A method of selecting a desired drop delay in a flow cytometer (100, 200), the method comprising: operating the flow cytometer (100, 200) with calibration particles during a plurality of drop delay periods each having a different selected drop delay from a range of potential selected drop delays; and deflecting charged droplets (118, 120) during the plurality of drop delay periods, wherein the method is characterized by: collecting non-deflected droplets (122, 222) during each drop delay period in waste tubing (126, 226, 302) to form a waste stream (123, 228, 304) in the waste tubing (126, 226, 302); illuminating the waste stream (123, 228, 304) in the waste tubing (126, 226, 302) to cause scattered light or fluorescent emissions (132, 212, 308) of the calibration particles in the waste stream (123, 228, 304) associated with each drop delay period; sensing the scattered light or fluorescent emissions (132, 212, 308) from the calibration particles with a detector (134, 220, 404) in association with each drop delay period; collecting data regarding a number of calibration particles sensed in the waste stream (123, 228, 304) in association with each of the different drop delay periods using the sensed scattered light or fluorescent emissions (132, 212, 308); determining which selected drop delay of the different selected drop delays results in the lowest rate of calibration particles in the waste stream (123, 228, 304) based on the number of calibration particles sensed in said waste stream (123, 228, 304); and using the determined selected drop delay as the desired drop delay. operating the flow cytometer (100, 200) with calibration particles during a plurality of drop delay periods each having a different selected drop delay from a range of potential selected drop delays; and deflecting charged droplets (118, 120) during the plurality of drop delay periods, wherein the method is characterized by: collecting non-deflected droplets (122, 222) during each drop delay period in waste tubing (126, 226, 302) to form a waste stream (123, 228, 304) in the waste tubing (126, 226, 302); illuminating the waste stream (123, 228, 304) in the waste tubing (126, 226, 302) to cause scattered light or fluorescent emissions (132, 212, 308) of the calibration particles in the waste stream (123, 228, 304) associated with each drop delay period; sensing the scattered light or fluorescent emissions (132, 212, 308) from the calibration particles with a detector (134, 220, 404) in association with each drop delay period; collecting data regarding a number of calibration particles sensed in the waste stream (123, 228, 304) in association with each of the different drop delay periods using the sensed scattered light or fluorescent emissions (132, 212, 308); determining which selected drop delay of the different selected drop delays results in the lowest rate of calibration particles in the waste stream (123, 228, 304) based on the number of calibration particles sensed in said waste stream (123, 228, 304); and using the determined selected drop delay as the desired drop delay. collecting non-deflected droplets (122, 222) during each drop delay period in waste tubing (126, 226, 302) to form a waste stream (123, 228, 304) in the waste tubing (126, 226, 302); illuminating the waste stream (123, 228, 304) in the waste tubing (126, 226, 302) to cause scattered light or fluorescent emissions (132, 212, 308) of the calibration particles in the waste stream (123, 228, 304) associated with each drop delay period; sensing the scattered light or fluorescent emissions (132, 212, 308) from the calibration particles with a detector (134, 220, 404) in association with each drop delay period; collecting data regarding a number of calibration particles sensed in the waste stream (123, 228, 304) in association with each of the different drop delay periods using the sensed scattered light or fluorescent emissions (132, 212, 308); determining which selected drop delay of the different selected drop delays results in the lowest rate of calibration particles in the waste stream (123, 228, 304) based on the number of calibration particles sensed in said waste stream (123, 228, 304); and using the determined selected drop delay as the desired drop delay.