paintObjects {EBImage} | R Documentation |
This function marks objects in images.
paintObjects(x, tgt, opac=c(1, 1), col=c('red', NA))
x |
An |
tgt |
An |
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 |
An Image
object or an array, containing the painted version
of tgt
.
Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007
bwlabel
, watershed
, link{getFeatures}
## 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')