A three-dimensional image of the eardrum is automatically registered. In one aspect, a three-dimensional image (e.g., depth map) of an eardrum is produced from four-dimensional light field data captured by a light field otoscope. The three-dimensional image is registered according to a predefined standard form. The eardrum is then classified based on the registered three-dimensional image. Registration may include compensation for out-of-plane rotation (tilt), for in-plane rotation, for center location, for translation, and/or for scaling.