scverse / scverse/spatialdata-io
Export the real global coordinates of cells (Xenium)
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- Dominant language
- Python
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- 103
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Description
Hi,
I am working with a Xenium dataset that includes an H&E image as well as an alignmentmatrix.csv file. I understand that this alignment matrix can be used to transform the image data into the global coordinate system.
I have successfully created an sdata object from this dataset.
How can I locate a specific cell within the H&E image? More specifically, now the H&E and the cell location are aligned, but how can I explicitly know the exact cell locations on the H&E image? Thanks for your time!!
Contributor guide
First steps
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Research direction
Start by reproducing the Xenium dataset workflow described in the issue, including the sdata object, H&E image, and alignmentmatrix.csv. Trace how cell locations and image transforms are represented, then identify the project entry point for exposing global cell coordinates; done means a documented or callable way to obtain exact cell positions in the H&E coordinate system.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 28/100