Package: GoodFibes 0.1.10

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

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).

Authors:Jessica Arbour [aut, cre]

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GoodFibes.pdf |GoodFibes.html✨
GoodFibes/json (API)

# Install 'GoodFibes' in R:

install.packages('GoodFibes', repos = c('https://jessica-arbour.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

ant.final - Ant muscle fibers finalized
ant.raw - Raw ant muscle fibers

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 244 downloads 17 exports 85 dependencies

Last updated 2 years agofrom:65d0db4030. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 10 2025
R-4.5-win	OK	Mar 10 2025
R-4.5-mac	OK	Mar 10 2025
R-4.5-linux	OK	Mar 10 2025
R-4.4-win	OK	Mar 10 2025
R-4.4-mac	OK	Mar 10 2025
R-4.4-linux	OK	Mar 10 2025
R-4.3-win	OK	Mar 10 2025
R-4.3-mac	OK	Mar 10 2025

Exports:check.overlap color.scale crop.stack equalize.stack fiber.angle fiber.curve fiber.lengths fibers.smoothed fuse.fibers fuse.fibers.auto good.fibes muscle.plot muscle.plot.multi muscle.plot.stl quality.check sequencePlot thresholdPlot

Dependencies:base64enc bmp bslib cachem class classInt cli codetools concaveman cpp11 curl data.table DBI diagram digest downloader dplyr e1071 evaluate fansi fastmap fontawesome fs future future.apply generics globals glue highr htmltools htmlwidgets igraph imager jpeg jquerylib jsonlite KernSmooth knitr lattice lava lifecycle listenv magrittr MASS Matrix memoise mime numDeriv parallelly pillar pkgconfig png prodlim progressr proxy purrr R6 rappdirs Rcpp RcppArmadillo readbitmap rgl rlang rmarkdown s2 sass sf shape splines2 SQUAREM stringi stringr survival tibble tidyselect tiff tinytex units utf8 V8 vctrs withr wk xfun yaml

Citation

Readme and manuals

Help Manual

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

Package: GoodFibes 0.1.10

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)