Xenium integration with post-xenium immunostaining and reference brain atlas

[Sverreg]

Hi,

This may not be the right place for this, I'm a noob and I appreciate any advice. I figure someone else must have done this before, so maybe I can save some effort.

I just ran my first Xenium samples, with a single immunostaining (+ dapi for alignment) after the run. I have multiple mouse brain samples (2 sections each from 5 untreated mice, and 3 treated mice), 297 genes. I want to correlate transcriptomics data to the immunostaining - my first question is how do I integrate the immunostaining data ( + or - staining per cell, but intensity quantification would also be great) in the xenium/squidpy/cellcharter dataframe for analysis?

Furthermore, I have aligned my Xenium brain slices to the Allen reference atlas using the Quint workflow - has anyone tried integrating this with spatial transcriptomics analysis?

Happy to share more information, as well as datasets.