Can I aggregate visium data from different samples using harmony?

Question

[oghzzang]

Dear Biostars users.

Can I aggregate visium data from different samples using harmony?

I saw a lot of tutorials and papers about the integration that combined multiple slide from same individual.

However, I didn't find the integration using multiple visium data derived from multiple individual.

Have you ever found the research paper???

Whatever,, My question is..

can I aggregate the multiple visium data from different samples using Harmony algorithm like scRNA-seq tutorial?

Thanks.

Answer 1

[bk11]

Hi,

Integration is the better term compared to aggregate here if you want to use Harmony algorithm. Yes, you can use harmony in Seurat V5 to integrate your visium data from different samples after you create a single Seurat object. It is recommended to check if you see batch effects before and after your data integration.

The following links will be helpful in your work-

https://satijalab.org/seurat/articles/spatial_vignette

https://satijalab.org/seurat/articles/seurat5_integration

[oghzzang]

Thank you so much for your reply!!

Thanks to you, I finally knew that Integrate visium data from multiple individuals are possible in a technical manner.

However, do you know why many scientific papers doesn't do that??

If you have ever seen any paper about integration multiple visium data from multiple individuals, can you share it???