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

Description Usage Arguments Value Author(s) References

View source: R/retina-package.r

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

1
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 brian.cohn@usc.edu, 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.