scverse / scverse/napari-spatialdata
Is "polygon_query" function working properly?
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- Python
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Description
Hi,
I'm using napari_spatialdata to segment regions of interest.
It seems the filtered table doesn't include the correct cell IDs.
I noticed all polygon shapes changed into rectangles.
I attached an example below. The triangle is the ROI I placed and the blue rectangle area shows cells obtained by polygon_query.
I'm using Seurat for clustering etc. So, I export the filtered table and add annotations as metadata.
This happens no matter what shapes of polygon I create.
However, "sdata.pl.render_images().pl.render_shapes(color='annotation').pl.show(coordinate_systems=["x"])" displays the actual polygon.
Why does this discrepancy happen (is this happening only to me?) and is there any way to solve this problem?
Thank you so much for your help!
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 tracing the polygon_query entry point and reproduce the discrepancy with the attached ROI example. Compare its selected cell IDs and polygon geometry with the polygon shown by sdata.pl.render_images().pl.render_shapes() and the exported table. Done means polygon_query preserves the ROI shape and returns the correct cell IDs.
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