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References:  <[log in to unmask]>
Content-Type: text/plain; charset="iso-8859-1"
Message-ID:  <004901c46262$17db46a0$75d96b86@PERICO>
Date:         Mon, 5 Jul 2004 09:31:31 +0200
Reply-To:     Pedro Ramos <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Pedro Ramos <[log in to unmask]>
Organization: Max Planck Institute for neurological research
Subject:      Re: Calculating average roundness

The following macro is not the most elegant approach to your problem, but it
works. You need a binary image (do Thresholding first) and then run the
macro. The system asks you to introduce a minimum value for the circularity
and for the perimeter of the particles (particles with a perimeter OR a
circularity lower than the specified ones are filtered out) and then it
measures area, circularity (roundness??) and perimeter of the remaining
particles, displaying the results. If you want to run the macro without
introducing the minimum perimeter and circularity any time just replace the
lines:

permin=getString("minimal perimeter","20");
circmin=getString("minimal circularity","0.8");

by

permin=20;
circmin=0.8;

where you can use any value you like instead of 20 and 0.8.

I hope something like this can help you. Cheers,

Pedro



//Definition of what a particle is (minimal perimeter and circularity)
permin=getString("minimal perimeter","20");
circmin=getString("minimal circularity","0.8");

//Main program
run("Rename...", "title=image01");
run("Set Measurements...", " circularity perimeter decimal=3");
run("Analyze Particles...", "minimum=1 maximum=1000 bins=0 show=Masks clear
record ");

for (i=0; i<nResults; i++) {
    x = getResult('XStart', i);
    y = getResult('YStart', i);
    circularity = abs(getResult('Circ.', i));
   perimeter = getResult('Perim.', i);
    if (circularity<circmin || perimeter<permin)  {
        doWand(x,y);
        run("Clear");
    }
}

selectWindow("Mask of image01");
run("Rename...", "title=image02");
run("Threshold");
run("Set Measurements...", "area       perimeter   circularity   display
redirect=None decimal=3");
run("Analyze Particles...", "minimum=1 maximum=1000 bins=0 show=Outlines
display     summarize");


------------------------------------------------------
Pedro Ramos Cabrer
Max Planck Institute for Neurological Research
Gleueler str. 50, 50931 Cologne, Germany
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