scverse / scverse/spatialdata-io
Visium HD: empty `dataset_id` default produces an unnamed coordinate system that napari-spatialdata can't select
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Description
Hi, and thanks for maintaining spatialdata-io!
When the Visium HD files have no filename prefix (e.g. feature_slice.h5) and dataset_id is not provided, visium_hd() falls back to dataset_id="".
Since dataset_id is used both as element prefix and as coordinate-system name, this yields an empty coordinate system that is problematic downstream: for instance, napari-spatialdata silently ignores it and shows it as a blank row, so the full-resolution image can't be displayed at all. This was reported as a Sopa bug in prism-oncology/sopa#446 before we traced it here.
That could be avoided by either defaulting to a non-empty identifier, or keeping "" but naming the coordinate system "global" when dataset_id is empty.
Thanks!
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Research direction
Start at the visium_hd() entry point and trace how an omitted dataset_id is used for element prefixes and coordinate-system naming. Reproduce the no-prefix case with feature_slice.h5, then verify that the resulting coordinate system has a selectable non-empty name and that downstream napari-spatialdata can display the full-resolution image.
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
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 58/100