threshIMG: Apply thresholding on image and save as RDS

In Russel88/RCon3D: Analysis of Confocal Images of Microbial Biofilms

Apply thresholding on image and save as RDS

Description

A single threshold is found for each image/z-stack.

Usage

threshIMG(
  imgs,
  method = "Manual",
  cores = 1,
  breaks = 100,
  opt = 0.1,
  thresh = rep(0, length(imgs)),
  BEM.opt = list(start = list(a = -1e+06, b = 0.1, c = 1e+06), control =
    nls.lm.control(maxiter = 1000))
)

Arguments

imgs	The paths of array files; i.e. output from loadIMG or findIMG functions.
method	Either Manual, Otsu, or BEM
cores	Integer. Number of cores to use for parallel computing.
breaks	Integer. Number of breaks for Otsu's threshold. Increase for increased precision
opt	Numeric. Between 0 and 1. Parameter for BEM method. Increase to decrease threshold
thresh	Numeric. Vector of thresholds for manual thresholding, one for each image.
BEM.opt	List. A list of options for model fitting for the BEM method. Passed to the nlsLM function.

Value

Prints thresholds. saves thresholded RDS files and outputs the path for the thresholded images.

Russel88/RCon3D documentation built on Dec. 14, 2022, 11:06 p.m.