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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.

...

Arguments passed to other functions.

Value

A validated Seurat object with misc$scop_spatial_input provenance.

See also

SpatialCellPlot