Stop motion video is created with a still camera or an animation camera on a tripod or, if you have a bunch of money in the budget, a motion control rig. You take a photo, move the elements in your scene, then take another and so on. Most stop motion is shot at 1 for 2. That means if you want one second of video at 24 frames per second you only shoot 12 pictures then in AE you interpret your image sequence as 12 fps and put it in a 24 fps comp.
That's the same trick used on most cell animation cartoons from Bugs Bunny (1940) to the Rocky and Bullwinkle Show (1959), to the Simpsons (1987). Stop motion projects from California Raisins (1989) to Wallis and Gromit use 1 for 2 techniques. The motion has a unique look and it cuts production time in half.