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Transport through quantum coherent conductors, such as atomic junctions, is described by conduction channels. Information about the number of channels and their transmissions can be extracted from various sources, such as multiple Andreev reflections, dynamical Coulomb blockade, or shot noise. We complement this set of methods by introducing the superconducting excess current as a new tool to continuously extract the transport channel transmissions of an atomic scale junction in a scanning tunneling microscope. In conjunction with ab initio simulations, we employ this technique in atomic aluminum junctions to determine the influence of the structure adjacent to the contact atoms on the transport properties.