Create Vizgen MERSCOPE largeImage — createMerscopeLargeImage • Giotto

Read MERSCOPE stitched images as giottoLargeImage. Images will also be transformed to match the spatial coordinate reference system of the paired points and polygon data.

createMerscopeLargeImage(
  image_file,
  transforms_file,
  name = "image",
  flip_axis = c("none", "y", "x", "both")
)

Arguments

image_file: character. Path to one or more MERSCOPE images to load
transforms_file: character. Path to MERSCOPE transforms file. Usually in the same folder as the images and named 'micron_to_mosaic_pixel_transform.csv'
name: character. name to assign the image. Multiple should be provided if image_file is a list.
flip_axis: character. Axis along which to reflect the image after the spatial shift: "none" (default), "y", "x", or "both". The reflection origin is the midpoint of the image extent in micron space.

Value

giottoLargeImage