A photon-accounting system for use with a flow cytometry system is disclosed which includes a signal shaping sub-system, including a differentiator configured to generate a differentiated output of photodiode signals into corresponding zero-crossings each associated with one of the received photons, a comparator configured to receive the differentiated signal and compare to a threshold to thereby generate a comparator output digital signal associated with the crossing of the differentiated signal about the threshold, a front-end synchronization system adapted to receive and synchronize the comparator generated digital signal to a clock, thereby generate synchronized photon data with the clock and associated with the asynchronized photodiode signal, and a timestamping system adapted to receive the synchronized data as a bit stream and generate a timestamp associated with each photon data.