A dual illumination system is disclosed for use with an imaging apparatus. The imaging apparatus defines a light-tight imaging compartment with an interior wall having a view port extending into the imaging compartment. This view port enables data acquisition of a biological specimen contained in the imaging compartment. The dual illumination system includes a first illumination assembly configured to direct structured light onto a first side of the specimen to enable structured light and surface topography measurements thereof. A second illumination assembly then directs light at the specimen wherein diffused fluorescent light emanates from a surface thereof for receipt through the view port to acquire fluorescence data of the specimen. The combination of structured light imaging and fluorescence imaging enables 3D diffuse tomographic reconstructions of fluorescent probe location and concentration.