paintObjects {EBImage}R Documentation

Marks objects in images

Description

This function marks objects in images.

Usage

  paintObjects(x, tgt, opac=c(1, 1), col=c('red', NA))

Arguments

x

An Image object in Grayscale color mode or an array containing object masks. Object masks are sets of pixels with the same unique integer value.

tgt

An Image object or an array, containing the intensity values of the objects.

opac

A numeric vector of two opacity values for drawing object boundaries and object bodies. Opacity ranges from 0 to 1, with 0 being fully transparent and 1 fully opaque.

col

A character vector of two R colors for drawing object boundaries and object bodies. By default, object boundaries are painted in red while object bodies are not painted.

Value

An Image object or an array, containing the painted version of tgt.

Author(s)

Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007

See Also

bwlabel, watershed, link{getFeatures}

Examples

  ## load images
  nuc = readImage(system.file('images', 'nuclei.tif', package='EBImage'))
  cel = readImage(system.file('images', 'cells.tif', package='EBImage'))
  img = rgbImage(green=cel, blue=nuc)
  if (interactive()) display(img, title='Cells')

  ## segment nuclei
  nmask = thresh(nuc, 10, 10, 0.05)
  nmask = opening(nmask, makeBrush(5, shape='disc'))
  nmask = fillHull(nmask)
  nmask = bwlabel(nmask)
  if (interactive()) display(normalize(nmask), title='Cell nuclei mask')

  ## segment cells, using propagate and nuclei as 'seeds'
  ctmask = opening(cel>0.1, makeBrush(5, shape='disc'))
  cmask = propagate(cel, nmask, ctmask)
  if (interactive()) display(normalize(cmask), title='Cell mask')

  ## using paintObjects to highlight objects
  res = paintObjects(cmask, img, col='#ff00ff')
  res = paintObjects(nmask, res, col='#ffff00')
  if (interactive()) display(res, title='Segmented cells')

[Package EBImage version 3.10.0 Index]