A flow cytometry system comprising: at least one sample illumination source, wherein each sample illumination source is configured to deliver light to a corresponding sample location, thereby causing sample light (206, 218) to be emitted by or scattered off of particles in the corresponding sample location; focusing optics (208, 242) that are configured to direct the sample light (206, 218) from each sample location along one or more optical paths, wherein each optical path passes through a corresponding one or more optical filter elements and terminates at a corresponding detector (222, 224, 226, 228, 230) that is configured to produce output data (232 234, 236, 238, 240) indicative of the measured intensity of light reaching that detector (222, 224, 226, 228, 230); characterized in that it comprises: a calibration light source that is configured to independently emit different spectral profiles of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) at different times, each spectral profile of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) having one or more peaks at different wavelengths, such that the emitted calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) is directed along at least a portion of each of the optical paths; one or more processors; and a memory that stores computer-executable instructions that, when executed by the one or more processors, cause the one or more processors to: receive the output data (232, 234, 236, 238, 240) from each of the detectors (222, 224, 226, 228, 230) responsive to that detector (222, 224, 226, 228, 230) receiving calibration light from the calibration light source, and determine filtering characteristics for the optical filter elements along each optical path by analyzing the output data (232, 234, 236, 238, 240) produced during the emission of at least two different spectral profiles of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) by the calibration light source. at least one sample illumination source, wherein each sample illumination source is configured to deliver light to a corresponding sample location, thereby causing sample light (206, 218) to be emitted by or scattered off of particles in the corresponding sample location; focusing optics (208, 242) that are configured to direct the sample light (206, 218) from each sample location along one or more optical paths, wherein each optical path passes through a corresponding one or more optical filter elements and terminates at a corresponding detector (222, 224, 226, 228, 230) that is configured to produce output data (232 234, 236, 238, 240) indicative of the measured intensity of light reaching that detector (222, 224, 226, 228, 230); characterized in that it comprises: a calibration light source that is configured to independently emit different spectral profiles of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) at different times, each spectral profile of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) having one or more peaks at different wavelengths, such that the emitted calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) is directed along at least a portion of each of the optical paths; one or more processors; and a memory that stores computer-executable instructions that, when executed by the one or more processors, cause the one or more processors to: receive the output data (232, 234, 236, 238, 240) from each of the detectors (222, 224, 226, 228, 230) responsive to that detector (222, 224, 226, 228, 230) receiving calibration light from the calibration light source, and determine filtering characteristics for the optical filter elements along each optical path by analyzing the output data (232, 234, 236, 238, 240) produced during the emission of at least two different spectral profiles of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) by the calibration light source. a calibration light source that is configured to independently emit different spectral profiles of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) at different times, each spectral profile of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) having one or more peaks at different wavelengths, such that the emitted calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) is directed along at least a portion of each of the optical paths; one or more processors; and a memory that stores computer-executable instructions that, when executed by the one or more processors, cause the one or more processors to: receive the output data (232, 234, 236, 238, 240) from each of the detectors (222, 224, 226, 228, 230) responsive to that detector (222, 224, 226, 228, 230) receiving calibration light from the calibration light source, and determine filtering characteristics for the optical filter elements along each optical path by analyzing the output data (232, 234, 236, 238, 240) produced during the emission of at least two different spectral profiles of calibration light (702, 704, 706, 708, 710, 712, 716, 718, 720) by the calibration light source.