spatialdata-db

Query 5114 spatial omics datasets and load them as SpatialData.

pip install git+https://github.com/theislab/spatialdata-db-client

from sddb import Catalog

hits = Catalog().query(technology="Visium", tissue="lung")
hits.summary()
smallest = min(hits, key=lambda ds: ds.size_bytes)
sdata = smallest.load(lazy=False)  # ~10 MB, copied to the local cache

Find & load

Filter the catalog by facets or free text and load datasets.

Find and load datasets

Cohorts

Freeze, split and reproduce sets of datasets.

Build, freeze and split cohorts

Agents & CLI

Use the catalog from the shell and from AI agents.

Command line and agents

API

Full reference for the Python API.

API reference

Using data from the DB? See Cite and license.