Create object of class HistologyImaging

Creates an object of class HistologyImaging that is used to store the image, image meta data and image annotations.

Located in slot @images in the SPATA2 object.

createHistologyImaging(
  image,
  id = "imageid",
  img_scale_fct = 1,
  meta = list(),
  pxl_scale_fct = NULL,
  coordinates = NULL,
  verbose = TRUE,
  ...
)

Arguments

image

Image input or character value. If character, input is interpreted as a directory to a file or to an URL and is read with EBImage::readImage(). The read image should be of type .png, .jpeg or .tiff. Capital letters work, too.

If not character, the function ensures that the input is - or is convertible - to class Image via EBImage::as.Image(). If that fails, an error is thrown.

id

Character value. Name of the HistologyImaging object.

img_scale_fct

Numeric value between 0 and 1. If lower than 1, is used to downscale the image before setting it.

coordinates

A data.frame of observational units that underlie the image in case of spatially resolved multi-omic studies. Should contain at least the two variables: x, y and a variable that identifies the observational units (e.g. barcodes).

Value

An object of class HistologyImaging.

See also

?HistologyImaging for the documentation of all slots.