Load a 10X Genomics Visium Image

Source: R/preprocessing.R

Load a 10X Genomics Visium Image

Read10X_Image(
  image.dir,
  image.name = "tissue_lowres_image.png",
  assay = "Spatial",
  slice = "slice1",
  filter.matrix = TRUE
)

Arguments

image.dir

Path to directory with 10X Genomics visium image data; should include files tissue_lowres_image.png, scalefactors_json.json and tissue_positions_list.csv

assay

Name of associated assay

filter.matrix

Filter spot/feature matrix to only include spots that have been determined to be over tissue

image.scale

PNG file to read in

Value

A VisiumV1 object