Scanning system and method for imaging and sequencing

A method for detecting a sequence of nucleotides of a polynucleotide, comprising:

• causing a first reaction in a flow cell, the flow cell comprising a plurality of fixed locations and a plurality of polynucleotides immobilized at the plurality of fixed locations, the first reaction involving a first group of polynucleotides of the plurality of polynucleotides;
• generating a first beam of radiation with an excitation source;
• modifying the first beam with modulating optics disposed between the excitation source and the flow cell;
• irradiating at least a portion of the flow cell with the modified first beam, wherein the modulating optics renders an intensity of irradiation of the modified first beam consistent over the at least the portion of the flow cell;
• scanning the flow cell with a scanning detector array, to detect a first radiation emitted from the first group of polynucleotides of the plurality of polynucleotides;
• causing a second reaction in the flow cell, the second reaction involving a second group of polynucleotides of the plurality of polynucleotides;
• irradiating at least a portion of the flow cell with a second beam of radiation subsequent to the second reaction;
• scanning the flow cell with the scanning detector array subsequent to the second reaction, to detect a second radiation emitted from the second polynucleotides of the plurality of polynucleotides;
• determining a sequence of nucleotides of the first group of polynucleotides of the plurality of polynucleotides based on the detected first radiation emitted from the first group of polynucleotides;
• and
• determining a sequence of nucleotides of the second group of polynucleotides of the plurality of polynucleotides based on the detected second radiation emitted from the second group of polynucleotides.