GoodFibes (version 0.1.12)

sequencePlot: 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)

Value

Returns a sequence of plots

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

Author

J. Arbour

References

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

See Also

thresholdPlot

Examples

# \donttest{

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)
# }