img.processor: Function to define a region of interest of a cell nucleus

In devSJR/micR: Image processing with micR

Description

Find nucleus of a cell.

Usage

img.processor(img.raw = NULL, gblur.sigma = 2, thresh.w = 20,
  thresh.h = 20, thresh.offset = 0.02, watershed.ext = 1)

Arguments

img.raw	is the raw image that will used for the detection of the nucleus
gblur.sigma	is the standard deviation of the Gaussian filter used for blurring (see gblur EBImage)
thresh.w	is the width of the moving rectangular window (see thresh EBImage)
thresh.h	is the height of the moving rectangular window (see thresh EBImage)
thresh.offset	is the thresholding offset from the averaged value (see thresh EBImage)
watershed.ext	is the radius of the neighborhood in pixels for the detection of neighboring objects. Higher value smoothes out small objects (see thresh EBImage)

Details

This function is a pipeline of EBImage function to process an image with the aim to find region of interest from nuclei.

Author(s)

Stefan Roediger

References

Pau G, Fuchs F, Sklyar O, Boutros M and Huber W (2010). EBImage –an R package for image processing with applications to cellular phenotypes. Bioinformatics, 26(7), pp. 979–981. http://doi.org/10.1093/bioinformatics/btq046.

devSJR/micR documentation built on May 15, 2019, 5:06 a.m.