Methods, storage mediums, and systems for correlating pulses generated from multiple interrogation regions in a flow cytometer to particular particles flowing through the flow cytometer are provided. Embodiments of the methods, storage mediums, and systems include configurations for calibrating a flow cytometer using a calibration particle having a unique signature to determine a time-of-flight for particles flowing through the flow cytometer. Based on the calculated time-of-flight and relative positions of interrogation regions corresponding to collectors of the flow cytometer, the methods, storage mediums, and systems may further include configurations for associating other signal pulses to particles of one or more different particle sets.