Separate H&E stain channels by colour deconvolution

Applies colour deconvolution to an H&E-stained image to separate the haematoxylin and eosin channels.

Usage

sg_stain_deconvolve(image, method = c("macenko", "ruifrok"), stains = NULL)

Arguments

image

An sg_image object with at least 3 colour channels (RGB).

method

Character string specifying the deconvolution method. One of "macenko" (default) or "ruifrok".

stains

Optional 3x3 numeric matrix whose columns are the stain vectors. If NULL, stain vectors are estimated from the image using the specified method.

Value

A named list of sg_image objects, one per stain channel. Typically hematoxylin and eosin, plus residual.

Examples

# \donttest{
# Requires a colour image
pixels <- array(runif(300), dim = c(10, 10, 3))
img <- new_sg_image(pixels, channels = c("R", "G", "B"))
stains <- sg_stain_deconvolve(img)
names(stains)
#> [1] "hematoxylin" "eosin"       "residual"   
# }