A quantum flow cytometer for detecting an analyte with photon-number statistics includes: a flow cytometer that: receives a pump light in a first direction; receives an analyte flow comprising the analyte in a second direction; and produces scattered light from scattering the pump light by the analyte; a single photon detector in optical communication with the flow cytometer and that: receives, in a third direction, the scattered light from the flow cytometer; provides a correlative time-of-arrival waveform comprising photon-number statistics as an amplitude and an integrated area, the integrated area being proportional to a number of photons received by the single photon detector, wherein the first direction, the second direction, and the third direction are arranged at oblique angles.