Explore validation for the orientation of visium images

[brianraymor]

Context

See cell-science-modalites.

@jahilton writes:

Solution is to reuse Visium’s in_tissue code. They annotate the image to determine in_tissue 0/1 We do the same with each image & see that it lines up with submitted in_tissue

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References

Space Ranger Algorithms: Image Processing.

Orientation issues may be mitigated by newer versions of space ranger per:

Finally, Space Ranger v2.0 onwards the automatic image analysis described here, will have --reorient-images=true by default which will automatically rotate and mirror the image such that the "hourglass" fiducial is in the upper-left (see details in Fiducial alignment)

@ivirshup shared:

HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis

[Bento007]

Related to aligning Visium data in cellxgene, here are some library we can look at

• https://slat.readthedocs.io/en/latest/tutorials/cross_technology.html This one might be open source, but no sure if it does what we need,
• 10x space ranger, this is proprietary and requires a license to use.
• https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md. Need to evaluate if it does what we need.