scverse / scverse/spatialdata-tutorials
Update Xenium dataset
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- Dominant language
- Jupyter Notebook
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Description
The Xenium notebook is using a previous dataset (for XOA 2.0). We should consider using on the following recent datasets, recommended by the 10x team:
- FFPE Human Pancreas with Xenium Multimodal Cell Segmentation
- Fresh Frozen Mouse Colon with Xenium Multimodal Cell Segmentation
In alternative we could use the preview data for the 5K panel:
Or even better,
- wait until a stable version of the 5K panel data is released and use that.
Contributor guide
No contributing guide indexed for this repository
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
Locate the Xenium notebook and inspect how the current XOA 2.0 dataset is referenced. Compare the linked 10x datasets and determine whether to use one of them or wait for stable 5K panel data; done means the notebook uses the selected dataset and still runs successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- data, documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100