Improve compatibility of cell segmentation output formats with downstream analysis tools
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- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
The cell segmentation （HD and stereoseq）results from spatialdata are currently difficult to integrate with downstream analysis software.
The main issue is with the saved format, especially the image/labels format, which doesn't connect well with many commonly used downstream tools (like Seurat, scanpy, and other spatial analysis packages).
Could the team consider:
Adding export functions to convert segmentation results to more widely-compatible formats
Providing clearer documentation on how to bridge spatialdata outputs with popular downstream tools
This would greatly improve the usability of spatialdata in standard spatial transcriptomics analysis workflows.
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 reviewing how spatialdata currently saves HD and stereoseq cell-segmentation image and labels results. Identify the compatibility requirements of Seurat, scanpy, and other spatial analysis tools, then determine whether export functions, bridging documentation, or both are needed. Done means segmentation results can be used more easily in standard spatial transcriptomics workflows.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100