scverse / scverse/spatialdata-io

Inquiry about Visium HD

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Python
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Description

Hi, I am working with the Visium HD colorectal cancer dataset. I have annotated a mask on the microscopic image with qupath and have it as a geoJSON file.
Could I please get instructions/ links to tutorials on how I can impose the mask on the microscopic image and extract the gene information.

I have done this with 10 X Visium datasets before but since the Visium HD datasets would need alignment, I am unsure if I would have to use the JSON file provided in visium to align the image, and if yes, how would I proceed with this.

Additionally, the tutorial here https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium_hd.html has loaded the full microscopic image onto the python pipeline however my microscopic image is 11.6 GB and therefore cannot be opened in my pipeline. Please do advise on how I may proceed.

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Research direction

Start with the linked Visium HD tutorial and the reported QuPath GeoJSON workflow, then compare its image-loading path with the stated 11.6 GB image constraint. Document whether the provided Visium JSON is needed for alignment, how to apply the mask and extract gene information, and a workable reference for large images.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, documentation
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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