The system includes a light source that emits partially coherent or coherent light split into a reference beam and an object beam and a stage that supports a workpiece in a path of the object beam that is transmitted through the workpiece. A first beam splitter combines the reference beam with the object beam transmitted through the workpiece into a combined beam, and a camera detects the combined beam. A processor generates a first interference image of the workpiece based on the combined beam, determines amplitude and phase information of the object beam based on the first interference image, generates a plurality of depth images of the workpiece based on the amplitude and phase information, determines a focus score of each pixel of the plurality of depth images, and generates a first 3D map of the workpiece based on the focus scores, which includes depth-integrated refractive index (DIRI) information.