1. A method for generating a three dimensional image from a plurality of two-dimensional bioluminescence images, comprising: acquiring a plurality of two-dimensional bioluminescence images using an imaging system; processing the plurality of two-dimensional bioluminescence images so that adjacent images are aligned with each other; identifying at least one feature common to each of the plurality of two-dimensional bioluminescence images; and applying an orthographic projection model to the at least one feature of each of the plurality of two-dimensional bioluminescence images to generate a three-dimensional image of the at least one feature.