input = getDirectory("Input directory");
output = getDirectory("Output directory");
processFolder(input);

print ("1");

function processFolder(input) {
    FolderList = getFileList(input);
	print ("processing" + input)
    for (i = 0; i < FolderList.length; i++) {

	folderItem = FolderList[i];
	print ("2");
	//isFolderDirectory is either true, or false
	isFolderItemADirectory = File.isDirectory(folderItem);
	print ("3");
		if(isFolderItemADirectory) {
    	//folderItem is a directory, process it a a folder
    	processFolder(input + "/" + FolderList[i]);
    	print ("4");
		}
	//folderItem is not a directory, so lets see if its an image
	doesFolderItemEndsWithTif = endsWith(folderItem, ".tif");
	print ("5");
		if(doesFolderItemEndsWithTif ) {
    	processFile(folderItem);
    	print ("6");
		}
	}
}

function processFile(folderItem) {
    run("Image Sequence...", "open=[folderItem]  number=300 starting=1 increment=1 sort ");
    print ("7");
    run("Set Scale...", "distance=1 known=6.6 pixel=1 unit=µm global");

    //Rescale: depth = number of images
    run("Scale...", "x=0.75 y=0.75 z=1.0 width=960 height=384 depth=300 interpolation=Bilinear average process create");

    run("Scale Bar...", "width=500 height=10 font=40 color=White background=None location=[Lower Right] bold overlay label");

    //Change label position depending on rescale
    run("Label...", "format=0 starting=0 interval=1 x=800 y=50 font=40 text=ms range=1-300 use");

    //Save as video
    saveAs("AVI... ", "compression=JPEG frame=30 output + File.separator + FolderList");
    close()
}

print ("done");