sequencePlot: Plot the path of a muscle fiber generated using good.fibes

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

Plot the path of a muscle fiber generated using good.fibes

Description

Plots images in sequence showing the image stack and the location of the muscle fiber path at each step in the fiber tracking algorithm in good.fibes

Usage

sequencePlot(fib.track, images, threshold = 0.1, sleep.time = 0.5)

Arguments

fib.track	A set of $fiber.points from a fiber list, generated by good.fibes
images	A character vector of image stack file names. Generated with list.files
threshold	A cutoff values under which voxels are set to black
sleep.time	Time in seconds between images, sets speed for plotting sequence

Value

Returns a sequence of plots

Author(s)

J. Arbour

References

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

See Also

thresholdPlot

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")

data(ant.raw)

sequencePlot(ant.raw[[2]]$fiber.points, images, 0 ,0.2)



setwd(olddir)

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