Use of Seurat in 3D

[MoussaKassim]

Dear Dr. Satija, I hope this message finds you well. I am writing to inquire about the possibility of using Seurat in a 3D context. Incorporating this feature would greatly enhance our work, and I would like to confirm whether this capability is available.

If Seurat does support 3D functionality, I would be grateful for any additional information or guidance on how to implement it.

Thank you in advance for your assistance.

Best regards,

[tkcaccia]

I have the same questions. I successfully created a spatial Seurat object but wondered if the function CreateCentroids can manage three-dimensional information (e.g., xyz).

  seu  <- CreateSeuratObject(counts = counts,
                                      meta.data = as.data.frame(metadata))

  segmentations.data <- list(
    "centroids" = CreateCentroids(xy)
  )

  coords <- CreateFOV(
    coords = segmentations.data,
    type = "centroids",
    assay="RNA"
  )

  seu[['RNA']] <- AddMetaData(seu[['RNA']], metadata=as.data.frame( metadata))
  seu@tools$platform <- "Visium"

  colnames(seu@meta.data) [colnames(seu@meta.data) %in% c("array_row","array_col")]=c("row","col")

  coords <- subset(x = coords, cells = Cells(x = seu))
  seu[["fov"]] <- coords