In working with video and animation in Jitter, it’s important to remember that the effect of continuous motion is achieved by successive discrete images, each somewhat different from the preceding one. You can create that effect in 2D animation by repositioning graphic objects for each frame, according to a particular trajectory, such that the objects seem to be moving.
To do animation in 3D, you need to learn about the jit.gl.* family of Jitter objects. To animate MIDI notes as 3D objects, you’ll need to decide what aspect of the note data you want to map to what aspect of the 3D objects. Here's about the simplest possible patch one could make for visualizing a MIDI note; the pitch of the most recently played note is used to determine the horizontal location of a sphere.