Write a Seurat object to SpatialData zarr format

Writes a Seurat object to the scverse SpatialData zarr specification. The expression data is written as an anndata table to tables/table/, spatial coordinates are written to shapes/, and tissue images are written to images/ in OME-NGFF format.

Usage

writeSpatialData(
  object,
  path,
  table = "table",
  region = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

object

A Seurat object

path

Path for the output .zarr directory

table

Name for the table (default: "table")

region

Name for the spatial region (default: auto-detect from image names, or "spots")

overwrite

If TRUE, overwrite existing output

verbose

Show progress messages

Value

Invisibly returns path