Unable to save subset spatialdata to zarr

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1

Hello,
I have subset a spatialdata using coordinates of a selection. This generated properly a new spatialdata (call it test) containing a subset of the SpatialElements initially present in the whole sdata, as desired.
When it comes to saving it to zarr, it does not work:
test.write(path_zarr+“Brain9_Female.zarr”, overwrite=True)

The error is:

RuntimeError: `anndata.settings.allow_write_nullable_strings` is False, because writing of `pd.arrays.{StringArray,ArrowStringArray}` is new and not supported in anndata < 0.11, still use by many people. Opt-in to writing these arrays by toggling the setting to True.
Error raised while writing key '_index' of <class 'zarr.core.group.Group'> to /tables/table/obs

Any help would be appreciated. I would like to further load this new subset on Xenium Explorer, amongst other downstream analysis.

2

Hi @npont, thanks for reaching out. Please can you report this bug in github (discourse is more for general use cases advice, not bug report) and add a complete copy-pastable reproducible example on a test datasets (from spatialdata.datasets import blobs). Thank you for your help in reporting the bug.