title_1=File.openDialog("Choose GFP file");
open(title_1);
dir_GFP=File.getParent(title_1)+File.separator;
name_GFP=File.nameWithoutExtension();
print(dir_GFP+name_GFP+".xls");
run("16-bit");
run("Despeckle");
run("Subtract Background...", "rolling=40");

title_2=File.openDialog("Choose mCherry file");
open(title_2);
dir_mC=File.getParent(title_2)+File.separator;
name_mC=File.nameWithoutExtension();
print(dir_mC+name_mC+".xls");
run("16-bit");
run("Despeckle");
run("Subtract Background...", "rolling=40");

run("Images to Stack", "name=Stack title=[] use");
run("Align slices in stack...");
selectWindow("Results");
IJ.renameResults("alignment clutter");
run("Close");

inputId = getImageID(); 
inputTitle = getTitle();
Stack.getDimensions(width, height, channels, slices, frames);
setSlice(1);
setTool("rectangle");
waitForUser("Identify ROIs, adding each to ROI Manager with 't' button.");
roiManager("Combine");
setBackgroundColor(0, 0, 0);
run("Clear Outside");
setSlice(2);
run("Clear Outside");
run("Select None");
roiManager("Reset");

setSlice(1);
run("Find Maxima...", "noise=2 output=[Maxima Within Tolerance]");
run("Create Selection");
roiManager("Add");
roiManager("Select", 0);
roiManager("Split");
roiManager("Select", 0);
roiManager("Delete");
close();
counter=0;
roiManager("Deselect");
objects=roiManager("Count");
setColor(255,1,1);
setLineWidth(4);
for(ii=0; ii<objects; ii++){
		roiManager("Select", ii);
 		run("To Selection");
 		Dialog.create("Answer");
  		Dialog.addCheckbox("Keep?", false);
  		Dialog.show();
  		response = Dialog.getCheckbox();
  		if (response == true){
  			run("Find Maxima...", "noise=2 output=[Point Selection]");
  			getSelectionCoordinates(x,y);
			run("Select None");
			inten1=getPixel(x[0],y[0]);
			setResult("Intensity",counter,inten1);
  			setResult("X1",counter,x[0]);
			setResult("Y1",counter,y[0]);
			counter++;
			drawOval(x[0]-10,y[0]-10,20,20);
  		}
	}	
updateResults();
selectWindow("Results");
IJ.renameResults(name_GFP);
saveAs("Results",dir_GFP+name_GFP+"_trueMatch"+".xls");
run("Close");
roiManager("Reset");
run("Select None");

selectWindow("Stack");
setSlice(2);
run("Find Maxima...", "noise=2 output=[Maxima Within Tolerance]");
run("Create Selection");
roiManager("Add");
roiManager("Select", 0);
roiManager("Split");
roiManager("Select", 0);
roiManager("Delete");
close();
counter=0;
roiManager("Deselect");
objects=roiManager("Count");
for(ii=0; ii<objects; ii++){
		roiManager("Select", ii);
 		run("To Selection");
 		Dialog.create("Answer");
  		Dialog.addCheckbox("Keep?", false);
  		Dialog.show();
  		response = Dialog.getCheckbox();
  		if (response == true){
  			run("Find Maxima...", "noise=2 output=[Point Selection]");
  			getSelectionCoordinates(x,y);
			run("Select None");
			inten1=getPixel(x[0],y[0]);
			setResult("Intensity",counter,inten1);
  			setResult("X1",counter,x[0]);
			setResult("Y1",counter,y[0]);
			counter++;
			drawOval(x[0]-10,y[0]-10,20,20);
  		}
	}	
updateResults();
selectWindow("Results");
IJ.renameResults(name_mC);
saveAs("Results",dir_mC+name_mC+"_trueMatch"+".xls");
roiManager("Reset");
run("Close");
run("Close All");