scverse / scverse/spatialdata-io
How to read BGI's STOmics spatial transcriptomics data?
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- Dominant language
- Python
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- 103
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- 65
- Avg merge
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Description
From user Jack on Zulip:
Does anyone know how to use spatialdata_io.stereoseq to read BGI's STOmics spatial transcriptomics data? Why is cell.cluster.h5ad required? The count output from SAW doesn't include this file. It seems that this file can only be obtained by continuing to use subsequent steps in SAW. Is it possible to only use the SAW count output? What does the standard input folder structure look like, and which data files should it include?
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 with the spatialdata_io.stereoseq entry point and trace why cell.cluster.h5ad is required. Compare that requirement with the SAW count output and the STOmics input described in the issue. Done means documenting the expected folder structure, required data files, and whether the SAW count output alone is supported.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100