LoadXenium error: "cells did not contain a segmentation_method column"

[elizabdv]

Hello, I am relatively new to Xenium and have been trying to troubleshoot this error. I have been able to load in this same file in the past with no errors so I am confused as to why this is happening now since there is no difference within the file. I used

object <- LoadXenium(object, fov = "fov", assay = "Xenium"

to load in my data and received the "Warning: cells did not contain a segmentation_method column. Skipping..." and then it continues to load in the object. However when I try to create crops of my object and visualize the outlines of individual cells in a plot using this function:

DefaultBoundary(object, fov = "fov", assay = "Xenium") <- "segmentation"

the segmentation data cannot be found. I was wondering if this was an issue with a new Seurat update that I am unaware of or if I can load the segmentation data in to outline the cells so that i may better visualize my tissue in an ImageDimPlot.

[bissacniaid]

Is there an answer for this question?

[Pancreas-Pratik]

Hi @elizabdv and @bissacniaid,

I just had this same error. In short, after asking ChatGPT, I found the solution to be specifying the type of segmentation (i.e. cell or nucleus) initially in LoadXenium(). See here: https://satijalab.org/seurat/reference/readxenium

So something like:

xenium.obj <- LoadXenium(path, fov = 'fov', segmentations = "cell")

or

xenium.obj <- LoadXenium(path, fov = 'fov', segmentations = "nucleus")

should allow you to use:

DefaultBoundary(xenium.obj[["fov"]]) <- "segmentation"

followed by ImageDimPlot() to see segmentations.