The MFISH fluorescence in situ hybridization analysis system is a new practical image software developed specifically for capturing and processing fluorescence microscopy images. The fluorescence in situ hybridization analysis system uses fluorescently labeled specific nucleic acid probes to hybridize with corresponding target DNA or RNA molecules in cells. By observing the fluorescence signal under a fluorescence microscope or confocal laser scanner, the morphology and distribution of stained cells or organelles after hybridization with the specific probe can be determined, or the DNA region or RNA molecule bound to the fluorescent probe can be localized in chromosomes or other organelles.