The image registration systems and methods according to this invention register reflectance and fluorescence hyperspectral imagery and provide the spatial image transformation between the reflectance and fluorescence hyperspectral imagery. A reflectance image is embedded into the fluorescence hyperspectral imagery and thereby resolves the resemblance problem of reflectance and fluorescence hyperspectral imagery. The reflectance image is embedded into the fluorescence hyperspectral imagery using (1) light from a narrow-band source embedded in Ultraviolet (UV) excitation light, (2) second order diffracted light, and/or (3) Ultraviolet (UV) excitation light reflectance. Resembling reflectance images are calculated from the reflectance hyperspectral imagery and the embedded reflectance image in the fluorescence hyperspectral imagery. The two respective reflectance images are pre-processed to maximize the resemblance between them. Image registration algorithms use the two pre-processed reflectance images and calculate the spatial image transformation that allows to map the spatial coordinates from the reflectance to the fluorescence hyperspectral imagery (and vice versa).