scverse / scverse/spatialdata-io
`xenium_aligned_image` assumes the image has 3 or 4 channels
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- Dominant language
- Python
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- 103
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- Avg merge
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Description
As mentioned in this issue, the xenium_aligned_image function assumes the image has 3 or 4 channels (i.e., typically, an H&E image).
It would be great to expand it, as we did recently here for Visium HD data. Let me know @LucaMarconato if you agree to have the same behavior as for Visium HD data, and I'll make a PR!
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 locating the xenium_aligned_image function and comparing its channel handling with the Visium HD behavior described in spatialdata-io PR #261. Align Xenium image handling with that behavior so images are not limited to three or four channels, then verify the resulting behavior with the relevant tests or examples.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100