1. A method for obtaining a representation of concentration of a fluorophore within an object, the method comprising: (a) administering to said object a known amount of probe comprising a fluorophore; (b) directing excitation light into and/or onto said object at multiple locations; (c) detecting excitation light emanating from or transmitted through at least part of said object, thereby acquiring an intrinsic image; (d) detecting fluorescent light emitted from said probe within or on a surface of said object, thereby acquiring a detected emission image; and (e) processing data from said intrinsic image and said detected emission image to provide a tomographically reconstructed raw representation of said region within said object, said raw representation compensating for waveguiding effects, wherein step (e) comprises: (i) creating an estimated emission image using at least said intrinsic image and altering said detected emission image using at least said estimated emission image; and (ii) determining a coincidence mask from said intrinsic image and said detected emission image and altering said detected emission image using at least said coincidence mask; (f) determining a scale factor associated with said fluorophore in the object; and (g) applying said scale factor to said raw representation to convert said raw representation into a scaled representation of concentration of said fluorophore in said region.