Abstract: A flow cytometer for detecting target particles such as microorganisms including biological cells and viruses as well as molecular species. The flow cytometer includes a detection system involving a CCD having a time delay integration capability to thereby increase the signal from the target particle and decrease the noise detected by the CCD. Calibration particles can be included in the sample stream of the flow cytometer for coordinating the readout of the CCD with the rate of flow of the sample stream to improve the detection capability of the CCD. Statistical analysis techniques can also be used to determine the rate of flow of target particles in the sample stream to thereby coordinate the readout rate of the CCD with the rate of flow of the target particles.