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JEFworks-Lab / STalign

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
https://jef.works/STalign/
GNU General Public License v3.0
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Align two Visium datas #21

Closed Lixinyoung closed 10 months ago

Lixinyoung commented 10 months ago

Is it possible to align two Visium-like datas? Like align a Visium to a DBiT data, or just align a Visium two another Visium data.

estellad commented 10 months ago

Hi there,

I have tried aligning Visium coordinates to Xenium HE (the other direction of their tutorial Xenium coordinates to Visium HE), so it is possible. To rasterize Visium, their function STalign.rasterize has an option 'g' that takes the RNA count of the cell. :)

Hope that helps :D

Sincerely, Estella

Lixinyoung commented 10 months ago

Thanks, @estellad:

I didn't realize that there is a 'g' option in the function STalign.rasterize. This solve my question perfectly!

Yours sincerely, Lixinyoung

JEFworks commented 10 months ago

Thanks @estellad! Appreciate it.