threshIMG | R Documentation |
A single threshold is found for each image/z-stack.
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)) )
imgs |
The paths of array files; i.e. output from |
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. |
Prints thresholds. saves thresholded RDS files and outputs the path for the thresholded images.
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