Emission tomography provides a method for the characterization of quantum states of those degrees of freedom of material quantum systems that are coupled to electronic states of the system. In such systems, the time-dependent fluorescence spectrum contains complete information about the non-electronic degree of freedom. Phase-space or, in certain cases, density matrix representations of the state can be reconstructed from the spectrum using standard methods of computer-assisted tomography or linear algebra. The principles and implementation of this procedure are described in detail and applied to the specific example of the reconstruction of the quantum state of the vibrational mode of a diatomic molecule excited into a non-stationary wavepacket state.