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Registering a new table with a coordinate system #573
I am playing around with Spatialdata and the Visium HD release and I want to do the following:
I have a Spatialdata object created with spatialdata.io.visium_hd and annotations from Napari.
I also have a new anndata object from this dataset that I created by segmenting the HE image and assigning bins to Nuclei.
This anndata object has (X,Y) centroids of segmented cells in adata.obsm["spatial"]
How can I correctly add this as a new table to the sdata, such that polygon_query will operate on the (X,Y) centroids?
Is it necessary to add the segmented shapes to which the centroids belong first?
Activity
pakiessling commentedon May 31, 2024
Nevermind.
When I added the segmented shapes first everything works nicely.
docs: clarify how coordinates stored in tables are treated (#1274)