docs.bioptimus.com/guides/reference/wsi-processing.md): Read whole-slide images: pyramid levels, MPP, regions, and thumbnails.
- [Tissue masking & tiling](https://docs.bioptimus.com/guides/workflows/preprocessing.md): Preprocess a slide before inference: segment tissue to drop background, then split it into model-sized tiles.
- [Tile embeddings & PCA](https://docs.bioptimus.com/guides/workflows/embeddings-pca.md): Extract tile embeddings (H-Optimus or M-Optimus) and visualize morphology with PCA.
- [Spatial transcriptomics](https://docs.bioptimus.com/guides/workflows/spatial-transcriptomics.md): Predict spatial gene expression from an H&E slide with M-Optimus, end to end.
- [Cohorts](https://docs.bioptimus.com/guides/workflows/cohort.md): Run a model over a cohort of slides with shared tissue masks and a structured workspace.
- [Common issues](https://docs.bioptimus.com/guides/get-started/troubleshooting.md): Common SDK issues: connecting to a server and diagnosing runs.
- [Logging](https://docs.bioptimus.com/guides/get-started/logging.md): Structured logging with zero setup: where logs go, the default format, and how to customize them.
- [Support bundles](https://docs.bioptimus.com/guides/get-started/support-bundles.md): Verify a deployed endpoint and build a redacted bundle to share with support.
- [bioptimus.data.cohort](https://docs.bioptimus.com/sdk-reference/data/cohort.md)
- [bioptimus.data.multi_modal.multi_modal_dataset](https://docs.bioptimus.com/sdk-reference/data/multi_modal/multi_modal_dataset.md)
- [bioptimus.data.omics.bulkrna](https://docs.bioptimus.com/sdk-reference/data/omics/bulkrna.md)
- [bioptimus.data.tile_spec](https://docs.bioptimus.com/sdk-reference/data/tile_spec.md)
- [bioptimus.data.wsi](https://docs.bioptimus.com/sdk-reference/data/wsi.md)
- [bioptimus.data.wsi.torch_dataset](https://docs.bioptimus.com/sdk-reference/data/wsi/torch_dataset.md)
- [bioptimus.data.wsi.wsi_dataset](https://docs.bioptimus.com/sdk-reference/data/wsi/wsi_dataset.md)
- [bioptimus.extraction.wsi](https://docs.bioptimus.com/sdk-reference/extraction/wsi.md)
- [bioptimus.extraction.wsi.megatile_extraction](https://docs.bioptimus.com/sdk-reference/extraction/wsi/megatile_extraction.md)
- [bioptimus.extraction.wsi.tile_extraction](https://docs.bioptimus.com/sdk-reference/extraction/wsi/tile_extraction.md)
- [bioptimus.extraction.wsi.types](https://docs.bioptimus.com/sdk-reference/extraction/wsi/types.md)
- [bioptimus.inference](https://docs.bioptimus.com/sdk-reference/inference.md)
- [bioptimus.inference.aggregate](https://docs.bioptimus.com/sdk-reference/inference/aggregate.md)
- [bioptimus.inference.inference](https://docs.bioptimus.com/sdk-reference/inference/inference.md)
- [bioptimus.inference.schemas](https://docs.bioptimus.com/sdk-reference/inference/schemas.md)
- [bioptimus.inference.writers](https://docs.bioptimus.com/sdk-reference/inference/writers.md)
- [bioptimus.io.omics](https://docs.bioptimus.com/sdk-reference/io/omics.md)
- [bioptimus.io.wsi](https://docs.bioptimus.com/sdk-reference/io/wsi.md)
- [bioptimus.io.wsi.factory](https://docs.bioptimus.com/sdk-reference/io/wsi/factory.md)
- [bioptimus.io.wsi.interface](https://docs.bioptimus.com/sdk-reference/io/wsi/interface.md)
- [bioptimus.io.wsi.metadata](https://docs.bioptimus.com/sdk-reference/io/wsi/metadata.md)
- [bioptimus.io.wsi.types](https://docs.bioptimus.com/sdk-reference/io/wsi/types.md)
- [bioptimus.models](https://docs.bioptimus.com/sdk-reference/models.md)
- [bioptimus.models.backbones](https://docs.bioptimus.com/sdk-reference/models/backbones.md)
- [bioptimus.models.clients](https://docs.bioptimus.com/sdk-reference/models/clients.md)
- [bioptimus.models.clients.aws](https://docs.bioptimus.com/sdk-reference/models/clients/aws.md)
- [bioptimus.models.clients.dispatch](https://docs.bioptimus.com/sdk-reference/models/clients/dispatch.md)
- [bioptimus.models.clients.hf](https://docs.bioptimus.com/sdk-reference/models/clients/hf.md)
- [bioptimus.models.clients.http](https://docs.bioptimus.com/sdk-reference/models/clients/http.md)
- [bioptimus.models.clients.local](https://docs.bioptimus.com/sdk-reference/models/clients/local.md)
- [bioptimus.models.config_loader](https://docs.bioptimus.com/sdk-reference/models/config_loader.md)
- [bioptimus.models.endpoint_model](https://docs.bioptimus.com/sdk-reference/models/endpoint_model.md)
- [bioptimus.models.types](https://docs.bioptimus.com/sdk-reference/models/types.md)
- [bioptimus.observability](https://docs.bioptimus.com/sdk-reference/observability.md)
- [bioptimus.observability.anonymize](https://docs.bioptimus.com/sdk-reference/observability/anonymize.md)
- [bioptimus.observability.context](https://docs.bioptimus.com/sdk-reference/observability/context.md)
- [bioptimus.observability.errors](https://docs.bioptimus.com/sdk-reference/observability/errors.md)
- [bioptimus.observability.fsboundary](https://docs.bioptimus.com/sdk-reference/observability/fsboundary.md)
- [bioptimus.observability.healthcheck](https://docs.bioptimus.com/sdk-reference/observability/healthcheck.md)
- [bioptimus.observability.log_export](https://docs.bioptimus.com/sdk-reference/observability/log_export.md)
- [bioptimus.observability.logging](https://docs.bioptimus.com/sdk-reference/observability/logging.md)
- [bioptimus.observability.probes](https://docs.bioptimus.com/sdk-reference/observability/probes.md)
- [bioptimus.preprocess.omics](https://docs.bioptimus.com/sdk-reference/preprocess/omics.md)
- [bioptimus.preprocess.omics.base](https://docs.bioptimus.com/sdk-reference/preprocess/omics/base.md)
- [bioptimus.preprocess.omics.factory](https://docs.bioptimus.com/sdk-reference/preprocess/omics/factory.md)
- [bioptimus.preprocess.omics.transforms](https://docs.bioptimus.com/sdk-reference/preprocess/omics/transforms.md)
- [bioptimus.preprocess.wsi](https://docs.bioptimus.com/sdk-reference/preprocess/wsi.md)
- [bioptimus.preprocess.wsi.models.base](https://docs.bioptimus.com/sdk-reference/preprocess/wsi/models/base.md)
- [bioptimus.preprocess.wsi.models.bioptimus_mask](https://docs.bioptimus.com/sdk-reference/preprocess/wsi/models/bioptimus_mask.md)
- [bioptimus.preprocess.wsi.provider.base](https://docs.bioptimus.com/sdk-reference/preprocess/wsi/provider/base.md)
- [bioptimus.preprocess.wsi.provider.precomputed](https://docs.bioptimus.com/sdk-reference/preprocess/wsi/provider/precomputed.md)
- [bioptimus.preprocess.wsi.provider.tiled](https://docs.bioptimus.com/sdk-reference/preprocess/wsi/provider/tiled.md)
- [bioptimus.runtime](https://docs.bioptimus.com/sdk-reference/runtime.md)
- [bioptimus.runtime.batch_scheduler](https://docs.bioptimus.com/sdk-reference/runtime/batch_scheduler.md)
- [bioptimus.runtime.loader](https://docs.bioptimus.com/sdk-reference/runtime/loader.md)
- [bioptimus.runtime.models](https://docs.bioptimus.com/sdk-reference/runtime/models.md)
- [bioptimus.runtime.models.m_optimus](https://docs.bioptimus.com/sdk-reference/runtime/models/m_optimus.md)
- [bioptimus.runtime.models.tissue_seg](https://docs.bioptimus.com/sdk-reference/runtime/models/tissue_seg.md)
- [bioptimus.runtime.pt2](https://docs.bioptimus.com/sdk-reference/runtime/pt2.md)
- [bioptimus.runtime.server_model](https://docs.bioptimus.com/sdk-reference/runtime/server_model.md)
- [bioptimus.utils](https://docs.bioptimus.com/sdk-reference/utils.md)
- [bioptimus.utils.pytorch](https://docs.bioptimus.com/sdk-reference/utils/pytorch.md)
- [bioptimus.utils.utils](https://docs.bioptimus.com/sdk-reference/utils/utils.md)
- [Bioptimus Inference Server](https://docs.bioptimus.com/api-reference/introduction.md): The REST API served by the Bioptimus Model Server, and the SageMaker dispatch endpoint.
- [Performance](https://docs.bioptimus.com/api-reference/performance.md): Model-server performance characteristics: what's fixed by the deployment, and what to expect.
- [Troubleshooting](https://docs.bioptimus.com/api-reference/troubleshooting.md): Diagnosing slow throughput or errors from the Model Server.
- [h1 embedding](https://docs.bioptimus.com/api-reference/models/h1-embedding.md)
- [m-optimus embedding](https://docs.bioptimus.com/api-reference/models/m-optimus-embedding.md)
- [h1 metadata](https://docs.bioptimus.com/api-reference/models/h1-metadata.md)
- [m-optimus metadata](https://docs.bioptimus.com/api-reference/models/m-optimus-metadata.md)
- [tissue-seg metadata](https://docs.bioptimus.com/api-reference/models/tissue-seg-metadata.md)
- [m-optimus prediction](https://docs.bioptimus.com/api-reference/models/m-optimus-prediction.md)
- [tissue-seg prediction](https://docs.bioptimus.com/api-reference/models/tissue-seg-prediction.md)
- [m-optimus prediction_with_embedding](https://docs.bioptimus.com/api-reference/models/m-optimus-prediction_with_embedding.md)
- [List available endpoints](https://docs.bioptimus.com/api-reference/discovery/list-available-endpoints.md)
- [Anonymized diagnostics or usage records](https://docs.bioptimus.com/api-reference/diagnostics/anonymized-diagnostics-or-usage-records.md): Returns selected anonymized diagnostics categories.

## OpenAPI Specs

- [openapi](/api-reference/openapi.json)

## Optional

- [GitHub](https://github.com/bioptimus)
- [Knowledge Base](https://www.bioptimus.com/knowledge-base)


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