Fluorescent biomarkers are used to detect target molecules within inhomogeneous populations of cells. When these biomarkers are found in trace amounts it becomes extremely challenging to detect their presence in a flow cytometer. Here, we present a framework to draw a detection baseline for single emitters and enable absolute calibration of a flow cytometer based on quantum measurements. We used single-photon detection and found the second-order autocorrelation function of fluorescent light. We computed the success of rare-event detection for different signal-to-noise ratios (SNR). We showed high-accuracy identification of the events with occurrence rates below 10-5 even at modest SNR levels, enabling early disease diagnostics and post-disease monitoring.