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Adaptive optics (AO) and optical coherence tomography (OCT) are powerful imaging modalities that, when combined, can provide high-resolution, 3-D, in vivo images of the retina. We will discuss general techniques for characterizing a vision science AO system, and we will describe the results of applying these techniques to measure the residual wavefront errors for the UC Davis AO-OCT system. Careful characterization of the AO system will lead to improved performance and inform the design of future systems.