Abstract: The present invention relates to a method and an automated fluorescent imaging system for digitizing a specimen with fluorescent target points on a microscope slide. The method uses the fluorescence microscope system for detecting and scanning said fluorescent target points. The method comprises the steps of marking the position of said specimen on said slide by visible marking means to define a specimen area containing said specimen and said fluorescent target points; capturing a bright field image of at least a portion of the slide at a first optical magnification, said portion(s) containing the specimen area and determining, from the visible marking means, a position of target fields falling within said specimen area; and scanning the target fields of the specimen area at a second optical magnification higher than said first optical magnification, said scanning including focusing on at least a part of said target fields.