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Load and validate Visium, Visium HD, or Xenium data

Source: R/SpatialInput.R
ReadSpatialData.Rd

Delegate file parsing to Seurat, validate each image against its assay, and record observation type, resolution and coordinate units. This function does not download data, normalize counts, segment cells, or install packages.

Usage

ReadSpatialData(
  data.dir,
  technology = c("visium", "visium_hd", "xenium"),
  bin.size = c(8L, 16L),
  sample_id = "sample1",
  ...
)

Arguments

data.dir

Existing vendor output directory.

technology

One of visium, visium_hd, or xenium.

bin.size

Positive integer HD bin sizes in microns. Ignored for other technologies; Seurat stores each resolution in a separate assay/image.

sample_id

Nonempty sample identifier stored in spatial_sample.

...

Extra arguments to Seurat's Load10X_Spatial or LoadXenium. Xenium defaults to cell segmentation and does not load molecule coordinates unless requested; cell segmentation must already exist in the vendor output.

Value

A validated Seurat object with misc$scop_spatial_input provenance.

See also

SpatialCellPlot