scverse / scverse/spatialdata-io
Segmented CODEX data in QuPath csv to squidpy
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- Python
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Description
Dear Community,
I have stitched CODEX images directly after the run and I segemented the image in QuPath. The result is a csv where each row is a cell with multiple columns of Marker Expressions, X and Y Centroids and other information such as in which compartment the cell is etc.
I want to start analyze the neighborhoods in squidpy or to start putting the file in spatialdata-io but I do fail generating the needed anndata object for it to run in squidpy.
Could you help me with some kind of support.
*I dont get the raw images or fcs file from the experiment. Only ome.tiffs that I segment etc. in QuPath.
Best wishes!!!!
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Research direction
The report mentions a QuPath CSV containing cell-level marker expressions and X/Y centroids, plus OME-TIFF inputs, but names no repository file, traceback, or test. Start by reproducing the attempted conversion to an AnnData object and determine which input structure Squidpy requires; done means a validated conversion path or a clearly documented missing-data limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100