Login  Register

Analyze Particles Overlay problems

Posted by Stein Rørvik on Dec 12, 2018; 10:12am
URL: http://imagej.273.s1.nabble.com/Analyze-Particles-Overlay-problems-tp5021557.html

I want to run Analyze Particles on a stack, but only on specific slices.
I want the results (which particles were analyzed or not) to be shown as an overlay.
If I say yes to process all slices, the results are as expected:
There is an individual overlay for each slice.

But if I want to analyze a single slice, the result overlay is "global"; that is, one overlay for the entire stack. So when I process another slice, the previous result overlay is lost. I think the overlay should have been applied to a single slice position in this case as well.

Am I missing an option somewhere? Or is this a bug?

Also, I cannot figure out where in the preferences/options to set the result overlay colors (outline color and label color), nor how to do this in a macro.

Demo macro, illustrating what I want to do:
------------------------------

//analyze entire stack
run("T1 Head (2.4M, 16-bits)");
setThreshold(350, 65535);
run("Analyze Particles...", "size=10-Infinity pixel show=Overlay stack");
setSlice(nSlices/2);
//results are as expected; an individual overlay for each slice

//analyze slice 30 and 60
run("T1 Head (2.4M, 16-bits)");
setThreshold(350, 65535);
setSlice(30);
run("Analyze Particles...", "size=10-Infinity pixel show=Overlay slice");
setSlice(60);
run("Analyze Particles...", "size=10-Infinity pixel show=Overlay slice");

setSlice(30);
//problem: overlay is per stack, not per slice, so the result overlay for slice 30 was lost

run("Tile");

------------------------------

I am using daily build ImageJ 1.52j with Java 1.6 on Windows 7/64-bit.


Stein


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html