1. A method for imaging a tumor in an animal, comprising (a) labeling an organ in the animal with a detectable label localized substantially exclusively to the organ, whereupon the labeled organ is capable of use as a fiducial marker in an image of the animal; (b) administering to the animal one or more detectably labeled probes that localize substantially exclusively to a marker of a tumor of interest in the body of the animal; (c) after labeling the organ according to step (a) and administering the one or more detectably labeled probes according to step (b), imaging the animal with a fluorescence molecular tomography (FMT) imager to generate an FMT image, and imaging the animal with a magnetic resonance (MR) imager to generate an MR image; and (d) aligning the FMT image and MR image using the fiducial marker as a reference point, thereby generating an image comprising a fusion of the FMT image and the MR image.