dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
headings="File name" + "\t" + "Puncta" + "\t" + "Nuclei" + "\t" + "Puncta per Nucleus" + "\t" + "Well Average";
File.append(headings, dir2+"Summary_FindMaxima.xls");
cluster=0;

list = getFileList(dir1);
setBatchMode(true);

for (i=0; i<list.length-2; i+=2) {
showProgress(i+2, list.length);
open(dir1+list[i]);
filename=getTitle;
	run("32-bit");
	run("Subtract Background...", "rolling=200 sliding");
	run("8-bit");
	//getStatistics(area, mean);
	run("Set Measurements...", "median"); 
	List.setMeasurements(); 
	median=List.getValue("Median");
	run("Set Measurements...", "  min redirect=None decimal=3");
	factor=10/median;
	run("Multiply...", "value=&factor");
	run("Find Maxima...", "noise=10 output=[Point Selection]");
	run("Enlarge...", "enlarge=3 pixel");
	run("Flatten");
	run("8-bit");
	setThreshold(0, 150);
	run("Convert to Mask");
	run("Analyze Particles...", "size=0-200 circularity=0.00-1.00 show=Nothing add");
	close(); 
	roiManager("Show All with labels");
	roiManager("Measure");
	count=0;
	for (a=0; a<nResults(); a++) {
	ROImin=getResult("Min",a);
	if (ROImin<12) {
	count=count+1;
	}
	}
	puncta=count;
	roiManager("Reset");
	run("Clear Results");
	selectWindow("Results"); 
	run ("Close");

	open(dir1+list[i+1]);
	run("32-bit");
	run("Subtract Background...", "rolling=50 sliding");
	run("8-bit");
	setAutoThreshold("Li dark");
	run("Convert to Mask");
	run("Median...", "radius=5");
	run("Watershed");
	run("Analyze Particles...", "size=0-Infinity pixel circularity=0.00-1.00 show=Nothing display");
	nuclei=nResults;
	run("Clear Results");
	selectWindow("Results"); 
	run ("Close");
	punctapernucleus=puncta/nuclei;
	row=filename + "\t" + puncta + "\t" + nuclei  + "\t" + punctapernucleus;
	File.append(row, dir2+"Summary_FindMaxima.xls");
	total=total+punctapernucleus;
	close();
	cluster=cluster+2;
	if (cluster==32) {
	average=total/16;
	row="\t" + "\t"+ "\t"+ "\t" + average;
	File.append(row, dir2+"Summary_FindMaxima.xls");
	total = 0;
	cluster = 0;
	}
}