scverse / scverse/spatialdata-io
Xenium cells with 2 nuclei
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xenium
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
Polynucleated cells are sometimes detected in Xenium when using the Multimodal Segmentation Kit. The xenium() XOA 2.0 reader has been developed on a preview version of the data which didn't include some of the metadata present in this case.
We should add support for them.
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 with the xenium() XOA 2.0 reader and inspect how it handles metadata from the Multimodal Segmentation Kit. Compare the preview data assumptions with the metadata present for Xenium cells containing two nuclei. Done means the reader supports polynucleated cells without losing the relevant metadata.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100