This imaging system provides high sensitivity for bioluminescence, fluorescence, photographic, and X-ray in vivo imaging. It includes a patented LED illumination source, 5 mouse capacity, 10 wavelengths/10 filter options, -90°C cooled camera, anesthesia compatible, absolute calibration, and Aura imaging software. The high throughput system captures images of luminescent sources or fluorescent reporters in subjects such as small animals, well plates, plants, bacterial colonies, electrophoresis gels, and western blots. The Aura Imaging Software allows for automated quantitative analysis of images.