Optical data manipulation technologies increasingly employ densely aperiodic optical 3D phase elements. Refinement of such technologies will require the capability to quantitatively characterize the volumetric dielectric modulation of an optical sample to a high level of precision and spatial resolution. We present a scanning transmission microscopy system that uses a position-sensitive detector to impart sensitivity to both the phase and absorption components. We describe the layout of the instrument and then derive its phase and absorption transfer functions. Simulations and experiments are presented to validate the analysis. For phase detection, the instrument possesses depth-sectioning properties similar to those of a confocal microscope without the use of a pinhole, enabling full 3D object reconstruction.