A system and method provide normalized fluorescence epi-illumination images and normalized fluorescence transillumination images. The normalization can be used to improve two-dimensional (planar) fluorescence epi-illumination images and two-dimensional (planar) fluorescence transillumination images. The system and method can also provide normalized bioluminescence epi-illumination images and normalized bioluminescence transillumination images. In some arrangements, the system and method can provide imaging of small animals, intro-operative imaging, endoscopic imaging, and/or imaging of hollow organs.
