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Last data update: 2014.03.03

R: Places detected objects into an image stack

stackObjects

R Documentation

Places detected objects into an image stack

Description

Places detected objects into an image stack.

Usage

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

Arguments

`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.

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.

Value

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.

Author(s)

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

Examples

  ## 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')

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)

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> library(EBImage)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/EBImage/stackObjects.Rd_%03d_medium.png", width=480, height=480)
> ### Name: stackObjects
> ### Title: Places detected objects into an image stack
> ### Aliases: stackObjects
> 
> ### ** Examples
> 
>   ## 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')
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
> 
>   ## 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')
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
> 
>   ## 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')
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
> 
>   ## stacked cells
>   st = stackObjects(cmask, img)
>   display(st, title='Stacked objects')
Only the first frame of the image stack is displayed.
To display all frames use 'all = TRUE'.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>