MuData Table for SpatialData object
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- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
Xenium version 4 and onward includes support for panels which assay for both gene expression and protein abundance. The spatialdata_io package can read these data in if gex_only is set to False, resulting in a table which contains gene expression and protein abundance measurements in the same AnnData object. This type of data seems like an intuitive fit for representation in the MuData format. Are there any plans to support SpatialData objects with MuData tables for this and other data types which might contain both multimodal measurements and spatial information?
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 represents tables and how MuData represents multimodal measurements, focusing on the Xenium case described in the issue. Determine the integration scope for tables containing gene expression and protein abundance alongside spatial information, then document the expected supported representation and validation coverage.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100