//qFunctions
function montageMaker(dir)	{
	// get name of original image and use a modified form for save at the end
	win = getTitle();
	// check how many slices/channels
	Stack.getDimensions(width, height, channels, slices, frames);
	getPixelSize(unit, pixelWidth, pixelHeight);
	run("Stack to Images");
	numImages = nImages;
	imgArray = newArray(numImages);
	colArray = newArray(numImages);
	mArray = newArray(numImages + 1);
	mArray[0] = "*None*";
	grayChoiceArray = newArray(numImages);
	for (i=0; i<numImages; i++)	{
		selectImage(i+1);
		run("Grays");
		imgArray[i] = getImageID();
		title = getTitle();
		colArray[i] = title;
		mArray[i+1] = title;
		grayChoiceArray[i] = d2s(i+1,0);
	}
	// give the option of making up to 2 merges
	Dialog.create("Montage Choice");
	Dialog.addMessage("How many grayscale panels?");
	Dialog.addChoice("Gray panels", grayChoiceArray);
	Dialog.addMessage("How many merge panels?");
	Dialog.addChoice("Merge panels", newArray("0","1","2"));
	Dialog.addCheckbox("Vertical montage?", false);
	Dialog.show();
	gPanels = Dialog.getChoice();
	mPanels = Dialog.getChoice();
	vChoice = Dialog.getCheckbox();

	setBatchMode(true);
	// if vertical montage, rotate all images left
	if (vChoice == true) {
		for (i = 0; i < numImages; i ++)	{
			selectImage(i+1);
			run("Rotate 90 Degrees Left");
		}
	}
	// Image choices
	gVar = parseInt(gPanels);
	mVar = parseInt(mPanels);
	// Make arrays to hold image choices
	gNameArray = newArray(gVar);
	if (mVar == 1) {
		m1NameArray = newArray(7);
	}
	else if (mVar == 2) {
		m1NameArray = newArray(7);
		m2NameArray = newArray(7);
	}

	// Next dialog
	grout = 8;
	Dialog.create("Pick your panels");
	Dialog.addMessage("Select order for grayscale");
	// variations based on number of files
	if (gVar==1)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
	}
	else if (gVar==2)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
	}
	else if (gVar==3)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
	}
	else if (gVar==4)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
	}
	else if (gVar==5)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
		Dialog.addChoice("G5 Gray Panel 5", colArray);
	}
	else if (gVar==6)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
		Dialog.addChoice("G5 Gray Panel 5", colArray);
		Dialog.addChoice("G6 Gray Panel 6", colArray);
	}
	else if (gVar==7)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
		Dialog.addChoice("G5 Gray Panel 5", colArray);
		Dialog.addChoice("G6 Gray Panel 6", colArray);
		Dialog.addChoice("G7 Gray Panel 7", colArray);
	}
	// variations based on merges
	if (mVar==0)	{
	}
	else if (mVar==1)	{
		Dialog.addMessage("Select channels for merge");
		Dialog.addChoice("Red", mArray);
		Dialog.addChoice("Green", mArray);
		Dialog.addChoice("Blue", mArray);
		Dialog.addChoice("Gray", mArray);
		Dialog.addChoice("Cyan", mArray);
		Dialog.addChoice("Magenta", mArray);
		Dialog.addChoice("Yellow", mArray);
	}
	else if (mVar==2)	{
		Dialog.addMessage("Select channels for 1st merge");
		Dialog.addChoice("R1 Red", mArray);
		Dialog.addChoice("G1 Green", mArray);
		Dialog.addChoice("B1 Blue", mArray);
		Dialog.addChoice("Gy1 Gray", mArray);
		Dialog.addChoice("Cn1 Cyan", mArray);
		Dialog.addChoice("Ma1 Magenta", mArray);
		Dialog.addChoice("Yw1 Yellow", mArray);
		Dialog.addMessage("Select channels for 2nd merge");
		Dialog.addChoice("R2 Red", mArray);
		Dialog.addChoice("G2 Green", mArray);
		Dialog.addChoice("B2 Blue", mArray);
		Dialog.addChoice("Gy2 Gray", mArray);
		Dialog.addChoice("Cn2 Cyan", mArray);
		Dialog.addChoice("Ma2 Magenta", mArray);
		Dialog.addChoice("Yw2 Yellow", mArray);
	}
	Dialog.addNumber("Grout size (pixels):", grout);
	Dialog.addNumber("dpi", 300);
	Dialog.addCheckbox("Include scale bar?", false);
	Dialog.addNumber("Scale bar size (µm):", 10);
	Dialog.addNumber("Scaling, 1 px is how many µm?", pixelWidth);
	Dialog.addMessage("If the scale is 0.069, check the actual pixel size of your image.")
	Dialog.show();
	// variations based on channels
	if (gVar==1)	{
		gNameArray[0] = Dialog.getChoice();
	}
	else if (gVar==2)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
	}
	else if (gVar==3)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
	}
	else if (gVar==4)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
	}
	else if (gVar==5)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
	}
	else if (gVar==6)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
		gNameArray[5] = Dialog.getChoice();
	}
	else if (gVar==7)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
		gNameArray[5] = Dialog.getChoice();
		gNameArray[6] = Dialog.getChoice();
	}
	// variations based on merges
	if (mVar==0)	{
	}
	else if (mVar==1)	{
		m1NameArray[0] = Dialog.getChoice();
		m1NameArray[1] = Dialog.getChoice();
		m1NameArray[2] = Dialog.getChoice();
		m1NameArray[3] = Dialog.getChoice();
		m1NameArray[4] = Dialog.getChoice();
		m1NameArray[5] = Dialog.getChoice();
		m1NameArray[6] = Dialog.getChoice();
	}
	else if (mVar==2)	{
		m1NameArray[0] = Dialog.getChoice();
		m1NameArray[1] = Dialog.getChoice();
		m1NameArray[2] = Dialog.getChoice();
		m1NameArray[3] = Dialog.getChoice();
		m1NameArray[4] = Dialog.getChoice();
		m1NameArray[5] = Dialog.getChoice();
		m1NameArray[6] = Dialog.getChoice();
		m2NameArray[0] = Dialog.getChoice();
		m2NameArray[1] = Dialog.getChoice();
		m2NameArray[2] = Dialog.getChoice();
		m2NameArray[3] = Dialog.getChoice();
		m2NameArray[4] = Dialog.getChoice();
		m2NameArray[5] = Dialog.getChoice();
		m2NameArray[6] = Dialog.getChoice();
	}
	grout = Dialog.getNumber();
	res = Dialog.getNumber();
	sbchoice = Dialog.getCheckbox();
	sblen = Dialog.getNumber();
	mag = Dialog.getNumber();
	// decisions collected

	// collect details from images
	newName = "mtg_" + safeName(win);
	if (mVar==0)	{
		m1NameArray = newArray(0);
		m2NameArray = newArray(0);
	}    else if (mVar==1)	{
		m2NameArray = newArray(0);
	}
	generateMontage(newName, vChoice, gVar, mVar, ww, hh, grout, res, sbchoice, sblen, mag, gNameArray, m1NameArray, m2NameArray);

	//save montage
	path = dir + newName;
	if(!endsWith(path, ".tif")) {
		path = path + ".tif";
	}
	saveAs("TIFF", path);
	setBatchMode(false);
	// close originals
	for (i = 0; i < imgArray.length; i ++)	{
		selectImage(imgArray[i]);
		close();
	}
}

// this function will either make a montage from every tif in the source Directory
// or it will make a stacked montage. opt is boolean to select behaviour
// dir1 is the input Directory
// dir2 is the output Directory
// origName is the originating filename, "none" if opt is true (not used)
function montageMakerMulti(dir1, dir2, opt, origName)	{

	list = getFileList(dir1);

	tiffnum = 0;
	if(opt == true) {
		// How many TIFFs do we have? Directory could contain other directories.
		for (i = 0; i < list.length; i ++) {
			if (endsWith(toLowerCase(list[i]), ".tif"))
				tiffnum = tiffnum + 1;
		}
	 	tifflist = newArray(tiffnum);
		mtglist = newArray(tiffnum);
		j = 0;
		for (i = 0; i < list.length; i ++) {
			if (endsWith(toLowerCase(list[i]), ".tif")) {
				tifflist[j] = list[i];
				mtglist[j] = "mtg_" + safeName(list[i]) + ".tif";
				j = j + 1;
			}
		}
	} else {
		// How many mmTemp TIFFs do we have? Directory could contain other directories.
		for (i = 0; i < list.length; i ++) {
			if (startsWith(list[i], "mmTemp") && endsWith(toLowerCase(list[i]), ".tif"))
				tiffnum = tiffnum + 1;
		}
	 	tifflist = newArray(tiffnum);
		mtglist = newArray(tiffnum);
		j = 0;
		for (i = 0; i < list.length; i ++) {
			if (startsWith(list[i], "mmTemp") && endsWith(toLowerCase(list[i]), ".tif")) {
				tifflist[j] = list[i];
				mtglist[j] = "mtg_" + list[i] + ".tif";
				j = j + 1;
			}
		}
	}
	// check we actually have tiffs to process
	if(tiffnum == 0) exit("No TIFFs to process!");

	// make the choice of what we will do
	Dialog.create("Montage Choice");
	Dialog.addMessage("How many grayscale panels?");
	Dialog.addChoice("Gray panels", newArray("1","2","3","4","5","6","7"));
	Dialog.addMessage("How many merge panels?");
	Dialog.addChoice("Merge panels", newArray("0","1","2"));
	Dialog.addCheckbox("Vertical montage?", false);
	Dialog.show();
	gPanels = Dialog.getChoice();
	mPanels = Dialog.getChoice();
	vChoice = Dialog.getCheckbox();

	// Image choices
	gVar = parseInt(gPanels);
	mVar = parseInt(mPanels);
	// Make arrays to hold image choices
	gNameArray = newArray(gVar);
	if (mVar == 1) {
		m1NameArray = newArray(7);
	}
	else if (mVar == 2) {
		m1NameArray = newArray(7);
		m2NameArray = newArray(7);
	}

	// for colArray and mArray we don't know what we have but we have 7 channel max
	colArray = newArray("C1","C2","C3","C4","C5","C6","C7");
	mArray = newArray("*None*","C1","C2","C3","C4","C5","C6","C7");

	//Next dialog
	grout = 8;
	Dialog.create("Pick your panels");
	Dialog.addMessage("Select order for grayscale");
	// variations based on number of files
	if (gVar==1)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
	}
	else if (gVar==2)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
	}
	else if (gVar==3)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
	}
	else if (gVar==4)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
	}
	else if (gVar==5)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
		Dialog.addChoice("G5 Gray Panel 5", colArray);
	}
	else if (gVar==6)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
		Dialog.addChoice("G5 Gray Panel 5", colArray);
		Dialog.addChoice("G6 Gray Panel 6", colArray);
	}
	else if (gVar==7)	{
		Dialog.addChoice("G1 Gray Panel 1", colArray);
		Dialog.addChoice("G2 Gray Panel 2", colArray);
		Dialog.addChoice("G3 Gray Panel 3", colArray);
		Dialog.addChoice("G4 Gray Panel 4", colArray);
		Dialog.addChoice("G5 Gray Panel 5", colArray);
		Dialog.addChoice("G6 Gray Panel 6", colArray);
		Dialog.addChoice("G7 Gray Panel 7", colArray);
	}
	// variations based on merges
	if (mVar==0)	{
	}
  else if (mVar==1)	{
		Dialog.addMessage("Select channels for merge");
		Dialog.addChoice("Red", mArray);
		Dialog.addChoice("Green", mArray);
		Dialog.addChoice("Blue", mArray);
		Dialog.addChoice("Gray", mArray);
		Dialog.addChoice("Cyan", mArray);
		Dialog.addChoice("Magenta", mArray);
		Dialog.addChoice("Yellow", mArray);
	}
	else if (mVar==2)	{
		Dialog.addMessage("Select channels for 1st merge");
		Dialog.addChoice("R1 Red", mArray);
		Dialog.addChoice("G1 Green", mArray);
		Dialog.addChoice("B1 Blue", mArray);
		Dialog.addChoice("Gy1 Gray", mArray);
		Dialog.addChoice("Cn1 Cyan", mArray);
		Dialog.addChoice("Ma1 Magenta", mArray);
		Dialog.addChoice("Yw1 Yellow", mArray);
		Dialog.addMessage("Select channels for 2nd merge");
		Dialog.addChoice("R2 Red", mArray);
		Dialog.addChoice("G2 Green", mArray);
		Dialog.addChoice("B2 Blue", mArray);
		Dialog.addChoice("Gy2 Gray", mArray);
		Dialog.addChoice("Cn2 Cyan", mArray);
		Dialog.addChoice("Ma2 Magenta", mArray);
		Dialog.addChoice("Yw2 Yellow", mArray);
	}

	Dialog.addNumber("Grout size (pixels):", 8);
	Dialog.addNumber("dpi", 300);
	Dialog.addCheckbox("Include scale bar?", false);
	Dialog.addNumber("Scale bar size (µm):", 10);
	Dialog.addNumber("Scaling,1 px is how many µm?", 0.069);
	Dialog.show();
	// variations based on channels
	if (gVar==1)	{
		gNameArray[0] = Dialog.getChoice();
	}
	else if (gVar==2)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
	}
	else if (gVar==3)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
	}
	else if (gVar==4)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
	}
	else if (gVar==5)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
	}
	else if (gVar==6)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
		gNameArray[5] = Dialog.getChoice();
	}
	else if (gVar==7)	{
		gNameArray[0] = Dialog.getChoice();
		gNameArray[1] = Dialog.getChoice();
		gNameArray[2] = Dialog.getChoice();
		gNameArray[3] = Dialog.getChoice();
		gNameArray[4] = Dialog.getChoice();
		gNameArray[5] = Dialog.getChoice();
		gNameArray[6] = Dialog.getChoice();
	}
	// variations based on merges
	if (mVar==0)	{
	}
	else if (mVar==1)	{
		m1NameArray[0] = Dialog.getChoice();
		m1NameArray[1] = Dialog.getChoice();
		m1NameArray[2] = Dialog.getChoice();
		m1NameArray[3] = Dialog.getChoice();
		m1NameArray[4] = Dialog.getChoice();
		m1NameArray[5] = Dialog.getChoice();
		m1NameArray[6] = Dialog.getChoice();
	}
	else if (mVar==2)	{
		m1NameArray[0] = Dialog.getChoice();
		m1NameArray[1] = Dialog.getChoice();
		m1NameArray[2] = Dialog.getChoice();
		m1NameArray[3] = Dialog.getChoice();
		m1NameArray[4] = Dialog.getChoice();
		m1NameArray[5] = Dialog.getChoice();
		m1NameArray[6] = Dialog.getChoice();
		m2NameArray[0] = Dialog.getChoice();
		m2NameArray[1] = Dialog.getChoice();
		m2NameArray[2] = Dialog.getChoice();
		m2NameArray[3] = Dialog.getChoice();
		m2NameArray[4] = Dialog.getChoice();
		m2NameArray[5] = Dialog.getChoice();
		m2NameArray[6] = Dialog.getChoice();
	}
	grout = Dialog.getNumber();
	res = Dialog.getNumber();
	sbchoice = Dialog.getCheckbox();
	sblen = Dialog.getNumber();
	mag = Dialog.getNumber();
	// decisions collected

	setBatchMode(true);
	for (i = 0; i < tifflist.length; i ++)	{
		input = dir1 + tifflist[i];
		output = dir2 + mtglist[i];
		open(input);
		win = getTitle();
		getDimensions(ww, hh, cc, ss, ff);
		okVar = checkImageForMontage(win);
		if (okVar == true) {
			newName = mtglist[i];
      // if vertical montage, rotate all images left
    	if (vChoice == true) run("Rotate 90 Degrees Left");
			// first we will split the stack and make an array of the correct order
			run("Stack to Images");
			theWinList = getListOfImages();
			gWinArray = convertChoicesToWindows(gNameArray,theWinList);
			if (mVar==0)	{
				m1WinArray = newArray(0);
				m2WinArray = newArray(0);
			}    else if (mVar==1)	{
				m1WinArray = convertChoicesToWindows(m1NameArray,theWinList);
				m2WinArray = newArray(0);
			}    else if (mVar==2)	{
				m1WinArray = convertChoicesToWindows(m1NameArray,theWinList);
				m2WinArray = convertChoicesToWindows(m2NameArray,theWinList);
			}
			generateMontage(newName, vChoice, gVar, mVar, ww, hh, grout, res, sbchoice, sblen, mag, gWinArray, m1WinArray, m2WinArray);
			// save montage
			if(!endsWith(output, ".tif")) {
				output = output + ".tif";
			}
			saveAs("TIFF", output);
			run("Close All");
		}
	}
	// if we are processing a stack montage, we need to stack them and clean up
	if (opt == false) {
		// stack the montages
		File.openSequence(dir2, "filter=(^mtg_mmTemp) step=1 scale = 100.0");
		newName = "mtg_" + safeName(origName);
		rename(newName);
		// clean up
		for (i = 0; i < tifflist.length; i ++) {
			ok = File.delete(dir1 + tifflist[i]);
		}
		for (i = 0; i < mtglist.length; i ++) {
			ok = File.delete(dir2 + mtglist[i]);
		}
		output = dir2 + newName;
		// save montage
		if(!endsWith(output, ".tif")) {
			output = output + ".tif";
		}
		saveAs("TIFF", output);
		run("Close All");
	}
	setBatchMode(false);
}

function mtgcomp()	{
	imgArray = newArray(nImages);
	rowArray = newArray(nImages);
	nameArray = newArray(nImages);
	widthArray = newArray(nImages);
	heightArray = newArray(nImages);
	for (i = 0; i < nImages; i ++)	{
		selectImage(i + 1);
		imgArray[i] = getImageID();
		title = getTitle();
		rowArray[i] = title;
		getDimensions(ww, hh, cc, ss, ff);
		widthArray[i] = ww;
		heightArray[i] = hh;
	}
	// check the widths are the same;
	Array.getStatistics(widthArray, min, max, mean, stdDev);
	if (stdDev != 0) exit ("Images have unequal widths");
	theWidth = mean;
	// check the widths are the same;
	Array.getStatistics(heightArray, min, max, mean, stdDev);
	if (stdDev != 0) exit ("Images have unequal heights");
	theHeight = mean;
	// vChoice is true if we will compile columns horizontally
	// vChoice is false (default) means compiling rows vertically
	vChoice = false;
	if (theHeight > theWidth) vChoice = true;
	len = imgArray.length;

	// Standard sizes
	grout = 16;
	res = 300;
	sblen = 10;
	mag = 0.069;
	// Make dialog box
	Dialog.create("Compile the montages");
	// variations based on number of files
	if (vChoice == true)	{
		Dialog.addMessage("Detected columns.\rSelect order for your compilation, left to right");
	}
	else {
		Dialog.addMessage("Detected rows.\rSelect order for your compilation, top to bottom");
	}
	for (i = 0; i < len; i ++)	{
		labStr = d2s(i+1,0);
		Dialog.addChoice(labStr, rowArray);
	}
	Dialog.addNumber("Row gap (px, default = 2 x grout):", 16);
	Dialog.addNumber("dpi", 300);
	Dialog.addCheckbox("Include scale bar?", false);
	Dialog.addNumber("Scale bar size (µm):", 10);
	Dialog.addNumber("Scaling, 1 px is how many µm?", 0.069);
	Dialog.addCheckbox("Force other orientation:", false);
	Dialog.show();
	// variations based on number of files
	for (i = 0; i < len; i ++)	{
		nameArray[i] = Dialog.getChoice();
	}
	grout = Dialog.getNumber();
	res = Dialog.getNumber();
	sbchoice = Dialog.getCheckbox();
	sblen = Dialog.getNumber();
	mag = Dialog.getNumber();
	forceChoice = Dialog.getCheckbox();
	// forceChoice reverses the logic of vChoice
	if(vChoice == true && forceChoice == true) vChoice = false;
	else if(vChoice == false && forceChoice == true) vChoice = true;
	// decisions collected
	setBatchMode(true);

	// setup for save
	win = getTitle();
	dir1 = getDirectory("image");
	newName = "cmp" + len + win;

	// get dimensions
	wArray = newArray(len);
	hArray = newArray(len);
	hPosArray = newArray(len+1);
	hPosArray[0] = 0;
	width = 0;
	height = 0;
	for (i=0; i<len; i++)	 {
		selectImage(nameArray[i]);
		if (vChoice == true)
			run("Rotate 90 Degrees Right");
		getDimensions(w, h, c, slices, frames);
		wArray[i] = w;
		hArray[i] = h;
		hPosArray[i+1] = hPosArray[i] + h;
		width = width + w;
		height = height + h;
	}
	// check widths are the same
	if (width / len != w)	{
		print("Check widths");
	}
	newImage(newName, "RGB", w, height + (grout * (len - 1)), 1);
	for (i=0; i<len; i++)	 {
		selectImage(nameArray[i]);
		run("Select All");
		run("Copy");
		close();
		selectImage(newName);
		makeRectangle(0, (hPosArray[i])+(grout*i), wArray[i], hArray[i]);
		run("Paste");
	}
	// now put back?
	if (vChoice == true)
		run("Rotate 90 Degrees Left");
	//add scale bar (height is same as grout)
	if (sbchoice==true)	{
		getDimensions(w, h, c, slices, frames);
		setColor(255,255,255);
		fillRect(w-((grout/2)+(sblen/mag)), h-(2*(grout/2)), sblen/mag, grout/2);
	}
	//specify dpi default is 300 dpi
	run("Set Scale...", "distance=res known=1 unit=inch");
	run("Select None");
	//save montage
	path = dir1 + newName;
	if(!endsWith(path, ".tif")) {
		path = path + ".tif";
	}
	saveAs("TIFF", path);
	// save a log file
	path = substring(path,0,lengthOf(path) - 4) + ".txt";
	f = File.open(path);
		print(f, "MONTAGE COMPILER");
		print(f, "Name of Montage:");
		print(f, newName);
		if(vChoice == true) {
			print(f, "Montage of columns (left to right):");
		} else{
			print(f, "Montage of rows (top to bottom):");
		}
		for (i=0; i<len; i++)	 {
			print(f, d2s(i+1,0) + " - " + nameArray[i]);
		}
		print(f, "Grout: " + grout);
		if(sbchoice == true) {
			print(f, "Scale bar: " + sblen + " um. Pixel size: " + mag);
		}
	File.close(f);
	setBatchMode(false);
}

function safeName(s)	{
	// need to replace some characters to allow save to work properly
	s = replace(s,"c:","");
	s = replace(s,"/","");
	s = replace(s,"\\(","");
	s = replace(s,"\\)","");
	s = replace(s,".tif","");
	s = replace(s," ","_");
	return s;
}

function checkImageForMontage(name)	{
	selectWindow(name);
	checker = false;
	// determine what we are dealing width
	getDimensions(ww, hh, cc, ss, ff);
	// warn if image is not square
	if (ww != hh) print("Input image is not square");
	//
	if (bitDepth() == 8 || bitDepth() == 16) {
		if (cc == 1) exit ("Need more than one channel");
		if (cc * ss * ff == 1) exit ("Need more than one channel, slice, or frame");
		if (ss > 1 && ff > 1) exit ("Reduce dimensions before making montage");
		if (cc > 1 && ss * ff == 1) checker = true;
		// if cc is 1 or more AND either ss or ff is > 1; checker stays false
	} else if (bitDepth() == 24 && ss * ff == 1)	{
		run("Split Channels");
		run("Images to Stack");
		checker = true;
	} else exit ("Input image does not meet requirements for montage");
	return checker;
}

function getListOfImages()	{
	numImages = nImages;
	winArray = newArray(numImages);
	for (i = 0; i < numImages; i ++)	{
		selectImage(i + 1);
		winArray[i] = getTitle();
		// ensure grayscale while we are here
		run("Grays");
	}
	return winArray;
}

function convertChoicesToWindows(choiceArray,winArray)	{
	convertedArray = newArray(choiceArray.length);
	for (i = 0; i < choiceArray.length; i ++)	 {
		arrayItem = choiceArray[i];
		if (choiceArray[i] == "*None*")	{
			convertedArray[i] = "*None*";
		} else	{
			lookupInteger = parseInt(replace(arrayItem,"C",""));
			convertedArray[i] = winArray[lookupInteger - 1];
		}
	}
	return convertedArray;
}

function generateMontage(newName, vChoice, gVar, mVar, width, height, grout, res, sbchoice, sblen, mag, gNameArray, m1NameArray, m2NameArray)	{
	len = gVar + mVar;
	newImage(newName, "RGB", ((width * len) + (grout * (len - 1))), height, 1);
	// paste in grayscales
	for (j = 0; j < gVar; j++)	 {
		wName = gNameArray[j];
		selectImage(wName);
		run("Copy");
		selectImage(newName);
		makeRectangle((width * j) + (grout * j), 0, width, height);
		run("Paste");
	}

	// build mergeString(s)
	merge1String = "";
	merge2String = "";

	for (i = 0; i < 7; i++)	 {
		if (mVar > 0) merge1String += "c" + d2s(i+1,0) + "=[" + m1NameArray[i] + "] ";
		if (mVar == 2) merge2String += "c" + d2s(i+1,0) + "=[" + m2NameArray[i] + "] ";
	}
	merge1String += "keep";
	merge2String += "keep";
	// make array to hold merge names
	mImgArray = newArray("merge1","merge2");

	// paste in the merge(s)
	for (i = 0; i < mVar; i++)	 {
		if (i == 0) {
			run("Merge Channels...", merge1String);
			rename("merge1");
		} else {
			run("Merge Channels...", merge2String);
			rename("merge2");
		}
		selectImage(mImgArray[i]);
		run("Copy");
		selectImage(newName);
		makeRectangle(((width * gVar) + (grout * gVar)) + ((width * i) + (grout * i)), 0, width, height);
		run("Paste");
	}
	selectImage(newName);
	// rotate right?
	if (vChoice == true)
		run("Rotate 90 Degrees Right");

	// add scale bar (height of bar is same as grout)?
	if (sbchoice==true)	{
		getDimensions(w, h, c, slices, frames);
		setColor(255,255,255);
		fillRect(w - (grout + (sblen / mag)), h - (2 * grout), sblen / mag, grout);
	}
	// specify dpi default is 300 dpi
	run("Set Scale...", "distance=" + res + " known=1 unit=inch");
	run("Select None");
}