A method of adjusting the timing and/or phase of a charge pulse signal for charging droplets from a fluid stream of sheath fluid in a flow cytometer, the method comprising: forming a fluid stream by flowing the sheath fluid through a nozzle, wherein the fluid stream separates into droplets after exiting the nozzle; applying a charge pulse signal to the nozzle during a calibration phase, wherein each droplet that separates from the stream when the charge pulse signal causes a charge to be applied to the nozzle becomes a charged droplet and each droplet that separates from the stream when the charge pulse signal does not cause a charge to be applied to the nozzle remains an uncharged droplet; receiving the charged and uncharged droplets in a charge collector during the calibration phase, collecting charges from the charged droplets during the calibration phase for a plurality of time periods using the charge collector, wherein a parameter selected from the group consisting of: timing, phase, and timing and phase of the charge pulse signal is different for each of the time periods; measuring the charges collected from the charged droplets during each of the time periods using the electrometer to create a plurality of corresponding collected charged droplet signals, each collected charged droplet signal indicative of an accumulated charge for the corresponding time period based on measurements by the electrometer; determining a collected charged droplet signal of the plurality of collected charged droplet signals that has the greatest magnitude; and operating the flow cytometer with a charge pulse signal timing, phase, or timing and phase based on the charge pulse signal timing, phase, or timing and phase for the time period that corresponds to the collected charged droplet signal that has the greatest magnitude. forming a fluid stream by flowing the sheath fluid through a nozzle, wherein the fluid stream separates into droplets after exiting the nozzle; applying a charge pulse signal to the nozzle during a calibration phase, wherein each droplet that separates from the stream when the charge pulse signal causes a charge to be applied to the nozzle becomes a charged droplet and each droplet that separates from the stream when the charge pulse signal does not cause a charge to be applied to the nozzle remains an uncharged droplet; receiving the charged and uncharged droplets in a charge collector during the calibration phase, collecting charges from the charged droplets during the calibration phase for a plurality of time periods using the charge collector, wherein a parameter selected from the group consisting of: timing, phase, and timing and phase of the charge pulse signal is different for each of the time periods; measuring the charges collected from the charged droplets during each of the time periods using the electrometer to create a plurality of corresponding collected charged droplet signals, each collected charged droplet signal indicative of an accumulated charge for the corresponding time period based on measurements by the electrometer; determining a collected charged droplet signal of the plurality of collected charged droplet signals that has the greatest magnitude; and operating the flow cytometer with a charge pulse signal timing, phase, or timing and phase based on the charge pulse signal timing, phase, or timing and phase for the time period that corresponds to the collected charged droplet signal that has the greatest magnitude.