We have developed an imaging system for high speed image acquisition in fluorescence microscopy. The use of a two- dimensional CCD array in a special operation mode called TDI (Time Delayed Integration) permits a significant increase in photon integration time compared to 1D scanners (higher signal-to-noise ratio) without compromising the total data throughput rate. Instead of a start–stop system we use continuous stage motion in the CCDs parallel shift direction. Synchronizing the parallel clock and the stage velocity guarantees a one-to-one relationship between a moving cell and its image onto the CCD. Compared to start-stop system, TDI scanning offers a speed improvement, negligible blurring in the scanning direction and a complete suppression of pixel variability boosting the SNR more than 10 dB.