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

Description Usage Arguments Details Author(s) References

Description

Find nucleus of a cell.

Usage

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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.