spatialdata-db

Central hub for SpatialData-DB. Two sibling repos are vendored as git submodules under extern/:

• extern/schemas → spatialdata-schemas — the lamin metadata contract (pinned at a release tag; external / read-only, do not edit in place).
• extern/curation → spatialdata-db-curation — dataset intake, registry, and UID assignment.

This repo (spatialdata_db) owns raw→zarr conversion, validation/curation, and lamin registration.

Getting the submodules

git clone --recursive https://github.com/theislab/spatialdata-db
# or, in an existing clone:
pixi run sync            # = git submodule update --init --recursive

Building the schema into the instance

pixi run -e schema build-schema   # runs extern/schemas' build_all() against the connected lamin instance

To advance the schema, bump the extern/schemas submodule to a newer tag and re-run.

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Currently focusing on the following datasets for diversity in testing:

• 10ktp: Visium, Mouse, Brain
• 4b368: Visium, Mouse, Lung
• m1v5v: Xenium, Human, Lung
• oeuwa: Xenium, Mouse, Brain
• jqmx8: VisiumHD, Mouse, Intestine

Setup vitessce

Currently, the SpatialDataWrapper is not yet merged and released. Therefore, we have to install it via

pip install anywidget starlette uvicorn
pip install git+https://github.com/vitessce/vitessce-python.git@ig/spatial_data

from Ilan's PR: vitessce/vitessce-python#333

UID logic

UIDs are owned by curation: the registry and generator live in extern/curation (registry/uids.csv, tools/mint_uids.py). This repo reads them read-only.

• Absolute ID will be a 5 char string of lowercase letters and digits -> 60466176 IDs
• Leaving out the letters [l, b, o, g, q] due to their similarity to [1, 6, 0, 9, 9] -> 28629151 IDs
• Reserve ID spaces for technology providers
  • 10 _ _ _ -> 29791 IDs for 10X Genomics
  • vg _ _ _ -> 29791 IDs for Vizgen
  • ns _ _ _ -> 29791 IDs for Nanostring
  • xx _ _ _ -> 29791 IDs for miscellaneous, such as publication