scverse / scverse/spatialdata-io
Problem of reading dbit-seq image
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- Python
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Description
Hi @LucaMarconato . Thanks for developing spatialdata-io, it is super helpful in processing spatial data. I wanted to use this package to process my dbit-seq data, but I had trouble reading the dbit-seq image with sd.models.Image2DModel.parse function. It said "ValueError: Wrong dims: ('y', 'x'). Expected ('c', 'y', 'x').". My image is (2000, 2000), and it seems that the Image2DModel doesn't work well with my data. Do you have any suggestions on this? Thanks very much!
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Research direction
Start with sd.models.Image2DModel.parse and reproduce the reported ValueError using the attached dbit-seq image shape, (2000, 2000). Determine whether the parser should accept this input or require different dimensions; done means the intended image can be read without the reported dims error, with coverage for the resolved behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100