Load a 10X Genomics Visium Image

Load a 10X Genomics Visium Image

Usage

Read10X_Image(
  image.dir,
  image.name = "tissue_lowres_image.png",
  assay = "Spatial",
  slice = "slice1",
  filter.matrix = TRUE,
  image.type = "VisiumV2",
  cells = NULL
)

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

image.name

PNG file to read in

assay

Name of associated assay

slice

Name for the image, used to populate the instance's key

filter.matrix

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

image.type

Image type to return, one of: "VisiumV1" or "VisiumV2"

cells

Optional barcode vector to restrict tissue positions before collection. NULL reads all eligible positions.

Value

A VisiumV2 object

See also

VisiumV2 Load10X_Spatial