Posted by
Krs5 on
Dec 12, 2018; 11:01am
URL: http://imagej.273.s1.nabble.com/Analyze-Particles-Overlay-problems-tp5021557p5021558.html
Dear Stein,
You can use the ROI Manger for this:
//analyze slice 30 and 60
roiManager("Associate", "true");
run("T1 Head (2.4M, 16-bits)");
setThreshold(350, 65535);
setSlice(30);
run("Analyze Particles...", "size=10-Infinity pixel add slice");
setSlice(60);
run("Analyze Particles...", "size=10-Infinity pixel add slice");
setSlice(30);
Best wishes
Kees
Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility
-----Original Message-----
From: Stein Rørvik <
[hidden email]>
Sent: 12 December 2018 10:12
To:
[hidden email]
Subject: Analyze Particles Overlay problems
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
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