Binary segmentation
Labels connected (connected sets) objects in a binary image.
bwlabel(x)
x |
An |
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.
A Grayscale Image object or an array, containing the
labelled version of x.
Gregoire Pau, 2009
## 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)')Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.