One or more embodiments of an apparatus, system and method of compensating image data for phase fluctuations caused by a wave deforming medium, and storage or recording mediums for use therewith, are provided herein. At least one embodiment of the method comprises capturing, by a sensor of an imaging system, first image data and second image data for each of a plurality of pixel positions of the sensor, the sensor capturing an object through a wave deforming medium causing a defocus disparity between the first image data and second image data; and determining the defocus disparity between the first image data and the second image data, the defocus disparity corresponding to a defocus wavefront deviation of the wave deforming medium. The method may further comprise compensating the image data captured by the sensor for phase fluctuations caused by the wave deforming medium using the determined defocus disparity.