spatialdata.write fails on Xenium sdata in env with pandas 3.0.0

[EmielGeeraerts]

I had some headaches trying to write a Xenium dataset as spatialdata object using write.

Error message:

anndata._io.specs.registry.IORegistryError: No method registered for writing <class 'pandas.arrays.ArrowStringArray'> into <class 'zarr.core.group.Group'>
Error raised while writing key '_index' of <class 'zarr.core.group.Group'> to /tables/table/obs

Turns out, with pandas 3.0.0 the default string type changed and a new writer is missing.

Resetting to pandas to "old behavior" did fix things for me, but just letting you know.

import pandas as pd
pd.options.mode.string_storage = "python"

import anndata as ad
ad.settings.allow_write_nullable_strings = True

I'm on spatialdata-io==0.5.1 and anndata==0.12.6 at the time of writing

[LucaMarconato]

Thanks for reporting and for sharing the workaround. I see there is a test failing for pandas 3.0.0 here https://github.com/scverse/integration-testing/actions/runs/21613728467/job/62287938878 (tests/io/test_readwrite.py::test_sdata_with_nan_in_obs), it may be related.

Could you please share which dataset you are using? If you could reproduce with a public one, or find a subset of the sdata object that leads to the bug it would be helpful.

[EmielGeeraerts]

I was able to reproduce the issue with the following public dataset, which is also created with Xenium Onboard Analysis 4.0.0
https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-carcinoma

curl -O https://s3-us-west-2.amazonaws.com/10x.files/samples/xenium/4.0.0/Xenium_V1_Human_Kidney_FFPE_Protein_updated/Xenium_V1_Human_Kidney_FFPE_Protein_updated_outs.zip
curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Kidney_FFPE_Protein_updated/Xenium_V1_Human_Kidney_FFPE_Protein_updated_xe_outs.zip

Below is the full error trace when I run the following:

import spatialdata_io as sio
sdata = sio.xenium(xenium_dir, cells_as_circles=True)
sdata.write(out_path, overwrite=True)

error_spatialdata-io_write.txt

pyproject.toml dependencies

"geosketch==1.3",
"harmonypy==0.2.0",
"igraph==0.11.8",
"pip>=23.2",
"popv==0.5.2",
"scanpy==1.12.0",
"scikit-misc==0.5.1",
"setuptools>=65.5",
"spatialdata[extra]==0.7.1",
"squidpy==1.8.0",
"wheel>=0.46.3"

Hope this helps!