Seurat (version 6.0.0)

Read10X_Segmentations: Load 10X Genomics Visium Cell Segmentations

Description

Load 10X Genomics Visium Cell Segmentations

Usage

Read10X_Segmentations(
  image.dir,
  data.dir,
  image.name = "tissue_lowres_image.png",
  assay = "Spatial.Polygons",
  slice = "slice1.polygons",
  segmentation.type = "cell",
  compact = TRUE,
  cells = NULL
)

Value

A VisiumV2 object with segmentations

Arguments

image.dir

Path to directory with 10X Genomics visium image data;

data.dir

Directory of the base spaceranger outs

image.name

Name of the tissue image to be plotted. tissue_lowres_image.png or tissue_hires_image.png

assay

Name of assay to associate segmentations to

slice

Name of the slice to associate the segmentations to

segmentation.type

Which segmentations to load, cell or nucleus. If using nucleus the full matrix from cells is still used

compact

Whether to store segmentations in only the sf.data slot in the corresponding Segmentation object (default TRUE) to save memory and processing time. If FALSE, segmentations are also stored in sp format in addition to the sf.data slot.

cells

Optional vector of cell barcodes to retain.