Read a SpatialData zarr store into a Seurat object

Reads a SpatialData zarr store following the scverse SpatialData specification. The expression data is read from the tables/ subdirectory (standard anndata zarr), spatial coordinates from shapes/ or points/, and tissue images from images/ in OME-NGFF format.

Usage

readSpatialData(path, table = "table", images = TRUE, verbose = TRUE)

Arguments

path

Path to the SpatialData .zarr directory

table

Name of the table within tables/ to read (default: "table")

images

Logical; if TRUE (default), attempt to read OME-NGFF images from the images/ directory

verbose

Show progress messages

Value

A Seurat object with spatial coordinates and optionally tissue images