GoodFibes (version 0.1.12)

fiber.angle: Experimental! Calculating the orientation of muscle fibers

Description

Calculating the angle of individual muscle fibers. This function can only calculate fiber angles around a central axis (x, y or z) or in reference to a particular "view" (plane). Fiber data is centered around the other axes.

Will eventually include an option for a tendon image stack. Not yet complete

Usage

fiber.angle(fib.list, axis, centered = TRUE, reference = "axis")

Value

A vector of angles in degrees corresponding to each fiber in the original list

Arguments

fib.list

A list of muscle fiber paths generated by good.fibes or from the various cleaning and processing function (must contain $fiber.points).

axis

The axis around which angles will be calculated as a deviation from. Default is 3 (z). This axis is treated as the "z" axis for "plane" options.

centered

Should the data be centered on the other two axes before calculation.

reference

Should the angles be calculated about an axis (specified by "axis") or in reference to a plane ("plane.xz" or "plane.yz", where z is the value of "axis").

Author

J. Arbour

References

Arbour, J. 2023. GoodFibes: an R package for the detection of muscle fibers from diceCT scans. Integrative Organismal Biology 5(1): obad030.

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.

Sullivan, S., McGechie, F., Middleton, K., and Holliday, C. 3D Muscle Architecture of the Pectoral Muscles of European Starling (Sturnus vulgaris).Integrative Organismal Biology 1(1):1-18.

See Also

fiber.lengths

Examples

# \donttest{
olddir<-getwd()

data(ant.final)
fangle<-fiber.angle(ant.final,3)
fangle

cols<-color.scale(fangle, "blue", "red")
muscle.plot.stl(ant.final, cols=cols, df = 1)

setwd(olddir)
# }