Biophotonic imaging is a novel, relatively low-cost method for in-vivo imaging of tumors in mouse models. This
technique, utilizing luminescent cancer cells, can improve productivity for cancer investigators and reduce the number of
mice needed to conduct an experiment by allowing longitudinal studies. However, many of the tools provided with these
systems are intended for interactive use and are time consuming to use when large numbers of images are captured.
Many studies require a specific determination of the location and tumor size, particularly relative to the anatomical
details of the mouse; whether this is the entire mouse body, single organs, or custom, user defined regions. An
automated method of registering mouse images to a whole body atlas mask with well defined anatomical details is
presented. Bilinear scaling is used within the registration process and is shown to be successful since the trapezoidal
shape chosen merges well with the natural shape of the mouse. After successful registration, quantification of the photon
flux can be performed for the whole body and specific regions using a summation of intensity levels and photon flux per
intensity level. Registration accuracy rates over 90% were achieved although results vary relative to the positioning of
the mouse. This work provides a base to explore 3D and temporal registration techniques for such data sets.