spherical_coords: ImageJ and Retistruction of Input Retinal Data from Flattened...

In yinscapital/retina-analysis-reference: Tools for plotting and analyzing vertebrate retinas.

Description

Converts flat retina to a spherical representation of the data. Spherical coords path must contain: outline.roi Datapoints in barycentric coordinates. P.csv Datapoints on reconstructed sphere in cartesian coordinates. T.csv Datapoints on reconstructed sphere in spherical coordinates. xyz.csv Cell density site locations with density measurements. Columns of x(integer column starting at 1 at the left) , y (integer column starting at 1 on the bottom) and z (counts)

Usage

spherical_coords(path, height, width, IJ_limits, falciform = TRUE)

Arguments

path	Directory which contains the retistruct files.
height	Height in microns of the stereologic counting frame
width	Width in microns of the stereologic counting frame
IJ_limits	data.frame with min, max and delta values for both X and Y with respect to the contour image in ImageJ coordiantes. For setting the calibration of the sampling sites to the sphere.
falciform	(boolean) True by default, meaning there is a file called falc.txt within the path.

Value

data.frame with phi(latitude), lambda(longitude) and Z (cells per square millimeter).

Author(s)

Brian Cohn [e-mail], Lars Schmitz

References

https://r-forge.r-project.org/scm/?group_id=1436

yinscapital/retina-analysis-reference documentation built on May 22, 2019, 12:40 p.m.