stackObjects {EBImage} | R Documentation |
Places detected objects into an image stack.
stackObjects(x, ref, index, combine=TRUE, rotate, bg.col='black', ext, centerby, rotateby)
x |
An |
ref |
An |
combine |
If |
bg.col |
Background pixel color. |
ext |
A numeric controlling the size of the output simage.
If missing, |
index, rotate, centerby, rotateby |
Deprecated. |
stackObjects
creates a set of nbobj
images of size
(2*ext+1
, 2*ext+1
), where nbobj
is the number of objects
in x
, and places each object of x
in this set.
If not specified, ext
is estimated using the 95% quantile of
2*sqrt(g.l1
), where g.l1
is the semi-major axis
descriptor extracted from hullFeatures
, taken over
all the objects of the image x
.
An Image
object containing the stacked objects contained in
x
. If x
contains multiple images and if combine
is TRUE
, stackObjects
returns a list of Image
objects.
Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007
## simple example x = readImage(system.file('images', 'shapes.png', package='EBImage')) x = x[110:512,1:130] y = bwlabel(x) if (interactive()) display(normalize(y), title='Objects') z = stackObjects(y, normalize(y)) if (interactive()) display(z, title='Stacked objects') ## 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(bwlabel(nmask)) ## segment cells, using propagate and nuclei as 'seeds' ctmask = opening(cel>0.1, makeBrush(5, shape='disc')) cmask = propagate(cel, nmask, ctmask) ## using paintObjects to highlight objects res = paintObjects(cmask, img, col='#ff00ff') res = paintObjects(nmask, res, col='#ffff00') if (interactive()) display(res, title='Segmented cells') ## stacked cells st = stackObjects(cmask, img) if (interactive()) display(st, title='Stacked objects')