Xenium multi sample data
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Entering edit mode
10 weeks ago

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.

Xenium batch-effect annotation • 330 views
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Entering edit mode
8 days ago
shh77735 • 0

I just found this below. Hopefully it is helpful!

https://github.com/MargoKapustina/XeniumSpatialAnalysis

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