GoodFibes-package {GoodFibes}

Detection and Reconstruction of Muscle Fibers from diceCT Image Data

Description

Reconstruction of muscle fibers from image stacks using textural analysis. Includes functions for tracking, smoothing, cleaning, plotting and exporting muscle fibers. Also calculates basic fiber properties (e.g., length and curvature).

Details

The DESCRIPTION file:

Package:	GoodFibes
Type:	Package
Title:	Detection and Reconstruction of Muscle Fibers from diceCT Image Data
Version:	0.1.10
Date:	2023-08-18
Authors@R:	person("Jessica", "Arbour", , "[e-mail]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4506-158X"))
Description:	Reconstruction of muscle fibers from image stacks using textural analysis. Includes functions for tracking, smoothing, cleaning, plotting and exporting muscle fibers. Also calculates basic fiber properties (e.g., length and curvature).
License:	GPL (>=2)
Depends:	R(>= 3.5.0), imager
Imports:	rgl, stats, graphics, grDevices, concaveman, prodlim, splines2
Author:	Jessica Arbour [aut, cre] (<https://orcid.org/0000-0003-4506-158X>)
Maintainer:	Jessica Arbour <[e-mail]>

Index of help topics:

GoodFibes-package       Detection and Reconstruction of Muscle Fibers
                        from diceCT Image Data
ant.final               Ant muscle fibers finalized
ant.raw                 Raw ant muscle fibers
check.overlap           Check if muscle fibers are redundant
color.scale             A simple wrapper to create colors for a
                        continuous variable
crop.stack              Automated imaging cropping
equalize.stack          Automated histogram equalization of image state
fiber.angle             *Experimental!* Calculating the orientation of
                        muscle fibers
fiber.curve             Calculate the relative curvature of muscle
                        fibers
fiber.lengths           Calculated the length of smoothed muscle fibers
fibers.smoothed         Smoothing of estimated fiber paths
fuse.fibers             Fuse incomplete fibers
fuse.fibers.auto        Automated repeated fusing of fiber paths
good.fibes              Automated detection of muscle fibers from
                        diceCT scans
muscle.plot             Plot a single muscle fiber
muscle.plot.multi       Plot multi muscle fibers with a muscle outline
muscle.plot.stl         Plot and export muscle fibers to stl
pointsGenerator         Line points generator
quality.check           Quality testing of possible muscle fibers
                        detected by good.fibes
sequencePlot            Plot the path of a muscle fiber generated using
                        good.fibes
thresholdPlot           Plot image from diceCT stack using thresholding

Functions in this package allow for the reconstruction of muscle fibers from diceCT image stacks. Fibers are detected using textural analysis, smoothed using splines and processed for path quality (grayscale variation). Muscle fibers can be plotted in 3D with or without the overall muscle outline, and the 3D muscle fibers can be exported as an STL file. Basic fiber architecture metrics can be calculated.

Author(s)

NA

Maintainer: NA

References

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