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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
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:
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.
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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.
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