Improvements to user interfaces for ophthalmic imaging systems, in particular Optical Coherence Tomography (OCT) systems are described to improve how diagnostic data are displayed, analyzed and presented to the user. The improvements include user customization of display and reports, protocol driven work flow, bookmarking of particular B-scans, accessing information from a reference library, customized normative databases, and ordering of follow-up scans directly from a review screen. A further aspect is the ability to optimize the contrast and quality of displayed B-scans using a single control parameter. Virtual real time z-tracking is described that maintains displayed data in the same depth location regardless of motion.