An integrated detection, flow cell and photonics device, comprising: a substrate having an array of pixel elements that sense photons during active sensing periods of a frame, the substrate and pixel elements forming an integrated circuit photon detection layer, wherein each pixel element includes a single photon avalanche diode (SPAD) and an in-pixel detection circuit, wherein the in-pixel detection circuit includes: a photon detector switch connected to an output node of the SPAD; a temporal accumulator capacitor electrically connected to the photon detector switch, the temporal accumulator capacitor configured to output an analog voltage proportional to a sum of arrival times for the photons sensed by the SPAD during the frame; an event counter switch connected to the output node of the SPAD; and an event counter capacitor electrically connected to the event counter switch, the event counter capacitor configured to output an other analog voltage proportional to a number of photons sensed by the SPAD during the frame; at least one wave guide formed on the IC photon detection layer as a photonics layer; an optical isolation layer formed over at least a portion of the wave guide; and a collection of photo resist walls patterned to define at least one flow cell channel that is configured to direct fluid along a fluid flow path, the at least one wave guide aligned to extend along the fluid flow path, the flow cell channel configured to receive samples and arranged with respect to the array of pixel elements so as to direct the samples to sample sites that align with the array of pixel elements. a substrate having an array of pixel elements that sense photons during active sensing periods of a frame, the substrate and pixel elements forming an integrated circuit photon detection layer, wherein each pixel element includes a single photon avalanche diode (SPAD) and an in-pixel detection circuit, wherein the in-pixel detection circuit includes: a photon detector switch connected to an output node of the SPAD; a temporal accumulator capacitor electrically connected to the photon detector switch, the temporal accumulator capacitor configured to output an analog voltage proportional to a sum of arrival times for the photons sensed by the SPAD during the frame; an event counter switch connected to the output node of the SPAD; and an event counter capacitor electrically connected to the event counter switch, the event counter capacitor configured to output an other analog voltage proportional to a number of photons sensed by the SPAD during the frame; a photon detector switch connected to an output node of the SPAD; a temporal accumulator capacitor electrically connected to the photon detector switch, the temporal accumulator capacitor configured to output an analog voltage proportional to a sum of arrival times for the photons sensed by the SPAD during the frame; an event counter switch connected to the output node of the SPAD; and an event counter capacitor electrically connected to the event counter switch, the event counter capacitor configured to output an other analog voltage proportional to a number of photons sensed by the SPAD during the frame; at least one wave guide formed on the IC photon detection layer as a photonics layer; an optical isolation layer formed over at least a portion of the wave guide; and a collection of photo resist walls patterned to define at least one flow cell channel that is configured to direct fluid along a fluid flow path, the at least one wave guide aligned to extend along the fluid flow path, the flow cell channel configured to receive samples and arranged with respect to the array of pixel elements so as to direct the samples to sample sites that align with the array of pixel elements.