Importing Mass Spec Imaging Data into SpatialData
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- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
I am currently trying to import mass spec imaging data by converting this to a .h5 to mimic the Visium file formatting. I have reached a point where the error is: ValueError: Versions older than V3 are not supported. Are there any suggestions for how to work with alternatively formatted data or mimicing the Visium V3 formatting? My data contains X and Y coordinates as well as feature intensities for each spot in my mass spec imaging dataset. This data is for spatial glycans, so I cannot easily use the metaspace_converter package. Thanks!
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 the existing Visium V3 import path and the handling that raises the version error. Compare its expected inputs with the X/Y coordinates and feature intensities described here, and check the metaspace_converter limitation. Done means establishing and documenting or implementing a supported import path for this alternative mass spectrometry imaging format.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100