trackdem (version 0.6)

findThreshold: Find threshold

Description

This function can help to find a threshold value to distinguish noise from particles of interest.

Usage

findThreshold(images, frame = 1, colorimages = NULL)

Value

Returns the number that is interactively chosen by the user. Use this threshold value in identifyParticles.

Arguments

images

Array containing images containing all moving particles, as obtained from subtractBackground.

frame

Number specifying which frame to use. Default is frame 1.

colorimages

Array containing original color images. By default, the original color images are obtained from the global environment.

Author

Marjolein Bruijning, Caspar A. Hallmann & Marco D. Visser

Examples

if (FALSE) {
dir.create("images")
## Create image sequence
traj <- simulTrajec(path="images",
                    nframes=30,nIndividuals=20,domain="square",
                    h=0.01,rho=0.9,
                    sizes=runif(20,0.004,0.006))
## Load images
dir <- "images"
allFullImages <- loadImages (dirPictures=dir,nImages=1:30)
stillBack <- createBackground(allFullImages,method="mean")
allImages <- subtractBackground(stillBack)
thr <- findThreshold(allImages,frame=10)
}