internal_smooth: internal smoothing function Function that does the smoothing...

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

internal smoothing function Function that does the smoothing on individual image array

Description

internal smoothing function Function that does the smoothing on individual image array

Usage

internal_smooth(
  image,
  method = c("median", "iso", "box"),
  iter = 1,
  sigma = 1,
  box = 20,
  threshold = 0,
  neuman = TRUE,
  gaussian = TRUE,
  na.rm = FALSE,
  across_levels = "min"
)

Arguments

image	cimg array
method	character describing smoothing method to use "median" , "iso" or "box" or a combination of them.
iter	numeric - number of smoothing iteration
sigma	numeric - standard deviation associated with isoblur (Gaussian)
box	numeric describing box size (centered around center pixel) for smoothing
threshold	numeric - discard pixels that are too low in value (cutoff threshold only applied in box/median blurs).
neuman	logical describing If Neumann boundary conditions should be used, Dirichlet otherwise (default true, Neumann)
gaussian	logical - use gaussian filter
na.rm	logical describing if NA values should be removed
across_levels	character - method used to account for multiple smoothing levels (see details). Select from: "min","mean", "max"

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