A sequencing chip comprising: a plurality of analytical devices, each analytical device having a reaction cell, an optical element and a detection element, wherein the reaction cell is a nanoscale aperture, a sample is disposed at the reaction cell, and the optical element is in optical communication with the reaction cell and the detection element; and one or more integrated waveguides (704, 706), in optical communication with a light source and the reaction cells to deliver a pulsed illumination to the reaction cells, wherein the pulsed illumination comprises two or more pulses at different wavelengths and different times, and the different wavelengths correspond to different excitation spectra of a plurality of fluorophores; wherein: the reaction cells, the optical elements, the detection elements and the one or more integrated waveguides (704, 706) are integrated components of the sequencing chip; and for each analytical device in the plurality of analytical devices: the pulsed illumination produces excitation events from the sample at the reaction cell, each excitation event producing an emitted signal; the optical element delivers the emitted signals to the detection element; and the detection element detects the emitted signals by correlating the timing of the emitted signals detected at the detection element with the timing of the excitation events, thereby identifying whether any fluorophore in the plurality of fluorophores is present or absent in the reaction cell. a plurality of analytical devices, each analytical device having a reaction cell, an optical element and a detection element, wherein the reaction cell is a nanoscale aperture, a sample is disposed at the reaction cell, and the optical element is in optical communication with the reaction cell and the detection element; and one or more integrated waveguides (704, 706), in optical communication with a light source and the reaction cells to deliver a pulsed illumination to the reaction cells, wherein the pulsed illumination comprises two or more pulses at different wavelengths and different times, and the different wavelengths correspond to different excitation spectra of a plurality of fluorophores; wherein: the reaction cells, the optical elements, the detection elements and the one or more integrated waveguides (704, 706) are integrated components of the sequencing chip; and for each analytical device in the plurality of analytical devices: the pulsed illumination produces excitation events from the sample at the reaction cell, each excitation event producing an emitted signal; the optical element delivers the emitted signals to the detection element; and the detection element detects the emitted signals by correlating the timing of the emitted signals detected at the detection element with the timing of the excitation events, thereby identifying whether any fluorophore in the plurality of fluorophores is present or absent in the reaction cell. the reaction cells, the optical elements, the detection elements and the one or more integrated waveguides (704, 706) are integrated components of the sequencing chip; and for each analytical device in the plurality of analytical devices: the pulsed illumination produces excitation events from the sample at the reaction cell, each excitation event producing an emitted signal; the optical element delivers the emitted signals to the detection element; and the detection element detects the emitted signals by correlating the timing of the emitted signals detected at the detection element with the timing of the excitation events, thereby identifying whether any fluorophore in the plurality of fluorophores is present or absent in the reaction cell. the pulsed illumination produces excitation events from the sample at the reaction cell, each excitation event producing an emitted signal; the optical element delivers the emitted signals to the detection element; and the detection element detects the emitted signals by correlating the timing of the emitted signals detected at the detection element with the timing of the excitation events, thereby identifying whether any fluorophore in the plurality of fluorophores is present or absent in the reaction cell.