scverse / scverse/spatialdata-io
Change points to shapes for stereo-seq
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
Hi,
We are using Stereo-seq a lot. It's more common to operate on the bin but not the cell_circles for most of the stereoseq users, because the cell segmentation performed badly as a result of both the experiment technology and algorithm limitations, could you change thePointstoShapesby default ?
Originally posted by @wangjiawen2013 in #97
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 by locating the Stereo-seq reader and the code that chooses the default between Points and Shapes; the issue does not name specific files or tests. Confirm how bin and cell_circles data are represented, then verify that Stereo-seq inputs default to Shapes without breaking existing reader behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100