scverse / scverse/spatialdata-io
VisiumHD: load scalefactor microns_per_pixel in anndata
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- Dominant language
- Python
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Description
Hello,
Segmentation of nuclei on VisiumHD H&E image might require (at least for StarDist segmentation model) to have the micron per pixel information (since pre trained models can be trained on H&E images with different micron per pixel ratio, it is sometimes needed to rescale the image).
Could it be possibe for the visiumHD reader to parse this info and store it somewhere in the Anndata ? Thank you very much !
Alexis
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Research direction
Start with the VisiumHD reader and inspect how image metadata is currently parsed and represented in AnnData. Identify the source of the microns-per-pixel value, store it in AnnData, and verify that VisiumHD loading preserves the value for downstream segmentation.
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
- 35/100