Some embodiments of the present inventive concept provide optical coherence tomography (OCT) systems for integration with a microscope. The OCT system includes a sample arm coupled to the imaging path of a microscope. The sample arm includes an input beam zoom assembly including at least two movable lenses configured to provide shape control for an OCT signal beam; a scan assembly including at least one scanning mirror and configured for telecentric scanning of the OCT signal beam; and a beam expander configured to set the OCT signal beam diameter incident on the microscope objective. The shape control includes separable controls for numerical aperture and focal position of the imaged OCT beam.