GoodFibes (version 0.1.12)

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).

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Version

Install

install.packages('GoodFibes')

Monthly Downloads

227

Version

0.1.12

License

GPL (>= 2)

Maintainer

J. Arbour

Last Published

October 13th, 2025

Functions in GoodFibes (0.1.12)

thresholdPlot

Plot image from diceCT stack using thresholding

pointsGenerator

Line points generator

muscle.plot

Plot a single muscle fiber

quality.check

Quality testing of possible muscle fibers detected by good.fibes

fuse.fibers

Fuse incomplete fibers

fuse.fibers.auto

Automated repeated fusing of fiber paths

equalize.stack

Automated histogram equalization of image state

fiber.angle

Experimental! Calculating the orientation of muscle fibers

crop.stack

Automated imaging cropping

fiber.curve

Calculate the relative curvature of muscle fibers

color.scale

A simple wrapper to create colors for a continuous variable

check.overlap

Check if muscle fibers are redundant

boundary.check

Check if muscle fiber is close to boundary of muscle

ant.raw

Raw ant muscle fibers

muscle.plot.multi

Plot multi muscle fibers with a muscle outline

muscle.plot.stl

Plot and export muscle fibers to stl

good.fibes

Automated detection of muscle fibers from diceCT scans

fiber.lengths

Calculated the length of smoothed muscle fibers

fibers.smoothed

Smoothing of estimated fiber paths

get.whites

An internal function determining grayscale values

ant.final

Ant muscle fibers finalized

GoodFibes-package

tools:::Rd_package_title("GoodFibes")

hemisphere.points

Finding end points of possible paths

sequencePlot

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