scverse / scverse/spatialdata-io
Wrong Visium radii?
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- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
Due to several insidious bugs in napari and napari-spatialdata concerning the radii of points in the macOS platform (we have to use points instead of the more intuitive shapes because of performance reasons) we generally overlooked the correct size of the Visium circles.
Today working on them I noticed that the Visium radius seems to be slightly bigger than the expected one. The correct expected sizes are the one shown in the images (55µm radii, 100µm center-to-center distances), as shown in the figure below. We should check this again after one crucial bug in napari-spatialdata on the points size is addressed: https://github.com/scverse/napari-spatialdata/issues/209.
In alternative, we could address this now by re-enabling the representation of circles as ellipses.
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 Visium radius handling and reproducing the rendering after napari-spatialdata issue 209 is addressed. Compare the displayed circles with the reference sizes of 55µm radii and 100µm center-to-center spacing; done means the point radii are correct or the ellipse representation is restored.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100