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docs: clarify how coordinates stored in tables are treated #1274

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ce6e0ae
docs: clarify how coordinates stored in tables are treated
jan-glx Oct 15, 2026
91e30b3
docs: say table coordinates are "currently" not processed
jan-glx Oct 15, 2026
960feba
docs: fix indentation so the tables bullet renders as a paragraph
jan-glx Oct 15, 2026
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6 changes: 4 additions & 2 deletions src/spatialdata/_core/spatialdata.py
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Expand Up @@ -108,8 +108,10 @@ class SpatialData:
- images and labels are stored as :class:`xarray.DataArray` or :class:`xarray.DataTree` objects.
- points are stored as :class:`dask.dataframe.DataFrame` objects.
- shapes are stored as :class:`geopandas.GeoDataFrame`.
- the table are stored as :class:`anndata.AnnData` objects, with the spatial coordinates stored in the obsm
slot.
- tables are stored as :class:`anndata.AnnData` objects. Tables have no coordinate system: coordinates
stored in a table (e.g. in ``obsm["spatial"]``, the squidpy/scanpy convention that several spatialdata-io
readers populate) are currently not transformed or used by spatial queries, and can get out of sync with
the SpatialElements the table annotates.

Tables can annotate SpatialElements (labels, shapes or points) and can be used to store additional
information. Points can also store annotations directly, as additional dataframe columns.
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