qPLMTiff: Produce Overview TIFFs From qPLM Arrays

In TobinH/microTransit: Quantitative Polarized Light Imaging and Analysis Tools

Produce Overview TIFFs From qPLM Arrays

Description

qPLMTiff creates greyscale .tiff images of out-of-plane orientation (theta), in-plane orientation (phi), transmittance (trans), and a false-color representation of combined orientation data (overview).

Usage

qPLMTiff(
  sample.name,
  qPLMarr,
  theta.scale = FALSE,
  theta.max = 90,
  invert.theta.scale = FALSE
)

Arguments

sample.name	An identifier for the sample, used as a stem for the output file names.
qPLMarr	A qPLMarr object, e.g., output from buildqPLM.
theta.scale	Boolean; if TRUE, automatically scales "_overview.tif" image color scale to peak at maximum measured theta value (default is FALSE).
theta.max	Numerical; if theta.scale is FALSE, specifies an upper end (degrees) for "_overview.tif" color scale (default is 90 degrees).
invert.theta.scale	Boolean; if TRUE, bright colors point toward viewer, brightness falls off as orientations go to parallel with the slide. Useful for sections with predominantly out-of-plane fibers (default is FALSE).

Details

The false-color image of the "overview" .tiff uses the LUV colorspace to produce a perceptually similar brightness for equal levels of theta, and encodes phi with different hues.

Value

Null; .tiff files saved to working directory.

See Also

Other qPLM Illustration Functions: acgEllipse(), qPLMKeymaker(), qPLMSphereSkinner()

TobinH/microTransit documentation built on Jan. 19, 2024, 5:21 a.m.