Posted by
Wayne Rasband on
Dec 07, 2006; 4:06pm
URL: http://imagej.273.s1.nabble.com/polygon-selection-tp3700848p3700849.html
> I'm trying to make a selection around segmented particles (with a
black
> background). When I make the normal selection, there is no problem and
> the selection follows the outline of the particle, but when I select
it as a polygon,
> on many particles, I get a rectangle instead of the outline of the
particle.
> Does any body have an idea why? Is it possible to get this polygon
selection properly?
> This is what I'm doing:
> setThreshold(1, 255);
> run("Create Selection");
> run("Enlarge...", "enlarge=0");
> getSelectionCoordinates(selX, selY);
> run("Select None");
> makeSelection("polygon", selX, selY);
ImageJ 1.38b fixes a bug that can cause this problem. From the release
notes:
Edit/Selection/Create Selection creates, if possible, a
non-composite selection. The "Issue with ROI closing"
workaround on the Documentation Wiki at
<
http://imagejdocu.tudor.lu/imagej-documentation-wiki/gui-commands/
selection>
no longer needed.
Isolated pixels, or pixels that are only corner-connected, can also
cause this problem. You can remove such pixels by doing binary erosion
with a count of 7, as in this example:
setThreshold(1, 255);
run("Convert to Mask");
run("Options...", "iterations=1 count=7");
run("Erode");
run("Create Selection");
getSelectionCoordinates(selX, selY);
makeSelection("polygon", selX, selY);
There is an example of a segmented particle with a single
corner-connected pixel at:
http://rsbweb.nih.gov/ij/images/8-connected-pixel.gif-wayne