I'm wanting to create a merged object in Seurat using 2 10x Visium 'slices'. However, when I create an object, Seurat assigns an identity "SeuratProject" to the objects (by default I'm guessing; see attached plot). This will be problematic when I attempt to merge the objects as there will be unintended duplicates of the objects.

Here's what I'm attempting to use to create the 10x Spatial Object:

brain1 <- Load10X_Spatial(data.dir = "~/xxx", filename = "filtered_feature_bc_matrix.h5", assay = "Spatial", slice = "slice1", filter.matrix = TRUE, to.upper = FALSE)

I'd need the ability to assign unique ident to each of these (and any subsequent) slices/data.

Thank you!!

Plot output showing the "SeuratProject" Identity


1 Answer 1


You can re-assign orig.ident after creating the object. For example:

brain1 <-Load10X_Spatial(data.dir = "~/xxx", filename = "filtered_feature_bc_matrix.h5", assay = "Spatial", slice = "slice1", filter.matrix = TRUE, to.upper = FALSE)
brain1$orig.ident <- "Visium"
  • $\begingroup$ Didn't work for me. I don't know what I did wrong. $\endgroup$
    Aug 26, 2021 at 22:14
  • $\begingroup$ The active.ident is still "SeuratProject", so also add Idents(brain1) <- "Visium". There should be a "project" option in Load_10X_Spatial to change the "SeuratProject" default $\endgroup$
    – Chris S.
    Dec 27, 2023 at 22:01

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.