equalize_image: equalise image histogram

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

equalise image histogram

Description

equalizeHistogram image enhancement via colour histogram equalization.

Usage

equalize_image(
  vesalius_assay,
  dimensions = seq(1, 3),
  embedding = "last",
  method = "BalanceSimplest",
  N = 1,
  smax = 1,
  sleft = 1,
  sright = 1,
  lambda = 0.1,
  up = 100,
  down = 10,
  verbose = TRUE
)

Arguments

vesalius_assay	a vesalius_assay object
dimensions	numeric vector of latent space dimensions to use.
embedding	character string describing which embedding should be used.
N	numeric describing how each colour channel will be mapped back to the image (Higher N = Higher greyscale contrast). Used with EqualizePiecewise
smax	numeric - upper limit if contrast stretching. Used with EqualizePiecewise
sleft	numeric - Range 0 - 100. Percentage of pixel to be saturated on the left side of the histogram. Used with BalanceSimplest
sright	numeric - Range 0 - 100. Percentage of pixel to be saturated on the right side of the histogram. Used with BalanceSimplest
lambda	numeric - strength of background correction. Used with SPE (Screened Poisson Equation).
up	numeric - color value threshold in the upper limit. Used with EqualizeDP.
down	numeric color value threshold in the lower limit. Used with EqualizeDP.
verbose	logical - progress message output.
type	character - histogram EQ type. Select from: BalanceSimplest, EqualizePiecewise, SPE, EqualizeDP, EqualizeADP, ECDF (see details)

Details

Histogram equalization ensures that image details are amplified. In turn, territories may be extract with greater precision. We recommend balancing the histogram prior to smoothing.

For further details on each method described here, please refer to https://cran.r-project.org/web/packages/imagerExtra/vignettes/gettingstarted.html

Value

a vesalius_assay object

Examples

## Not run: 
data(vesalius)
# First we build a simple object
ves <- build_vesalius_object(coordinates, counts)
# We can do a simple run
ves <- build_vesalius_embeddings(ves)

# simple EQ
ves <- equalisz_image(ves, embedding = "PCA")

## End(Not run)

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.