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This is not only a problem in mechanics but first and foremost a problem in style. A Disney-like animation and claymation such as Wallace & Gromet, for example, or figures such as the Muppets present radically different qualities of style. Imagine Disney's Beauty and the Beast as a claymation cartoon, or W&G with Big Bird.
Once you've decided how you want your figure to look you can determine how to move it. Stop motion — shooting a single frame at a time, then moving the puppet — could be a way of animating this project; very time-consuming and not for the faint of heart. Or you could have the puppet sit in front of the camera until there was a logical moment in the action for it to move, move it to a new position, continue shooting. Or you could use rods attached to limbs like the Muppets.
I would prefer a bunraku approach. This style was developed by Japanese performers in the 17th century and has been used ever since. A large articulated figure is moved about by a person clad entirely in black (body, hands, head and face.) Performed against a black background the human all but disappears. Of course we know it's there but our focus is entirely on the figure(s) being animated. Think Jeff Dunham, who animates his puppet figures while he talks. We know its only a puppet but each puppet character comes "alive" before us.
In your question you imply that having the manipulator be seen is to be avoided. Why not embrace a style which includes the manipulator?