paintObjects {EBImage}R Documentation

Marking detected objects in reference images

Description

This function allows to mark objects detected with getFeatures or watershed in colour for preview.

Usage


  ## S4 method for signature 'IndexedImage, Image':
  paintObjects(x, tgt, opac=c(0.4, 0.05, 0.4), col=c("#FFC72C","#5BABF6","#FF372C"), ...)

Arguments

x An object of IndexedImage in the Grayscale mode with integer-absed object encoding, as returned by watershed.
tgt A reference grayscale image to calculate object intensity. Should be TrueColor to produce coloured output.
opac A numeric vector of opacity values for foreground (object boundary), object background and edges of object contacts. At least 3 values in the above sequence must be supplied. Opacity range is [0,1] with 0 being fully transparent.
col A character vector of full colours (before opacity applied), colour names supported, to draw object boundaries, object background and edges of object contacts. At least 3 values must be supplied. Default color scheme is yellow for edges, blue for background and red for object contacts and object on image edges.
... Reserved.

Value

A copy of tgt in the same colour mode with objects marked on top of the image. features of x are not transfered – this result is for visualization only.

Author(s)

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

See Also

IndexedImage, Image, watershed, getFeatures

Examples


  ## load images of nuclei (seed points later)
  f <- paste( system.file(package="EBImage"), "images/Gene1_G.tif", sep="/" )
  ii = readImage(f)
  ## normalize images
  ii = normalize(ii, separate=TRUE)
  ## segment
  mask = thresh(ii, 25, 25, 0.02)
  ## refine segmentation with morphology filters
  mk3 = morphKern(3)
  mk5 = morphKern(5)
  mask = dilate(erode(closing(mask, mk5), mk3), mk5)
  ## index objects with 'watershed'
  io = watershed( distmap(mask), 1.5, 1)

  ## load images of cells (the ones to segment with propagate)
  f <- paste( system.file(package="EBImage"), "images/Gene1_R.tif", sep="/" )
  xi = readImage(f)
  ## normalize images
  xi = normalize(xi, separate=TRUE)
  ## segment
  mask = thresh(xi, 40, 40, 0.0)
  ## refine segmentation with morphology filters
  mk7 = morphKern(7)
  mask = dilate(erode(closing(mask, mk7), mk5), mk7)
  ## index objects of xi with 'propagate' using ii as seeds
  xo = propagate(xi, io, mask, 1e-5, 1.5)
  
  ## create an RGB preview of a combination of ii and xi
  rgb = channel(ii, "asred") + channel(xi, "asgreen")
  ## paint cells on the preview
  rgb = paintObjects(xo, rgb)
  ## paint nuclei on the preview
  rgb = paintObjects(io, rgb)
  if (interactive()) display(rgb)
  

[Package EBImage version 2.6.0 Index]