MCP tools

sddb-mcp serves the catalog to agents over stdio (Model Context Protocol). It needs the optional extra:

pip install "spatialdata-db[mcp] @ git+https://github.com/theislab/spatialdata-db-client"
sddb-mcp

The query tool caps its output at MAX_ROWS = 200 records; genes is not capped. download writes only to a server-controlled directory: $SDDB_MCP_DOWNLOAD_DIR, or a cache subdirectory when unset.

Tool	Description	Parameters
query	Filter datasets by facets, ranges (min_obs/min_features), gene (expressing) and free-text search.	organism, tissue, disease, technology, assay, tier, validation (default pass), expressing, min_fraction, search, min_obs, min_features
describe	Catalog row and element shapes for one dataset uid.	uid
genes	Datasets expressing one or more genes (symbols or Ensembl ids; mode all=AND, any=union), optionally filtered by organism/tissue/disease/assay. Bronze datasets are included by default.	symbols, organism, tissue, disease, assay, mode (default all), include_bronze (default true)
facets	List facet columns, or the distinct values of a facet field.	field (optional)
cite	BibTeX for the studies of a filtered cohort.	organism, tissue, disease, technology, assay, tier, search, expressing, min_fraction, validation
download	Plan (sizes) or fetch a filtered cohort to the server download dir.	same filters as cite, plus download (default false: plan only)