Package: GoodFibes 1.0.0

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, angle and curvature).

Authors:Jessica Arbour [aut, cre]

GoodFibes_1.0.0.tar.gz
GoodFibes_1.0.0.zip(r-4.7)GoodFibes_1.0.0.zip(r-4.6)GoodFibes_1.0.0.zip(r-4.5)
GoodFibes_1.0.0.tgz(r-4.6-any)GoodFibes_1.0.0.tgz(r-4.5-any)
GoodFibes_1.0.0.tar.gz(r-4.7-any)GoodFibes_1.0.0.tar.gz(r-4.6-any)
GoodFibes_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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.

1.48 score 555 downloads 18 exports 130 dependencies

Last updated from:4cacf47fcc. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	202
source / vignettes	OK	254
linux-release-x86_64	OK	218
macos-release-arm64	OK	134
macos-oldrel-arm64	OK	160
windows-devel	OK	175
windows-release	OK	107
windows-oldrel	OK	131
wasm-release	OK	184

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

Dependencies:abind backports base64enc bmp boot broom bslib cachem car carData class classInt cli codetools colorspace concaveman cowplot cpp11 curl data.table DBI Deriv diagram digest doBy downloader dplyr e1071 evaluate farver fastmap fontawesome forecast Formula fracdiff fs future future.apply generics ggplot2 globals glue gtable highr htmltools htmlwidgets igraph imager isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv lme4 lmtest magrittr MASS matlib Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr nlme nloptr nnet numDeriv parallelly pbkrtest pillar pkgconfig png prodlim progressr proxy purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readbitmap reformulas rgl rlang rmarkdown rstudioapi s2 S7 sass scales sf shape SparseM splines2 SQUAREM stringi stringr survival tibble tidyr tidyselect tiff timeDate tinytex units urca utf8 V8 vctrs viridisLite withr wk xfun xtable yaml zoo

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
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
Find endpoints for the line of action of a muscle	find.endpoints
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 1.0.0

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)