Read10X_Segmentations: Load 10X Genomics Visium Cell Segmentations

In Seurat: Tools for Single Cell Genomics

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
)

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; see Load10X_Spatial for details

Value

A VisiumV2 object with segmentations

Seurat documentation built on Dec. 14, 2025, 9:07 a.m.