equalize.stack: Automated histogram equalization of image state

In GoodFibes: Detection and Reconstruction of Muscle Fibers from diceCT Image Data

Automated histogram equalization of image state

Description

Conducts histogram equalization to adjust the contrast of the image stack. May improve visibility of muscle fibers prior to fiber detection. Optionally automatically save new image stack in working directory.

Usage

equalize.stack(images, n, save.images = FALSE)

Arguments

images	A vector of png image file names, created using list.files
n	The number of the image in the stack to be equalized and plotted
save.images	Should the whole image stack be equalized and plotted?

Value

Creates a plot and optionally saves an image stack

Author(s)

J. Arbour

References

Arbour, J. In Prep. GoodFibes: an R package for the detection of muscle fibers from diceCT scans

See Also

crop.stack

Examples

olddir<-getwd()

#### this downloads the ant dataset image stack
#### if you have it already downloaded you can navigate to that folder
setwd(tempdir())
download.file(url=
"https://github.com/jessica-arbour/Ant-Muscle-Image-Stack/raw/main/Ant_data.zip",
destfile="antdata.zip")

unzip("antdata.zip")
setwd(paste0(getwd(),"/Ant data"))
####

images<-list.files(pattern=".png")
equalize.stack(images, 100)  


setwd(olddir)

GoodFibes documentation built on Aug. 19, 2023, 1:06 a.m.