// This Macro counts particles inside specific Roi and otputs the number to TAB separated Log window which after saving can be imported to excel.  
print ("RoiNumber","	","SliceLabel","	","RoIName","	","Count","	","RoIArea","	","RoIPerimeter","	"," ParticlesCoveredArea","	","AreaFraction") ;
setAutoThreshold("Default dark");       
 n = roiManager("count");
        for (i=0; i<n; i++)  {
        roiManager("select", i);
        run("Set Measurements...", "area perimeter redirect=None decimal=4");
	run("Measure");
	r=getResult("Area");
	u=getResult("Perim.");
run("Set Measurements...", "area area_fraction limit display redirect=None decimal=4");
run("Measure");
s=getResult("Area");
t=getResult("%Area");
run("Analyze Particles...", "size=0-infinity circularity=0.00-1.00 show=Nothing display clear ");
	m=nResults;
 	q=getInfo("slice.label");
	print (i,"	",q,"	",call("ij.plugin.frame.RoiManager.getName", i),"	",m,"	",r,"	",u,"	",s,"	",t) ;
}	
          



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