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gao-lab / SLAT

Spatial-Linked Alignment Tool
https://slat.readthedocs.io/en/latest/
MIT License
71 stars 7 forks source link

preprocessing methods for Xenium and Visium datasets #11

Closed guoyang-github closed 1 month ago

guoyang-github commented 2 months ago

Thanks for your excellent tool! I noticed that in your tutorial available at https://slat.readthedocs.io/en/latest/tutorials/cross_technology.html, we need Xenium.h5ad and Visium.h5ad for the cross technology alignment. I wonder what is the pre-processing method from raw data to h5ad for Xenium and Visium? Thanks.

xiachenrui commented 1 month ago

Hi, thanks for your interests !

We followed the common single cell pre-process pipeline in Scanpy. Please note we used shared genes of Xenium and Visium dataset.

Best, Chen-Rui