# US 2021/0277469 A1 · Sequencing and high resolution imaging > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2021/0277469 A1 - Document ID: US20210277469A1 - Status: Published application - Kind: A1 - Application number: 17/327,588 - Filed: 2021-05-21 - Published: 2021-09-09 - Earliest claimed: 2017-03-17 - Assignees: Apton Biosystems, Inc. - Applicants: Apton Biosystems, Inc. - Inventors: Bryan P. STAKER; Niandong LIU; Manohar R. FURTADO; Rixun FANG; Norman BURNS; Windsor OWENS - Web page: https://patentgrep.com/patent/US20210277469A1 ## CPC - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - G06T 7/73: using feature-based methods - G06V 20/69: Microscopic objects, e.g. biological cells or cellular parts - G16B 25/30: Microarray design - G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids - G16B 30/10: Sequence alignment; Homology search - G06F 2218/18: by plotting the signal segments against each other, e.g. analysing scattergrams - G06T 2207/20056: Discrete and fast Fourier transform, [DFT, FFT] - G06T 2207/30072: Microarray; Biochip, DNA array; Well plate - G06V 20/695: {Preprocessing, e.g. image segmentation} - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G06T: IMAGE DATA PROCESSING OR GENERATION, IN GENERAL - G06V: IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N) ## Abstract Disclosed herein are methods and systems for detection and discrimination of optical signals from a densely packed substrate. There have broad applications for biomolecule detection near or below the diffraction limit of optical systems, including in improving the efficiency and accuracy or polynucleotide sequencing applications. ## Claims ### Claim 1 A method for processing or analyzing a plurality of analytes, comprising: (a) providing a substrate that supports said plurality of analytes immobilized adjacent thereto at a density of at least 1 molecule per square micrometer (b) obtaining at least one optical signal from said substrate over at least one cycle of probes binding to one or more analytes of said plurality of analytes immobilized adjacent to said substrate; (c) processing said at least one optical signal to identify said one or more analytes of said plurality of analytes; wherein at least 10% of said plurality of analytes are separated from one another by less than λ/(2*N.A.) of said at least one optical signal. ### Claim 2 (depends on 1) The method of claim 1, wherein (b) further comprises configuring an image processing module to overlay said at least one optical signal from said at least one cycle of probes binding to said one or more analytes of said plurality of analytes, and wherein (c) further comprises applying an optical distribution model to said overlay of said at least one optical signal to identify said one or more analytes of said plurality of analytes. ### Claim 3 (depends on 2) The method of claim 2, further comprising using said image processing module to generate an oversampled image from said at least one optical signal with a higher pixel density from a field image for said at least one cycle of probes binding to said one or more analytes of said plurality of analytes. ### Claim 4 (depends on 1) The method of claim 1, wherein said plurality of analytes is immobilized adjacent to said substrate at a density of at least 2 molecules per square micrometer. ### Claim 5 (depends on 1) The method of claim 1, wherein said plurality of analytes is immobilized adjacent to said substrate at a density of at least 4 molecules per square micrometer. ### Claim 6 (depends on 1) The method of claim 1, wherein said at least one optical signal is obtained by an optical imagine module at a resolution of one pixel per 250 nanometers or lower. ### Claim 7 (depends on 1) The method of claim 1, wherein at least one analyte of said plurality of analytes is a nucleic acid molecule. ### Claim 8 (depends on 1) The of claim 1, wherein at least one analyte of said plurality of analytes is a protein or polypeptide. ### Claim 9 (depends on 1) The method of claim 1, wherein said at least one optical signal is a fluorescent signal. ### Claim 10 (depends on 1) The method of claim 1, wherein said at least one optical signal is a plurality of optical signals. ### Claim 11 (depends on 1) The method of claim 1, wherein said at least one cycle is a plurality of cycles. ### Claim 12 A system for processing or analyzing a plurality of analytes, comprising: a substrate configured to support said plurality of analytes immobilized adjacent thereto at a density of at least 1 molecule per square micrometer; an optical imaging module configured to obtain at least one optical signal from said substrate over at least one cycle of probes binding to one or more analytes of said plurality of analytes immobilized adjacent to said substrate; and an image processing module configured to process said at least one optical signal to identify said one or more analytes of said plurality of analytes; wherein at least 10% of said plurality of analytes are separated from one another by less than λ/(2*N.A.) of said at least one optical signal. ### Claim 13 (depends on 12) The system of claim 12, wherein said image processing module is configured to overlay said at least one optical signal from said substrate over said at least one cycle of probes binding to said one or more analytes of said plurality of analytes, and apply an optical distribution module of said overlay of said at least one optical signal to identify said one or more analyses of said plurality of analytes. ### Claim 14 (depends on 13) The system or claim 13, wherein said image processing module is further configured to generate an oversampled image from said at least one optical signal with a higher pixel density from a field image for said at least one cycle of probes binding to said one or more analytes of said plurality of analytes. ### Claim 15 (depends on 12) The system or claim 12, wherein said plurality of analytes is immobilized adjacent to said substrate at a density of at least 2 molecules per square micrometer. ### Claim 16 (depends on 15) The system of claim 15, wherein said plurality of analytes is immobilized adjacent to said substrate at a density of at least 4 molecules per square micrometer. ### Claim 17 (depends on 12) The system of claim 12, wherein at least one analyte of said plurality of analytes is a nucleic acid molecule. ### Claim 18 (depends on 12) The system of claim 12, wherein at least one analyte of said plurality of analytes is a protein or polypeptide. ### Claim 19 (depends on 12) The system of claim 12, wherein said at least one optical signal is a fluorescent signal. ### Claim 20 (depends on 12) The system of claim 12, wherein said at least one optical signal is a plurality of optical signals.