A method and apparatus for equalizing gain in an array of electron multiplication (EM) pixels is disclosed, each pixel having one or more impact ionization gain stages with implants to achieve charge transfer directionality and comprising a phase 1 clocked gate, an EM clocked gate, and two DC gates formed between the phase 1 clocked gate and the EM clocked gate, comprising the steps of (a) applying initial voltages to each of the DC gates and the EM clocked gates of at least two pixels of a plurality of pixels; (b) clocking phase 1 clock gates and an EM clock gates associated with the at least two pixels of the plurality of pixels a predetermined number of times to achieve an average pixel intensity value after impact ionization gain; and (c) selectively adjusting the difference in voltage between the DC gate and corresponding EM clocked gate of the at least two pixels of the plurality of pixels until the difference between the resulting pixel intensity values and the average pixel intensity value needed to produce a desired uniform gain image is below a predetermined threshold.