ant.raw {GoodFibes}

Raw ant muscle fibers

Description

Preliminary muscle fibers detected from the mandibular muscle of an ant (Monomorium pharaonis). No quality checking or processing.

Usage

data("ant.raw")

Format

A list with 247 entries, each representing a muscle fiber reconstructed from an image stack (dataset available in examples below) and a partial, subsampled stack is available in extdata. Each entry contains $fiber.points, the raw reconstructed fiber paths, and $fiber.smoothed, the smoothed paths.

Details

These are the initial possible fibers detected using good.fibes. Also see ant.final for the processed fibers.

Source

Fiber paths were generated from the ant dataset in Katzke et al (2022). Original image files are stored under extdata (and see example).

References

Katzke, J., Puchenkov, P., Stark, H., and Economo, E. 2022. A Roadmap to Reconstructing Muscle Architecture from CT Data. Integrative Organismal Biology 4(1): 1-16.

Examples

data(ant.raw)
fl<-fiber.lengths(ant.raw, res = 0.000673107, df = 1)

#### this downloads the ant dataset image stack to a temp folder
olddir<-getwd()
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"))

setwd(olddir)