omicverse.space.sync_visium_hd_seg_geometries

omicverse.space.sync_visium_hd_seg_geometries(adata, sample=None)[source]

Synchronize adata.uns["spatial"][sample]["geometries"] with current adata.obs_names.

This utility is intended for AnnData objects loaded by read_visium_hd_seg. After subsetting AnnData, adata.obs and adata.obsm are subset automatically, but the geometry table stored in adata.uns["spatial"][sample]["geometries"] may still contain rows for cells that are no longer present. This function filters that GeoDataFrame by current cell IDs and updates it in place.

Parameters:

  • adata (sc.AnnData) – A (possibly subsetted) AnnData object containing spatial segmentation metadata.

  • sample (str, optional) – Sample key under adata.uns["spatial"]. If None, the first available key is used (with a warning when multiple samples exist).

Returns:

The same adata object, modified in place.

Return type:

sc.AnnData