Combining stop motion clips into one?

Hi I am trying to create a stop motion music video(1 minute long) but considering what is the best method to take. Everything in the scene will be moving through stop motion. Can I create separate motion clips for each element in the movie and then combine them in layers in after effects and using the transparency to get rid of the background information in each clip(im using just a white background)
OR will I need to do the stop motion with all the elements moving together?
Help! Thanks

You could do it that way, using a white background and making that transparent. Making white disappear is not trivial.
But "create separate motion clips for each element in the movie and then combine them in layers in after effects and using the transparency to get rid of the background information" is a highly unusual way to approach stop motion. You would only do it that way if your individual elements or characters do not interact with each other in any physical or implied way on your set. I think most of us would use a dedicated stop motion application with onion skinning and variable playback to an external monitor, create scenes with all active elements, edit the scenes together with music and sound effects and dialog in a video editor and use After Effects for effects and compositing.
Have you done stop motion before? If so, what made you decide to, or what about this particular project suggests that you try this approach?

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