A flow cytometry apparatus comprising: a detector configured to produce a detector signal responsive to detecting light during operation of the flow cytometer; a first pulse processor configured to receive the detector signal from the detector and to output detector data characterizing pulse heights of pulses in the detector signal; a second pulse processor configured to also receive the detector signal from the detector and to output a pulse height data signal, a pulse width data signal, and a pulse area data signal for desired pulses in the detector signal, wherein the desired pulses are the pulses for which the pulse height data signal, the pulse width data signal, and the pulse area data signal are to be stored in a data storage device and, for each desired pulse: the second pulse processor is configured to output the pulse height data signal, the pulse width data signal, and the pulse area data signal for that desired pulse responsive to a set of one or more trigger conditions being met, and the set of one or more trigger conditions at least includes a trigger condition involving a comparison of the pulse height for that desired pulse with a trigger threshold value; a real-time trigger module configured to receive the detector data from the first pulse processor and to generate periodic histogram data from the detector data during a predetermined time period; and a threshold selector configured to receive the periodic histogram data from the real-time trigger module and to provide the trigger threshold value. a detector configured to produce a detector signal responsive to detecting light during operation of the flow cytometer; a first pulse processor configured to receive the detector signal from the detector and to output detector data characterizing pulse heights of pulses in the detector signal; a second pulse processor configured to also receive the detector signal from the detector and to output a pulse height data signal, a pulse width data signal, and a pulse area data signal for desired pulses in the detector signal, wherein the desired pulses are the pulses for which the pulse height data signal, the pulse width data signal, and the pulse area data signal are to be stored in a data storage device and, for each desired pulse: the second pulse processor is configured to output the pulse height data signal, the pulse width data signal, and the pulse area data signal for that desired pulse responsive to a set of one or more trigger conditions being met, and the set of one or more trigger conditions at least includes a trigger condition involving a comparison of the pulse height for that desired pulse with a trigger threshold value; a real-time trigger module configured to receive the detector data from the first pulse processor and to generate periodic histogram data from the detector data during a predetermined time period; and a threshold selector configured to receive the periodic histogram data from the real-time trigger module and to provide the trigger threshold value. the second pulse processor is configured to output the pulse height data signal, the pulse width data signal, and the pulse area data signal for that desired pulse responsive to a set of one or more trigger conditions being met, and the set of one or more trigger conditions at least includes a trigger condition involving a comparison of the pulse height for that desired pulse with a trigger threshold value; a real-time trigger module configured to receive the detector data from the first pulse processor and to generate periodic histogram data from the detector data during a predetermined time period; and a threshold selector configured to receive the periodic histogram data from the real-time trigger module and to provide the trigger threshold value.