scverse / scverse/spatialdata-io
Nanostring TileDB export, new format
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- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
Description
Nanostring CosMx datasets have a new file export format through TileDB, https://nanostring.com/wp-content/uploads/2023/01/LiverPublicDataRelease.html
They no longer give .csv files for expression matrix and metadata. We are able to generate h5ad files no problem, but the spatial coordinates are different now. Are there any plans to update the tutorial with the new file format? thank you so much, love squidpy and hoping to continue using it for these new datasets.
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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 tutorial and the current handling of expression-matrix and metadata CSV files alongside generated h5ad files. Compare those assumptions with Nanostring CosMx's TileDB export and its different spatial-coordinate representation. Done means the tutorial and relevant workflow explain how to use the new format, or clearly document the remaining limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data, documentation
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100