spatialdata-db

Lean read client for the spatialdata-db spatial-omics collection: query the catalog in pandas and load datasets as SpatialData objects from anonymous S3.

Early development (0.x): the API may change.

Install

pip install spatialdata-db

Usage

import sddb

Getting the catalog

Either way you get a Catalog you can query():

# (a) Default: the published catalog (DEFAULT_CATALOG_URL, or $SDDB_CATALOG_URL),
#     served from this repo's latest GitHub release — live, anonymous, no account.
cat = sddb.Catalog()

# (b) Local: download catalog.parquet, then point the client at it.
cat = sddb.Catalog.from_file("catalog.parquet")  # equivalent: sddb.Catalog(url="catalog.parquet")
cat.query(organism="human")

from_file accepts absolute or relative paths and file:// URLs, and validates the file against the catalog schema.

Remote datasets: query the catalog, inspect with elements() (no download), or load fully with load(lazy=False) (copies the store to the cache). Lazy/partial remote open is not supported yet (spatialdata upstream limitation); local stores open lazily.