macro "Batch Measure Plate Area Action Tool - T3e16X"{
 n = 0;
 input = getDirectory("Choose an input folder");
 output = input+"ImageJ"+File.separator;
 suffix = ".JPG";
 File.makeDirectory(output);

run("Set Measurements...", "area redirect=None decimal=3");
processFolder(input);
setBatchMode(false);
selectWindow("Results"); 
saveAs("Results", output +"Results"+".csv");
close()
waitForUser("Processing Complete!");

function processFolder(input) {
	list = getFileList(input);
	list = Array.sort(list);
	for (i = 0; i < list.length; i++) {
/*		if(File.isDirectory(input + File.separator + list[i]))
			processFolder(input + File.separator + list[i]);*/
		if(endsWith(list[i], suffix))
			processFile(input, output, list[i]);
	}
}
	
function processFile(input, output, file) {	
	if(n == 0){
	roiManager("reset");
	setBatchMode(false);//allows for user interaction
	setTool("line");//Draw scalebar
	open(input + File.separator + file); //open photo
	waitForUser("Draw scalebar, check global on next screen");//pause and popup	
	run("Set Scale...");//set scale
	setTool(0);//Box selection
	waitForUser("Select petri plate");//select crop area or ROI
	roiManager("add")
	roiManager("Select", 0);//select crop area
	run("Crop");//crop to ROI
	run("8-bit");//turn 8 bit greyscale
	setThreshold(0, 225);
	run("Convert to Mask");// turn b&w
	run("Fill Holes");//Fill holes
	setThreshold(250, 255);//Find colony
	run("Create Selection");//select colony
	run("Measure");//measure colony area
	setBatchMode(true);//Headless
	n++;
} else {
	open(input + File.separator + file);
	run("8-bit");//turn 8 bit greyscale
	roiManager("Select", 0);//select crop area
	run("Crop");//crop to ROI
	setThreshold(0, 225);
	run("Convert to Mask");// turn b&w
	run("Fill Holes");//Fill holes
	setThreshold(250, 255);//Find colony
	run("Create Selection");//select colony
	run("Measure");//measure colony area
}
save(output+ File.separator + file);
}
}
}