Load a Stereo-seq GEF file into a Seurat object — LoadStereoSeqGef • scConvert

Pure-R native reader for BGI Stereo-seq .gef and .cellbin.gef HDF5 files. No Python or stereopy dependency.

Usage

LoadStereoSeqGef(file, bin_size = 50, assay = "Spatial", verbose = TRUE)

Arguments

file: Path to a .gef or .cellbin.gef file
bin_size: Bin size to read for square-bin files (default 50, ignored for cellbin)
assay: Seurat assay name (default "Spatial")
verbose: Print progress messages

Value

A Seurat object with spatial coordinates in meta.data$spatial_x/y and provenance in @misc$stereo_seq

Details

The function auto-detects square-bin versus cell-bin layouts from the root bin_type attribute. Square-bin files are read at the requested bin size (typically 50 or 100 for downstream analysis; bin1 is raw DNB-level data and can be very large). Cell-bin files are read into a gene x cell sparse matrix using the cell segmentation table.

Examples

if (FALSE) { # \dontrun{
seurat_obj <- LoadStereoSeqGef("mouse_embryo.gef", bin_size = 50)
scConvert(seurat_obj, "mouse_embryo.h5ad")
} # }