scverse / scverse/spatialdata-io
Recommended approach for reading multiple Xenium slides with mutual panel at once
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- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
We have an in-house developed visualisation platform that can import multiple spatial biology ROIs/slides for spatial transcriptomics assays such as 10x Visium and Xenium. The current spatialdata Visium reader is able to inherently support multiple Visium slides in one spatialdata zarr directory (and we have successfully rendered multiple Visiums in our software with this structure), but it appears that the Xenium spatialdata structure has one zarr store per slide/ROI.
We have a project comprised of multiple Xenium slides with a shared panel, and would like to have a streamlined approach for being to read all slides into our visualization software in one go. Is there a recommended approach for how to manage this? Would it make the most sense to read a directory of zarr sub-directories, parsing each sub-directories to look for a zarr store that has a Xenium slide? Or can the spatialdata/spatialdata-io API support multiple Xenium slides in one zarr.
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 comparing the linked spatialdata Visium reader and Xenium spatialdata structure, focusing on how each represents multiple slides or ROIs. Determine whether a directory of Xenium zarr stores or one combined zarr is the intended model, then document the recommended approach or the API change needed to support it.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100