Load a 10x Xenium output bundle into a Seurat object

Thin R-only wrapper around Seurat::LoadXenium() that validates the bundle layout, sets the scConvert spatial-technology tag, and returns a Seurat object ready for conversion to h5ad / h5Seurat / Zarr via scConvert.

Usage

LoadXenium(data.dir, fov = "fov", assay = "Xenium", verbose = TRUE)

Arguments

data.dir: Path to the Xenium output directory
fov: FOV name attached to the resulting Seurat object (default "fov")
assay: Seurat assay name (default "Xenium")
verbose: Print progress messages

Value

A Seurat object with an FOV slot containing cell centroids, segmentation boundaries, and transcript molecules

Details

The bundle directory must contain the canonical 10x Xenium output files (cell_feature_matrix.h5 or cell_feature_matrix/, cells.csv.gz or cells.parquet, and optional transcripts.parquet / cell_boundaries.parquet / nucleus_boundaries.parquet).

Examples

if (FALSE) { # \dontrun{
seurat_obj <- LoadXenium("/path/to/xenium_lung/")
scConvert(seurat_obj, "xenium_lung.h5ad")
} # }