Spatialdata does not seem to be interoperable with squidpy image pipelines
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- Dominant language
- Python
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Description
For example, I can't figure out how to use segmentation algorithms with squidpy with the images stored in the spatial data. I know I can load these images in straight from the image file, but it would be nice to have the object be self contained.
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First steps
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Research direction
Start by reproducing a squidpy segmentation workflow using images stored in a SpatialData object, then determine where the interoperability breaks. Define the integration needed so the object remains self-contained and segmentation can operate on its stored images; done means the workflow works without loading the image separately.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100