Abstract: The methods described herein are methods to ascertain motion contrast within optical coherence tomography data based upon phase variance. The phase variance contrast observes the nanometer scale motion of scatterers associated with Brownian motion and other non-flow motion. The inventive method of calculating motion contrast from the phase variance can differentiate regions of different mobility based on the motion contrast differences, and can use the phase information to characterize mobility properties of the scatterers. In flow regions, the inventive method for acquiring and analyzing motion contrast can identify the regions as well as characterize the motion. Furthermore, the inventive method can determine quantitative flow estimation, the index of refraction variations, and absorption variations within flow regions.