Here is what Orion Tait, CD at Buck NYC had to say about the process:
Footage was used as an animation guide for the main character. Augenblick studios animated the main character,
and our team did the rest (as a hybrid of 2d cel and 3d animation). For the character, we shot Thomas on a treadmill and constructed an edit. We then illustrated style-frames based on stills from that edit (which you can see up on the site).
The edit and style frames then went to Aaron and his team for cel animation. They are very traditional in their approach, which you can really see from their work on superjail. They used the footage as reference to layout key frames, and then started closing the gap with in-betweens, until they got to a fluid 30fps animation. This allowed them to nail the timing and loose look of the illustration and introduce the morphing animation, all while maintaining nice fluid, stylish animation that most rotoscoping lacks.