scverse / scverse/spatialdata-io
Error reading Xenium data: morphology file missing
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xenium
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Description
While trying to read Xenium data with spatialdata_io.xenium(), I get the following error:
The file "path/to/xenium/data/morphology_mip.ome.tif" does not exist.
Inspecting the folder shows that the file is actually named:
morphology.ome.tif
The dataset and software versions are the same as in issue #361:
spatialdata_ioversion: 0.6.0- Xenium platform: Xenium Onboard Analysis 4.0.0
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 by reproducing the failure through spatialdata_io.xenium() with the Xenium Onboard Analysis 4.0.0 dataset described here, then compare the behavior with issue #361. Trace how the reader locates the morphology image; done means a dataset containing morphology.ome.tif can be read without looking for morphology_mip.ome.tif.
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
- 42/100