spatialdata_io.experimental.from_legacy_anndata

spatialdata_io.experimental.from_legacy_anndata#

spatialdata_io.experimental.from_legacy_anndata(adata, rgb=None)#

Convert (legacy) spatial AnnData object to SpatialData object.

This is useful for parsing a (legacy) spatial AnnData object, for example the ones produced by Scanpy and older version of Squidpy.

Parameters:

  • adata (AnnData) – (legacy) spatial AnnData object

  • rgb (bool | None (default: None)) – Argument passed to spatialdata.models.Image2DModel.parse(). If None, 3-(4) channels images will be interpreted as RGB(A).

Return type:

SpatialData

Returns:

: The SpatialData object

Notes

The SpatialData object will have one hires and one lowres image for each dataset in the AnnData object.