An imaging system for inspection of a sample includes an illumination module, which irradiates a surface of the sample with pulsed optical radiation. A mechanical scanner translates at least one of the sample and part of the imaging system so as to scan an area irradiated by the pulsed optical radiation over the surface in order to irradiate successive, partially overlapping frames on the surface by respective successive pulses of the pulsed radiation. A collection module collects the optical radiation scattered from the surface so as to capture a sequence of images of the irradiated frames. A system controller varies a configuration of the imaging system in alternation between at least first and second different optical configurations in synchronization with the pulsed optical radiation.