1. A method of calibrating a pupil center in scatterometry overlay measurements, comprising: acquiring one or more scatterometry overlay (SCOL) measurements via an overlay metrology tool; calculating, with one or more processors, one or more fluctuations from a first statistical figure of merit of a per pixel overlay signal at a pupil plane of the overlay metrology tool based on the one or more SCOL measurements; adjusting, with one or more processors, the one or more calculated fluctuations based on a second statistical figure of merit of the per pixel overlay signal at the pupil plane; determining, with the one or more processors, a pupil calibration value that reduces the one or more adjusted fluctuations; and providing the determined pupil calibration value to calibrate one or more coordinates of one or more detectors located at the pupil center of the pupil plane of the overlay metrology tool.