Convert Seurat to SpatialExperiment — srt_to

Create a lightweight SpatialExperiment from a spatial Seurat object using one assay layer, metadata, and resolved spatial coordinates.

Usage

srt_to_spe(
  object,
  assay = NULL,
  layer = "counts",
  coord.cols = c("col", "row"),
  image = NULL,
  include_meta = TRUE,
  coordinate_space = c("raw", "legacy_display"),
  srt = NULL
)

Arguments

object: A Seurat object.
assay: Assay to export. If NULL, the default assay is used.
layer: Assay layer to export.
coord.cols: Metadata coordinate columns. By default, SCOP resolves x/y first and then col/row.
image: Optional Seurat image name. When present, image-derived coordinates are used.
include_meta: Whether to include Seurat metadata as colData.
coordinate_space: Coordinate space exported to spatialCoords. "legacy_display" preserves the historical scaled/y-flipped behavior; "raw" (the default) preserves analysis distances. The source and transform are stored in metadata(spe)$scop_spatial_coordinates so that an explicit display export can be inverted by spe_to_srt().
srt: Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A SpatialExperiment.