RCTD for Xenium data

[balthasar0810]

Dear all,

I was applying the vignette:
https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2#mouse-brain-10x-genomics-xenium-in-situ

Annotations are extracted by:
annotations.df <- RCTD@results$results_df
annotations <- annotations.df$first_type

from the RCTD object produced by spacexr. Inspecting results_df, there is a column named "spot_class". For some cells, this column gives "doublet_certain".

However, in the Seurat vignette, there is no differentiation between singlets and doublets, is there any reason for that?

Thanks, best, Chris