1. A method for imaging a tumor in an animal, comprising (a) labeling an organ in the animal with a first detectable label that localizes substantially exclusively to the organ by specifically hybridizing or binding with a receptor or antigen at the organ, whereupon the labeled organ is capable of use as a first fiducial marker in an image of the animal and the first detectable label is detectable by both fluorescence molecular tomography (FMT) and magnetic resonance (MR); (b) administering to the animal one or more detectably labeled probes that localize substantially exclusively to a region of interest in the body of the animal separate from the labeled organ; (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 FMT imager to generate an FMT image, and imaging the animal with a MR imager to generate an MR image; and (d) aligning the FMT image and MR image using the first fiducial marker as a first reference point in the FMT image and in the MR image, thereby generating an image comprising a fusion of the FMT image and the MR image.