scverse / scverse/spatialdata-io
store probe set for image-based transcriptomics in spatialdata
Open
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
after discussion with @LouisK92 and @timtreis we realized it would be useful for spatialdata to also store the probe set used to target mRNA transcripts. Where should that be stored, unclear, maybe uns?
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
The issue does not name files, tests, or entry points. First review how spatialdata currently stores image-based transcriptomics data and resolve whether the probe set belongs in an existing structure or a new one with maintainers; done means the probe set can be stored and retrieved consistently.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100