Mark objects in images
Higlight objects in images by outlining and/or painting them.
paintObjects(x, tgt, opac=c(1, 1), col=c('red', NA), thick=FALSE, closed=FALSE)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 |
thick |
A logical indicating whether to use thick boundary contours. Default is |
closed |
A logical indicating whether object contours should be closed along image edges or remain open. |
An Image object or an array, containing the painted version of tgt.
Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007 Andrzej Oles, andrzej.oles@embl.de, 2015
## 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')Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.