paintObjects {EBImage} | R Documentation |
This function allows to mark objects detected with getFeatures
or
watershed
in colour for preview.
## S4 method for signature 'IndexedImage, Image': paintObjects(x, tgt, opac=c(0.4, 0.05, 0.4), col=c("#FFC72C","#5BABF6","#FF372C"), ...)
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. |
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.
Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007
IndexedImage, Image, watershed, getFeatures
## 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)