scverse / scverse/spatialdata-io
Xenium Fails to read third party segmentation
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- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
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Description
spatialdata_io.xenium() assumes the dataset contains both nucleus and cell segmentation masks as in the standard Xenium structure. E.g. Proseg-imported segmentation only contains a single segmentation mask and therefore cant be loaded properly. Also setting
cells_labels=False
nucleus_boundaries=False
does not solve the issue.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start at the spatialdata_io.xenium() entry point and reproduce the failure with a Proseg-imported dataset containing only one segmentation mask. Trace how cells_labels and nucleus_boundaries are handled, then verify that supported single-mask datasets load correctly without breaking standard Xenium structures.
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
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100