bwlabel: Binary segmentation

In EBImage: Image processing and analysis toolbox for R

Description

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

Usage

bwlabel(x)

Arguments

x	An Image object or an array. x is considered as a binary image, whose pixels of value 0 are considered as background ones and other pixels as foreground ones.

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')

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

Example output

Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
Number of nuclei= 77,84,94,90 

EBImage documentation built on Nov. 8, 2020, 5:41 p.m.