A computer-implemented method of determining tag signals from measured intensities, the measured intensities collected by light sensors or pixels (206, 208, 210, 212, 214) in a sensor array overlaid by nano wells (256, 258, 260, 262, 264) on a sample surface, the sample surface including pixel areas (206', 208', 210', 212', 214'), wherein each pixel area is associated with a corresponding light sensor or pixel, and the nano wells holding a plurality of clusters (206A, 206B; 208A, 208B; 210A, 210B; 212A, 212B; 214A, 214B) during a sequence of sampling events, wherein one or more nano wells are present in each pixel area, and wherein each light sensor or pixel is directed to and measures intensity from one of the pixel areas during each sampling period, the computer-implemented method including: determining an adjustment to the measured intensities collected by a light sensor or pixel in sampling periods for crosstalk from adjoining nano wells, as collected by corresponding light sensors or corresponding pixels, by applying crosstalk estimations to measured intensities collected by light sensors or pixels for the adjoining nano wells in respective sampling periods; determining a further adjustment to the measured intensities collected by the light sensor or pixel in the sampling periods for background intensity; and determining the tag signals originating from the light sensor or pixel in the sampling periods, taking into account the adjustment and the further adjustment to the measured intensities, combined with modifying at least the measured intensities to take into account signal decay over progress of the sequence of sampling events and for phasing and pre-phasing, including: modifying the measured intensities in the sampling periods by a progressive decay function that takes into account how late each sampling period occurs in the sequence of sampling events; and applying a distribution function to at least current, prior, and subsequent measured intensities, using signal presence ground truth for the light sensor or pixel in the sampling periods, and separating intensity contributions due to phasing and pre-phasing from contribution of a current tag signal to a current measured intensity. determining an adjustment to the measured intensities collected by a light sensor or pixel in sampling periods for crosstalk from adjoining nano wells, as collected by corresponding light sensors or corresponding pixels, by applying crosstalk estimations to measured intensities collected by light sensors or pixels for the adjoining nano wells in respective sampling periods; determining a further adjustment to the measured intensities collected by the light sensor or pixel in the sampling periods for background intensity; and determining the tag signals originating from the light sensor or pixel in the sampling periods, taking into account the adjustment and the further adjustment to the measured intensities, combined with modifying at least the measured intensities to take into account signal decay over progress of the sequence of sampling events and for phasing and pre-phasing, including: modifying the measured intensities in the sampling periods by a progressive decay function that takes into account how late each sampling period occurs in the sequence of sampling events; and applying a distribution function to at least current, prior, and subsequent measured intensities, using signal presence ground truth for the light sensor or pixel in the sampling periods, and separating intensity contributions due to phasing and pre-phasing from contribution of a current tag signal to a current measured intensity. modifying the measured intensities in the sampling periods by a progressive decay function that takes into account how late each sampling period occurs in the sequence of sampling events; and applying a distribution function to at least current, prior, and subsequent measured intensities, using signal presence ground truth for the light sensor or pixel in the sampling periods, and separating intensity contributions due to phasing and pre-phasing from contribution of a current tag signal to a current measured intensity.