stackObjects: Places detected objects into an image stack
In EBImage: Image processing and analysis toolbox for R

Description Usage Arguments Details Value Author(s) See Also Examples

Places detected objects into an image stack.

1	stackObjects(x, ref, combine=TRUE, bg.col='black', ext)

`x`	An `Image` object or an array containing object masks. Object masks are sets of pixels with the same unique integer value.
`ref`	An `Image` object or an array, containing the intensity values of the objects.
`combine`	If `x` contains multiple images, specifies if the resulting list of image stacks with individual objects should be combined using `combine` into a single image stack.
`bg.col`	Background pixel color.
`ext`	A numeric controlling the size of the output image. If missing, `ext` is estimated from data. See details.

stackObjects creates a set of n images of size (2*ext+1, 2*ext+1), where n is the number of objects in x, and places each object of x in this set.

If not specified, ext is estimated using the 98% quantile of m.majoraxis/2, where m.majoraxis is the semi-major axis descriptor extracted from computeFeatures.moment, taken over all the objects of the image x.

An Image object containing the stacked objects contained in x. If x contains multiple images and if combine is TRUE, stackObjects returns a list of Image objects.

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

combine, tile, computeFeatures.moment

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

  ## 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)
  display(img, title='Cells')

  ## segment nuclei
  nmask = thresh(nuc, 10, 10, 0.05)
  nmask = opening(nmask, makeBrush(5, shape='disc'))
  nmask = fillHull(bwlabel(nmask))

  ## segment cells, using propagate and nuclei as 'seeds'
  ctmask = opening(cel>0.1, makeBrush(5, shape='disc'))
  cmask = propagate(cel, nmask, ctmask)

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

  ## stacked cells
  st = stackObjects(cmask, img)
  display(st, title='Stacked objects')