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Export xenium to seurat rds

Export Xenium to Seurat (RDS)

Data Type

Spatial transcriptomics datasets produced on the 10X Xenium platform may be exported automatically to Seurat objects using the "Export Seurat Object (RDS)" pipeline.

As part of this pipeline, the raw Xenium data may optionally be processed using the analysis described in the Mouse Brain: 10X Genomics Xenium In Situ vignette from the Seurat documentation. This includes:

  • SCTransform
  • RunPCA
  • RunUMAP
  • FindNeighbors
  • FindClusters

Note: The FindClusters tool uses a tunable parameter for resolution of the clusters that are assigned. The default value is 0.3. Use a larger value if you want to find a larger number of clusters, and a smaller value if you want to find a smaller number of clusters.

Images generated automatically as part of this analysis process include:

DimPlot: Showing the UMAP coordinates for each cell with cluster assignments annotated

example UMAP with cluster annotations

ImageDimPlot: Showing the spatial coordinates for each cell with cluster assignments annotated

example spatial coordinates with cluster annotations