Fluorescence in situ hybridization (FISH) is a powerful tool for visualizing and detecting genetic abnormalities. Manual scoring FISH analysis is a tedious and labor-and-time-consuming task. Automated image acquisition and analysis provide an opportunity to overcome the difficulties. However, conventional fluorescence microscopes, the mostly used instrument for FISH imaging, have deficiencies. A multi-spectral image modality must be employed in order to visualize fluorescently dyed FISH probes for analysis, and the existing technologies are either two expensive, too slow, or both. Aiming at upgrading the current employed cytogenetic instrumentation, we developed a new imaging technique capable of simultaneously imaging multiple color spectra. Using the principle, we implemented a prototype system and conduct various characterization experiments. Experiment results (<1% peripheral geometric distortion, consistent signal response linearity, and ~2000 lp/mm spatial resolution) show no significant compromise in terms of optical performance. A detector alignment scheme was developed and performed to minimize registration error. The system has significantly faster acquisition speed than conventional fluorescence microscopes albeit the extra cost is quite insignificant.