An inspection system comprises a beam generator module for deflecting spots across scan portions of a specimen. The system also includes detection channels for sensing light emanating from a specimen in response to an incident beam directed towards such specimen and generating a detected image for each scan portion. The system comprises a synchronization system comprising clock generator modules for generating timing signals for deflectors of the beam generator module to scan the spots across the scan portions at a specified frequency and each of the detection channels to generate the corresponding detected image at a specified sampling rate. The timing signals are generated based on a common system clock and cause the deflectors to scan the spots and the detection channels to generate a detected image at a synchronized timing so as to minimize jitter between the scan portions in the response image.