Microparticle-based analytical methods, systems and applications are provided. A system controller of the system sets a focus zone on the point of interest and adjusts the aperture and apodization for the range of interest. Changes in the reference optical signal detected at the monitor optical signal detector are used for controlling the optical signal generator of the transceiver. An atomic layer deposition tool includes a subatmospheric load chamber, a subatmospheric transfer chamber and a plurality of atomic layer deposition chambers.