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Preprocess an image

Source: R/preprocess.R
sg_preprocess.Rd

Applies a chain of preprocessing steps to an sg_image object, including optional stain normalisation, denoising, and contrast enhancement.

Usage

sg_preprocess(
  image,
  stain_normalize = c("none", "macenko", "reinhard", "vahadane"),
  denoise = FALSE,
  contrast = c("none", "clahe", "stretch"),
  target_resolution = NULL
)

Arguments

image

An sg_image object.

stain_normalize

Character string specifying the stain normalisation method. One of "none" (default), "macenko", "reinhard", or "vahadane".

denoise

Logical; if TRUE, a simple mean filter is applied for denoising. Default is FALSE.

contrast

Character string specifying contrast enhancement. One of "none" (default), "clahe", or "stretch".

target_resolution

Numeric scalar or NULL. If not NULL, the image is resampled to this target resolution (microns per pixel) using bilinear interpolation.

Value

A new sg_image object with its history field updated to record the preprocessing steps applied.

Examples

pixels <- matrix(runif(400), nrow = 20, ncol = 20)
img <- new_sg_image(pixels)
img2 <- sg_preprocess(img)
img3 <- sg_preprocess(img, contrast = "stretch", denoise = TRUE)