The self-energy for a given electrode (Left or Right) is computed as ƩL(E)=(HCL - ESCL) g(E) (HLC - ESLC), where g(E) is the surface Green's function of the semi-infinite (Left) electrode, and HLC is the part of the Hamiltonian that couples the left electrode (L) with the central region (C), and likewise for the overlap matrix, SLC.
If you are interested in the self-energy (matrix) you can get it like this:
sigma_L = calculateSelfEnergy(device_configuration, energy=0.0*eV, contribution=Left)
Notice, that you can also get access to the Hamiltonian, Green's functions and other quantities as described in this tutorial : http://quantumwise.com/documents/tutorials/latest/LowLevelEntities/index.html/chap.intro.html#sect.intro.hs
The self-energy is a complex matrix. The real part gives rise to a shift of the molecular energy levels, while the imaginary part gives the broadening (finite life time) of the molecular energy levels.
Sometimes the coupling parameter (matrix) is referred to as ҐL(E) = i(ƩtL(E) - ƩL(E)), which is responsible for the energy broadening.
Since Ґ is a matrix, that depends on energy, the actual broadening of a particular molecular orbital should be obtained from the width of the spectral function A(E) = Gr(E)( ҐL(E) + ҐR(E)) Ga(E), where Gr/a(E) is the retarded/advanced Green's function, which can also be obtained (see link above).