Advances in the detection and quantification for 3D optical tomography of bioluminescent and fluorescent reporters to quantify in terms of either cell number or absolute pmol concentration will be discussed. These methods include enhancing the detected signal levels using slight compression which reduces the amount of tissue light propagates through. Calibration techniques to improve signal location by reducing the excitation light artifacts, the amount of detected autofluorescence and techniques to quantify 3D reconstruction results in terms of biological activity will be demonstrated.