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Error with spatialdata_io.xenium() reader #361
Description
Hi,
I was trying to read a Xenium dataset donwloaded from the 10XGenomics portal at https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-biomarkers, with Xenium version 4.0.0. with the xenium reader, but I get this error:
'The file "/path/to/xenium/folder/morphology_focus.ome.tif" does not exist.'
I noticed the source code reads the "analysis_sw_version" of the '.xenium' file to asses the current version and it expects "xenium-4.0.0" for this case, but what I read in my 'experiment.xenium' is "analysis_sw_version": "R&D". I believe this might be the reason of this error occurring.
Reacted by LucaMarconato
Activity
LucaMarconato commentedon Feb 1, 2026
Thanks for reporting. Seems indeed to be an error in the metadata for that dataset. Looping in @stephenwilliams22
A
xenium_versionoptional argument may be added to thexenium()reader to let the user manually specify a version in cases like this when the version is known but it cannot be inferred by the dataset metadata.stephenwilliams22 commentedon Feb 2, 2026
Thanks @LucaMarconato. We're looking into this.