A mouse brain Visium two-slice spatial example dataset — visium_mouse_brain_slices

A compact two-slice subset of the 10x Genomics mouse brain serial sagittal Visium dataset distributed as stxBrain.SeuratData. The object contains 1000 tissue spots from each of the anterior serial sections anterior1 and anterior2, with a Spatial assay, two Visium images, and tissue coordinates in metadata columns x and y. Metadata column sample stores the original slice label and is intended for multi-slice spatial integration examples that require a real sample.by column. To keep the package data small, the object retains the top 4000 genes ranked by total counts across the two selected slices.

Format

A Seurat object with 4000 genes, 2000 spots, and two Visium images named anterior1 and anterior2.

Source

Derived from the 10x Genomics mouse brain serial section 1 sagittal anterior Visium dataset distributed through SeuratData as stxBrain.SeuratData version 0.1.2 under the CC BY 4.0 license. The Seurat spatial vignette describes loading these slices with SeuratData::LoadData("stxBrain", type = "anterior1").

Examples

data(visium_mouse_brain_slices_sub)
table(visium_mouse_brain_slices_sub$sample)
#> 
#> anterior1 anterior2 
#>      1000      1000 
SeuratObject::Images(visium_mouse_brain_slices_sub)
#> [1] "anterior1" "anterior2"
head(visium_mouse_brain_slices_sub@meta.data[, c("sample", "x", "y")])
#>                                 sample    x    y
#> anterior1_AAACACCAATAACTGC-1 anterior1 8553 2788
#> anterior1_AAACAGGGTCTATATT-1 anterior1 7116 2375
#> anterior1_AAACATTTCCCGGATT-1 anterior1 8793 8156
#> anterior1_AAACCGTTCGTCCAGG-1 anterior1 7715 4371
#> anterior1_AAACCTAAGCAGCCGG-1 anterior1 9272 7193
#> anterior1_AAACGGGCGTACGGGT-1 anterior1 9272 7743
SpatialSpotPlot(
  visium_mouse_brain_slices_sub,
  group.by = "sample",
  split.by = "sample",
  image = "anterior1",
  overlay_image = FALSE
)