macro "NEW_Segmentaion" {
	s = File.separator;
	count = 0;
	Ritems = newArray("multiple KCs","single KC");

	Dialog.create("Segmentation");
	Dialog.addRadioButtonGroup("", Ritems, 1, 2, "multiple KCs")
	//Dialog.addCheckbox("Input Directory = Output Directory", true);
	Dialog.addMessage("Extract Mean Gray Values from ROI:");
	items = newArray("_C2_Reg", "_C2_to_C1_Reg_C2_Spl");
	Dialog.addChoice("Extract From:", items, "_C2_to_C1_Reg_C2_Spl");
	items1 = newArray("Maximum Intensity", "Average Intensity");
	Dialog.addChoice("Projection for ROI:", items1, "Average Intensity");
	//Dialog.addMessage("Delete Files:");
	Dialog.show();
	KC = Dialog.getRadioButton();
	//inDisOutD=Dialog.getCheckbox();
	ExtrFrom=Dialog.getChoice();
	Projection="Average Intensity";//Dialog.getChoice();

	inDir=getDirectory("Choose the Raw Data Containing Folder");

	inDisOutD=true;
	outDir=inDir;
	


	if (KC == "single KC") {
	MeanGrayValueExtraction(inDir);
	}
	else {
		multipleKCSegmentation(inDir);
	}
	
	function MeanGrayValueExtraction(inDir) {
	list = getFileList(inDir);
	for (i=0; i<list.length; i++) {
		if (endsWith(list[i], "/")) {
			MeanGrayValueExtraction(inDir+list[i]);	
		}
		else if ((endsWith(list[i], ExtrFrom+".tif"))&&(!File.exists(replace(outDir+s+list[i], ExtrFrom+".tif", ExtrFrom+"_RoiSet.zip")))) {
			open(inDir+list[i]);
			name=File.getName(inDir+list[i]);
			selectWindow(name);
			run("Z Project...", "projection=["+Projection+"]");
			//selectWindow("AVG_"+name);
			run("Duplicate...", "title=Mask");
			selectWindow("Mask");
			run("Make Binary");
			setTool("wand");
			run("ROI Manager...");
			
			waitForUser("Select the Cell/ROI please");
			
			roiManager("Add");
			roiManager("Select", 0);
			roiManager("Rename", "Cell");
			run("Make Inverse");
			roiManager("Add");
			roiManager("Select", 1);
			roiManager("Rename", "Background");
			roiManager("Select", newArray(0,1));
			roiManager("Save", outDir+s+File.nameWithoutExtension+"_Roiset.zip");//replace(inDir+s+list[i], ExtrFrom+".tif", ExtrFrom+"_RoiSet.zip"));						
			selectWindow(name);
			close(name);
			close("Results");
			roiManager("Select", newArray(0,1));
			roiManager("Delete");
			run("Close");
		run("Close All");
		
		}
	}
}
	
	function multipleKCSegmentation(inDir) {
		list = getFileList(inDir);
		for (i=0; i<list.length; i++) {
		//print("Liste: "+i+1+"/"+list.length);
		if (endsWith(list[i], "/")) {
			multipleKCSegmentation(inDir+list[i]);
		}
		else if ((endsWith(list[i], ExtrFrom+".tif"))&&(!File.exists(replace(outDir+s+list[i], ExtrFrom+".tif", ExtrFrom+"_RoiSet.zip")))) {
			count++;
			//File.makeDirectory(outDir+s+"Test");
			open(inDir+list[i]);
			name=File.getName(inDir+list[i]);
			selectWindow(name);					//Background first
			run("Z Project...", "projection=["+Projection+"]");
			run("Duplicate...", "title=Enhanced_Contrast");
			selectWindow("Enhanced_Contrast");		
			run("Enhance Contrast", "saturated=20.00");
			//run("Duplicate...", "title=Background");
			//run("Options...", "iterations=50 count=4 do=Nothing");
			//run("Make Binary");
			run("In [+]");
			run("In [+]");
			setTool("freehand");
			makeRectangle(0, 0, 0, 0);
			while (selectionType() == -1) {
				waitForUser("Outline non- Background");
			}
			//roiManager("add");
			run("Make Inverse");
			roiManager("add");
			roiManager("select", 0);
			roiManager("rename", "Background");
			makeRectangle(1, 1, 0, 0);
			
			//close("Enhanced_Contrast");

			
			
			//selectWindow(name);
			//run("Z Project...", "projection=["+Projection+"]");
			//run("Duplicate...", "title=Enhanced_Contrast");
			selectWindow("AVG_"+name);		
			run("Subtract...", "value=20 slice");
			selectWindow("Enhanced_Contrast");		
			//run("Enhance Contrast", "saturated=20.00");
			//run("In [+]");
		//	run("In [+]");
			
			//selectWindow(name);
			//run("Duplicate...", "title=Cells");
			//run("Measure");
			//w = getResult("Mean", 0);
			//run("Subtract...", "value="+w+" slice");
			//selectWindow("Enhanced_Contrast");
			setTool("Seg Tool 2");
			waitForUser("Click on the Cells");
			z = roiManager("count");
			for (c = 1; c < z; c++) {
				roiManager("select", c);
				roiManager("rename", "Cell"+c);
			}
			roiManager("Save", inDir+s+File.nameWithoutExtension+"_Roiset.zip");
			close("*");
			roiManager("reset");
			
			
			
			
			
			
			
			
			//roiManager("Multi Measure");
			//N=nSlices;
			//for (k=1; k<N; k++) {
			//	Background=getResult("Mean(Background)", 0);
			//	print(Background);
				//print(k);
				//Stack.setSlice(k);
				
				//run("Subtract...", "value="+Background);
				//}
			//run("Close-");
			//a = getHeight();
			//b = getWidth();
			//doWand(a/2, b/2);
			//run("Dilate");
			//run("Create Selection");
			//wait(3000);
			
		}
	}
	close("ROI Manager");
	//for (i = 0; i < count; i++) {
	//	File.copy(path1, path2)
	//}
}
}