Methods and a computer readable medium for deriving a quantitative phase contrast tomographic image of a specimen. The specimen is illuminated and a focus of the illuminating light is scanned to a plurality of depths within the specimen. Light transmitted through the specimen is spatially Fourier transformed at each of the plurality of depths to form a spatially transformed image, and at least one of the phase and amplitude of a plurality of spatial frequency components of the spatially transformed image is spatially modulated. An intensity image of the specimen plane as modulated with respect to spatial frequency components is detected and deconvolved at a plurality of spatially modulated instances to obtain a three-dimensional phase representation of the specimen at each of the plurality of distances relative to a fiducial plane.