Tutorial request: Stereo-seq (BGI STOmics) analysis — bin vs cellbin
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 598
- Forks
- 121
- Avg merge
- 3d 11h
- Merged PRs (30d)
- 3
Description
Description of feature
First, thanks for squidpy — the per-platform tutorials (Visium, Xenium, MERFISH,
seqFISH, Slide-seqV2, Vizgen, IMC, MIBI-TOF, CosMx, 4i) are extremely useful.
One major platform is missing: Stereo-seq (BGI / STOmics). It's one of the
most widely used spatial transcriptomics technologies (large-FOV whole-organ /
whole-embryo atlases), and many of us run squidpy on it, but there is no official
guidance — so people keep guessing at the correct setup. Would the maintainers
(or community) consider adding a Stereo-seq tutorial? I'm happy to help and can
provide real data for testing.
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
Review the existing per-platform tutorials in Squidpy and determine what Stereo-seq data and setup guidance are needed for bin versus cellbin analysis. A suitable outcome is an official Stereo-seq tutorial with reproducible examples and clear recommendations for both workflows; the issue offers real data for testing but names no files or tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 45/100