An imaging sensor system includes a single photon avalanche diode (SPAD) imaging array including N pixels formed in a first semiconductor layer of a first wafer. Substantially an entire thickness of the first semiconductor layer of each pixel is fully depleted such that a multiplication region included in each pixel near a front side is configured to be illuminated with photons through a back side and through the substantially entire thickness of the fully depleted first semiconductor layer. Deep n type isolation regions are disposed in the first semiconductor layer between the pixels to isolate the pixels. N digital counters are formed in a second semiconductor layer of a second wafer that is bonded to the first wafer. Each of the N digital counters is coupled to the SPAD imaging array and coupled to count output pulses generated by a respective one of the pixels.