Which reporter gene should I use for whole animal imaging?
Mice: you can use optical imaging (luciferase or fluorescent proteins) or nuclear imaging (NIS). Biolumonescence imaging is very sensitive and there is no issue with background signals. Due to issues with autofluorescence from fur or rodent chow, fluorescence imaging in living animals can be challenging as it requires you to first subtract the background fluorescence signals. If you want to obtain high resolution 3D true tomographic data, you should use nuclear reporter genes (e.g. NIS) with SPECT/CT or PET/CT imaging for best quantitative results.
Rats or larger: Due to inability of light to penetrate deep tissues and scatter, nuclear reporter genes (e.g. NIS) are the ideal genes for in-life imaging of living animals. If you need to monitor the genes long term, you will need to ensure that you use an immunogenic reporter gene (e.g. species specific NIS) to prevent host immune mediated rejection of NIS transduced cells.