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Filter table by coordinate system #431

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Filter table by coordinate system#431

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@sokratiag
sokratiag
opened on Jan 16, 2024

Hello,

I am going through your tutorials and I have one question regarding the 'Use landmark annotations to align multiple omics layers' one. I want to filter the visium breast cancer data by the 'downscaled_hires' coordinate system using:

visium_sdata.filter_by_coordinate_system("downscaled_hires",filter_table=True)

What i want to achieve is to have a new spatialdata object with only the aligned barcodes (only the overlapping xenium/visium region) but instead, the above filtering function return a spatial object with equal size as the original one (4992 spots). Is it possible to filter the anndata so that I only include the spots that fall in the aligned area?

Thanks!

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