Hello everyone

I'm currently dealing with spatial transcriptome data using the Xenium platform, where each slide contains several tissue sections.

1. Initially, I conducted separate analyses for each sample and identified numerous clusters of interest.
2. Now, I'm aiming to integrate these multiple samples, removing batch effects, and performing integrative cluster analysis. Should I adopt strategies similar to those used in single-cell analysis for multiple samples?
3. Regarding cluster annotation, some studies have utilized a marker-based approach. Would it be acceptable for Xenium if I utilize single-cell data for cell type annotation ?

I'm new to working with Xenium and want to ensure the approach I take for steps 2 and 3 is appropriate.

I would appreciate all the suggestions.