Binary segmentation

Description

Labels connected (connected sets) objects in a binary image.

Usage

bwlabel(x)

Arguments

Details

All pixels for each connected set of foreground (non-zero) pixels in x are set to an unique increasing integer, starting from 1. Hence, max(x) gives the number of connected objects in x.

Value

A Grayscale Image object or an array, containing the labelled version of x.

Author(s)

Gregoire Pau, 2009

See Also

computeFeatures, propagate, watershed, paintObjects, colorLabels

Examples

  ## simple example
  x = readImage(system.file('images', 'shapes.png', package='EBImage'))
  x = x[110:512,1:130]
  display(x, title='Binary')
  y = bwlabel(x)
  display(normalize(y), title='Segmented')

  ## read nuclei images
  x = readImage(system.file('images', 'nuclei.tif', package='EBImage'))
  display(x)

  ## computes binary mask
  y = thresh(x, 10, 10, 0.05)
  y = opening(y, makeBrush(5, shape='disc'))
  display(y, title='Cell nuclei binary mask')

  ## bwlabel
  z = bwlabel(y)
  display(normalize(z), title='Cell nuclei')
  nbnuclei = apply(z, 3, max)
  cat('Number of nuclei=', paste(nbnuclei, collapse=','),'\n')

  ## recolor nuclei in colors
  cols = c('black', sample(rainbow(max(z))))
  zrainbow = Image(cols[1+z], dim=dim(z))
  display(zrainbow, title='Cell nuclei (recolored)')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(EBImage)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/EBImage/bwlabel.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bwlabel
> ### Title: Binary segmentation
> ### Aliases: bwlabel
> 
> ### ** Examples
> 
>   ## simple example
>   x = readImage(system.file('images', 'shapes.png', package='EBImage'))
>   x = x[110:512,1:130]
>   display(x, title='Binary')
>   y = bwlabel(x)
>   display(normalize(y), title='Segmented')
> 
>   ## read nuclei images
>   x = readImage(system.file('images', 'nuclei.tif', package='EBImage'))
>   display(x)
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
> 
>   ## computes binary mask
>   y = thresh(x, 10, 10, 0.05)
>   y = opening(y, makeBrush(5, shape='disc'))
>   display(y, title='Cell nuclei binary mask')
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
> 
>   ## bwlabel
>   z = bwlabel(y)
>   display(normalize(z), title='Cell nuclei')
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
>   nbnuclei = apply(z, 3, max)
>   cat('Number of nuclei=', paste(nbnuclei, collapse=','),'\n')
Number of nuclei= 76,86,94,89 
> 
>   ## recolor nuclei in colors
>   cols = c('black', sample(rainbow(max(z))))
>   zrainbow = Image(cols[1+z], dim=dim(z))
>   display(zrainbow, title='Cell nuclei (recolored)')
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>