Multimodal system able to detect Bioluminescence, Multi-wavelength fluorescence, CT, Reflected Light, and Cherenkov Radiation. Equipped with 10 excitation filters (490 to 850nm) and 18 emission filters. Spectral scanning of filters and the use of spectral unmixing algorithms helps reduce autofluorescence. Single-view 3D surface topography from structured light and 3D diffuse tomographic reconstructions for both bioluminescence and fluorescence.