Atomic synapses represent a special class of memristors whose operation relies on the formation of metallic nanofilaments bridging two electrodes across an insulator. Due to the magnifying effect of this narrowest cross section on the device conductance, a nanometer-scale displacement of a few atoms grants access to various resistive states at ultimately low energy costs, satisfying the fundamental requirements of neuromorphic computing hardware. However, device engineering lacks the complete quantum characterization of such filamentary conductance. Here we analyze multiple Andreev reflection processes emerging at the filament terminals when superconducting electrodes are utilized. Thereby, the quantum PIN code, i.e., the transmission probabilities of each individual conduction channel contributing to the conductance of the nanojunctions, is revealed. Our measurements on Nb2O5 resistive switching junctions provide profound experimental evidence that the onset of the high conductance ON state is manifested via the formation of truly atomic-sized metallic filaments.

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