I do have another question: I was able to obtain cropped images for all the images using a batch process (thanks again), and now I am hoping I can take all of these outputted images and create an animated gif or a video. I know this is possible to do with a stack of images, but is this also possible using an output directory from a batch process? I am a little foggy about when to use batch processes vs stacks vs virtual stacks.
You can do File > Import > Image Sequence… to load all of your TIFFs as a stack. (Default is to load all the images in a file. Order is determined by filenames.)
Then File > Save As > AVI or Animated GIF.
Hope this helps.