scverse / scverse/napari-spatialdata
Very Strange Triangulation of Segmentation, Cannot Globally Update Marker Size or Face Color
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- Dominant language
- Python
- Stars
- 90
- Forks
- 25
- Avg merge
- 22m
- Merged PRs (30d)
- 1
Description
I tried out napari-spatialdata on a Xenium project and I noticed a few usability issues. I wonder if these are specific to me (maybe my workstation doesn't have sufficient resources? I have an M1 macbook with 16GB memory). Overall the program was very laggy/non-responsive so that makes me suspect a resource limitation.
The first thing is that the triangulation of the segmentation shapes seems kind of wonky. This is not at all what the nuclear segments look like in the Xenium browser. Is there some configuration parameter I can pass to get a higher poly rendering of the segments?
After that there were a few usability issues, like not being able to change the size of the transcript dots globally, however adjusting the opacity globally seemed to work fine.
https://github.com/scverse/napari-spatialdata/assets/105746884/3036634e-91b9-422c-9d51-9821bdcfad2d
It seems I need to actually select the dots to change their size, but when I try and use cmd-A to select them all the software crashed (hung indefinitely).
https://github.com/scverse/napari-spatialdata/assets/105746884/3919c69d-4a6f-47e1-b0de-19d8efef69c0
Maybe these issues are not relevant to this software project directly but I'm just curious if something is horribly wrong with my installation or if this is expected. If I'm viewing a full Xenium slide should I maybe downsample to just one quadrant of the image maybe?
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 reproducing the report with a full Xenium project, using the two linked videos to inspect the segmentation triangulation, global marker controls, and cmd-A hang. Compare behavior with a downsampled or single-quadrant view; the issue is done when the rendering and global controls work reliably without the software hanging.
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
- 25/100