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timtreis
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@timtreis timtreis commented Mar 4, 2025

Users can easily break SpatialData objects by filtering the contained AnnData tables using scanpy - this might remove observations that are still present in other elements, such as Shapes. This function properly filters the entire object, enabled things such as shown here:

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@LucaMarconato
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LucaMarconato commented Mar 5, 2025

Hi thanks. Can you show an example of error that occurs after the legacy filtering? Such mismatch between tables and shapes are supported by design, so I think the broken behavior is a bug.

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Function to subset the entire spatialdata object
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