scverse / scverse/spatialdata-io
Xenium read error
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- Python
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Description
Hi,
I am using spatialdata-io v0.3.0 and trying to read the data from the Xenium bundle with this command
xenium_bundle_path = "/path/to/xenium/data"
zarr_path = "/path/to/workdir"
sdata = xenium(xenium_bundle_path)
but I got this error:
ValueError: Expected files in the morphology focus directory to be named as morphology_focus_0000.ome.tif to morphology_focus_0003.ome.tif, found {'ch0000_dapi.ome.tif', 'ch0001_atp1a1_cd45_e-cadherin.ome.tif', 'ch0003_alphasma_vimentin.ome.tif', 'ch0002_18s.ome.tif'}
I think this may have happened because I am using new Xenium version and spatialdata-io doesn't support it yet:
Instrument software version | 4.0.1.4
Analysis version | xenium-4.0.1.0
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start from the xenium(xenium_bundle_path) entry point and reproduce the reported ValueError with the Xenium bundle format and software versions listed in the issue. Trace how morphology focus files are discovered and validated, then confirm that the reader accepts the reported filenames without breaking existing bundles.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100