scverse / scverse/spatialdata-io
Error with spatialdata_io.xenium() reader
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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.
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Research direction
Start at the spatialdata_io.xenium() reader and inspect how the experiment.xenium file's analysis_sw_version is interpreted for the Xenium 4.0.0 dataset. Reproduce the reported missing morphology_focus.ome.tif error with the linked 10X Genomics dataset; done means the reader handles this metadata correctly without requesting a nonexistent file.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100