paintObjects {EBImage} | R Documentation

## Mark objects in images

### Description

Higlight objects in images by outlining and/or painting them.

### Usage

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

### 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.
`thick` | A logical indicating whether to use thick boundary contours. Default is `FALSE`.
`closed` | A logical indicating whether object contours should be closed along image edges or remain open.

### Value

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

### Author(s)

Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007 Andrzej Oles, andrzej.oles@embl.de, 2015

### See Also

`bwlabel`, `watershed`, `computeFeatures`, `colorLabels`

### 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)
      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)
      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)
      display(normalize(cmask), title='Cell mask')

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

[Package EBImage version 4.20.1 Index]