//Identify source directory
sdir=getDirectory("Choose source directory ");
list = getFileList(sdir);

//Identify appropriate image file extension type
Dialog.create("Specify File extension");
Dialog.addString("File extension","JPG",3);
Dialog.show();
ext=Dialog.getString();

//Identify destination directory
ddir=getDirectory("Choose destination directory ");

//Identify ROI directory
roidir=getDirectory("Locate appropriate ROI files ");

//Get lower thresholding value
Dialog.create("Specify lower value for thresholding ");
Dialog.addString("Lower Threshold Value","70",3);
Dialog.show();
lowthresh = Dialog.getString();

//Get name of output file
Dialog.create("Specify name of output file ");
Dialog.addString("Output file","ImageJ_detailed_output.xls",30);
Dialog.show();
outfile = Dialog.getString();

//Prepare output file with column headings
File.append("Area" + "\t" + "Major" + "\t" + "Minor" + "\t" 
+ "Feret" + "\t" + "ImageName" + "\t" + "PatchRichness" + "\t"
, ddir + "\\" + outfile);

//Identify regions of interest
run("ROI Manager...");
roiManager("Open", roidir + "\\FullArena.roi");
roiManager("Open", roidir + "\\LowRed.roi");
roiManager("Open", roidir + "\\ModerateYellow.roi");
roiManager("Open", roidir + "\\HighGreen.roi");


for (i=0; i<list.length; i++) {
        if (endsWith(list[i],ext)){
               
open(sdir+list[i]);

//Delete irrelevant part of image
roiManager("Select", 0);
run("Clear Outside");
run("8-bit");

run("Set Measurements...", "area fit feret's display redirect=None decimal=3");

//Apply threshold adjustment
setThreshold(lowthresh, 255);

//Count in patch 1
roiManager("Deselect");
roiManager("Select", 1);
run("Analyze Particles...", "size=6-100 circularity=0.00-1.00 clear");
NoResults = nResults;
for
(row=0;row<NoResults;row++) {
	ImageName = getTitle();
	PatchRichness = "LowRed";
	datum1 = getResult("Area", row);
	datum2 = getResult("Major", row);
	datum3 = getResult("Minor", row);
	datum4 = getResult("Feret", row);
	File.append(datum1 + "\t" + datum2 + "\t" + datum3 + "\t" 
	+ datum4 + "\t" + ImageName + "\t" + PatchRichness + "\t"
	, ddir + "\\" + outfile);
	}
//Count in patch 2
roiManager("Deselect");
roiManager("Select", 2);
run("Analyze Particles...", "size=6-100 circularity=0.00-1.00 clear");
NoResults = nResults;
for
(row=0;row<NoResults;row++) {
	ImageName = getTitle();
	PatchRichness = "ModerateYellow";
	datum1 = getResult("Area", row);
	datum2 = getResult("Major", row);
	datum3 = getResult("Minor", row);
	datum4 = getResult("Feret", row);
	File.append(datum1 + "\t" + datum2 + "\t" + datum3 + "\t" 
	+ datum4 + "\t" + ImageName + "\t" + PatchRichness + "\t"
	, ddir + "\\" + outfile);
	}
//Count in patch 3
roiManager("Deselect");
roiManager("Select", 3);
run("Analyze Particles...", "size=6-100 circularity=0.00-1.00 clear");
NoResults = nResults;
for
(row=0;row<NoResults;row++) {
	ImageName = getTitle();
	PatchRichness = "HighGreen";
	datum1 = getResult("Area", row);
	datum2 = getResult("Major", row);
	datum3 = getResult("Minor", row);
	datum4 = getResult("Feret", row);
	File.append(datum1 + "\t" + datum2 + "\t" + datum3 + "\t" 
	+ datum4 + "\t" + ImageName + "\t" + PatchRichness + "\t"
	, ddir + "\\" + outfile);
	}

close();

        }
}
print(" -- Finished -- ");