run("Close All");


inDir = getDirectory("Choose Directory Containing Files "); 
fileList = getFileList(inDir);
print(fileList.length);

Area = newArray(fileList.length);
Spotnumber = newArray(fileList.length);
SampleName = newArray(fileList.length);

Dialog.create("Channels");
	Dialog.addMessage("Please enter the Channels");
	Dialog.addString("Fluorescent Channel: ", "fl");
	Dialog.addString("Brightfield Channel: ", "tl");


	Dialog.show();

	CH1=Dialog.getString();
	CH2=Dialog.getString();

/********************
 * Loop over files 
 ********************/
runNumber = 0;
 
for (l=0; l<fileList.length; l++){
	////Cut Imagename
	inFileCut = lengthOf(fileList[l])-4;
	//print(inFileCut);
	saveName=substring(fileList[l],0,inFileCut);
	Name=fileList[l];
	file = inDir + fileList[l];
	//print(fileList[i]); 
	//print(Name);

			
		////Cut Imagename
		Name=fileList[l];
		file = inDir + fileList[l];
		print(fileList[l]); 
		//Slicecut = lengthOf(Slice1);
		
		////Check for Filename
		Run = 0;
		matching=(endsWith(Name, CH1 +  ".tif"));
		if (matching==1) {
			Run=1;	
			matching=(lastIndexOf(Name, CH1));
			inFileCut = matching;
			saveName=substring(fileList[l],0,inFileCut);

		}
		else {};

	
	//print("Run = " + Run);

	////Open files to merge

	if (Run == 1){
		setBatchMode(true);
		roiManager("reset");
		
	////Open and save projection image
		ImgCH1 = inDir + saveName + CH1 + ".tif"  ;
		run("Bio-Formats Importer", "open=["+ImgCH1+"] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
		//rename("CH1");

		ImgCH2 = inDir + saveName + CH2 + ".tif"  ;
		run("Bio-Formats Importer", "open=["+ImgCH2+"] color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
		rename("CH2");
		run("Duplicate...", "title=Mask");
		
		run("Median...", "radius=3");
		setAutoThreshold("Otsu dark");
		setOption("BlackBackground", true);
		run("Convert to Mask");
		run("Set Measurements...", "area mean standard min display redirect=" + Name +" decimal=2");
		run("Analyze Particles...", "size=1950-3750 display add");

		run("Merge Channels...", "c1=" + Name + " c2=CH2 create");
		saveAs("Tiff", inDir + saveName + "Merge.tif");

		run("From ROI Manager");
		run("Flatten");

		saveAs("Jpeg", inDir + saveName + "Segment.tif");


		run("Close All");

		
		}
		
}

saveAs("Results", inDir + "Results.csv");
run("Clear Results");