A system for operating an electrokinetic device includes a support configured to hold and operatively couple with the electrokinetic device, an integrated electrical signal generation subsystem configured to apply a biasing voltage across a pair of electrodes in the electrokinetic device, and a light modulating subsystem configured to emit structured light onto the electrokinetic device. The system can further include a thermally controlled flow controller, and/or be configured to measure impedance across the electrokinetic device. The system can be a light microscope, including an optical train. The system can further include a light pipe, which can be part of the light modulating subsystem, and which can be configured to supply light of substantially uniform intensity to the light modulating subsystem or directly to the optical train.