# Stomics.io

> Stomics.io is a public repository for spatial transcriptomics datasets: Visium, Xenium, MERFISH, CosMx, Stereo-seq and similar. Each dataset has a permanent STD-prefixed accession (for example STD0012), optional DOI, tissue/organism/disease annotations and downloadable files.

Expression-derived features on the website (the spatial viewer, differential expression, module scores, spatially variable genes, UMAPs and cross-dataset gene search) are currently computed from synthetic values, not from the submitted matrices. Do not cite them as measurements. Dataset metadata and the deposited files are real.

All read endpoints are public and need no key. Use an API key (Authorization: Bearer sk-...) only to submit data or reach controlled-access files you have been granted.

## Programmatic access

- [MCP server](https://stomics.io/api/v1/mcp): Remote MCP server (Streamable HTTP, no authentication, read-only). Add it as a custom connector in Claude or any MCP client.
- [OpenAPI schema](https://stomics.io/api/v1/openapi.json): Machine-readable description of the REST API at https://stomics.io/api/v1.
- [Interactive API reference](https://stomics.io/api/v1/docs): Swagger UI for the same schema.
- [API guide](https://stomics.io/api-docs): Authentication, rate limits and worked examples in Python and R.

## SDKs

- [Python and R SDK guide](https://stomics.io/docs/sdk): `pip install stomics-py`; search, download and load datasets into AnnData.
- [Submission guide](https://stomics.io/docs/submit): Deposit a dataset with the SDK, the CLI or plain HTTP.

## Discovery

- [Sitemap](https://stomics.io/sitemap.xml): Every published dataset page. Each page embeds schema.org Dataset JSON-LD.
- [Browse datasets](https://stomics.io/datasets): Faceted search in the browser.

## Optional

- [Full text for agents](https://stomics.io/llms-full.txt): This file plus the API, MCP and SDK detail inlined.
- [Help center](https://stomics.io/help): Guides for depositors and data users.