1. A system for stereoscopically imaging at least a portion of one or more samples, comprising: a stage configured to support a sample; an illumination source configured to illuminate at least a portion of the sample; collection optics defining a collection path, the collection optics configured to receive illumination transmitted through or reflected from a surface of the sample, and further configured to direct a first portion of the illumination along a first imaging path to a first detector and a second portion of the illumination along a second imaging path to a second detector; a wave front coder disposed along the collection path, the wave front coder configured to induce one or more imaging effects, at least by phase shifting the illumination directed along the collection path; and at least one computing system communicatively coupled to the first detector and the second detector, the at least one computing system configured to acquire a first image from the first detector and a second image from the second detector, and further configured to filter the first image and the second image to remove at least a portion of the one or more imaging effects induced by the wave front coder.