I started with a 2D illustration I had done of open heart surgery. All of the art was done in Photoshop, except for the device. The animation was done in Flash, almost entirely with bitmaps instead of vector art. I took apart some of the anatomy within the chest cavity of the image and made some PNG files with transparency. Then I brought them into Flash and scaled and warped them to create the simulation of the heart beating. This short series of symbols were then looped in the background so the heart would beat throughout.
I used Strata 3D to create the bitmaps of the device. I rotated the model and output images as I needed. When I needed a true rotation of the device in the animation, I would set it up in my 3d app and output a series of bitmaps (PNG's with transparency) to be imported to the Flash timeline to achieve the rotation.
For the surgeon's hands, I used my own gloved hands and photographed them, photoshoped them to match the art style, and broke them apart into palm, fingers, and thumb. I put those parts on different layers in Flash so that I could appear to hold things in the animation. If my hand or thumb needed to appear to rotate, them I took extra photos at several angles of rotation, and used them as a series of frames in Flash.
I used Swift3D for the rotating logo.
I have done another of this type of animation, where I stood in both for the patient and the surgeon's hands. You can view it at http://www.paulpetersen.net/biopsy