# US 11,112,591 B2 · Reduced dimensionality structured illumination microscopy with patterned arrays of nanowells > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 11,112,591 B2 - Document ID: US11112591B2 - Status: Granted - Kind: B2 - Application number: 16/621,122 - Filed: 2019-01-22 - Published: 2020-04-02 - Granted: 2021-09-07 - Earliest claimed: 2018-01-24 - Assignees: Illumina, Inc.; Illumina Cambridge Limited - Applicants: Illumina, Inc.; Illumina Cambridge Limited - Inventors: Gary Mark Skinner; Geraint Wyn Evans; Stanley S. Hong - Web page: https://patentgrep.com/patent/US11112591B2 ## CPC - G02B 21/06: Means for illuminating specimens - B01L 3/5085: {for multiple samples, e.g. microtitration plates} - G01N 21/05: Flow-through cuvettes (G01N21/09 takes precedence; handling fluid samples G01N1/10) - G02B 21/16: adapted for ultraviolet illumination {; Fluorescence microscopes (G02B21/0076 takes precedence)} - G02B 21/365: {Control or image processing arrangements for digital or video microscopes (G02B21/361, G02B21/362 take precedence)} - G02B 27/425: {in illumination systems (mask illumination systems in photolithographic systems G03F7/70158)} - B01L 2300/0654: Lenses; Optical fibres - B01L 2300/0663: Whole sensors - B01L 2300/0893: having a very large number of wells, microfabricated wells - B01L 2300/0896: Nanoscaled - G02B: OPTICAL ELEMENTS, SYSTEMS OR APPARATUS - B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) ## Abstract Techniques are described for reducing the number of angles needed in structured illumination imaging of biological samples through the use of patterned flowcells, where nanowells of the patterned flowcells are arranged in, e.g., a square array, or an asymmetrical array. Accordingly, the number of images needed to resolve details of the biological samples is reduced. Techniques are also described for combining structured illumination imaging with line scanning using the patterned flowcells. ## Claims ### Claim 1 A method of imaging a biological sample, comprising: projecting an optical pattern onto a biological sample and capturing a first image of the optical pattern overlaid on the biological sample, the biological sample being contained in an asymmetrically patterned flowcell comprising a plurality of elongated nanowells, wherein each of the elongated nanowells is elliptically shaped or rectangularly shaped; phase shifting the projected optical pattern relative to the biological sample and capturing at least a second image of the phase shifted optical pattern overlaid on the biological sample; and reconstructing a high resolution image representative of the biological sample based upon the first captured image and the at least second captured image. ### Claim 2 (depends on 1) The method of claim 1, wherein each of the plurality of elongated nanowells are oriented such that along a first axis of the asymmetrically patterned flowcell, resolution is increased to resolve information representative of the biological sample. ### Claim 3 (depends on 2) The method of claim 2, wherein each of the plurality of elongated nanowells are oriented such that along a second axis of the asymmetrically patterned flowcell, resolution is not increased to resolve information representative of the biological sample. ### Claim 4 (depends on 1) The method of claim 1, wherein the capturing of the first and the at least second images comprises performing line scanning imaging. ### Claim 5 (depends on 4) The method of claim 4, further comprising: directing light through an optical diffraction grating in a first phase and angle orientation, wherein the optical pattern projected onto the biological sample is an optical diffraction grating pattern generated by the light being directed through the optical diffraction grating, wherein phase shifting the projected optical pattern relative to the biological sample comprises phase shifting the optical diffraction grating. ### Claim 6 (depends on 5) The method of claim 5, wherein the phase shifting of the optical diffraction grating comprises phase shifting the optical diffraction grating along the first angle orientation. ### Claim 7 (depends on 6) The method of claim 6, wherein the phase shifting of the optical diffraction grating occurs perpendicularly to a direction of the line scanning imaging. ### Claim 8 (depends on 1) The method of claim 1, further comprising: directing light through an optical diffraction grating in a first phase and angle orientation, wherein the optical pattern projected onto the biological sample is an optical diffraction grating pattern generated by the light being directed through the optical diffraction grating, wherein phase shifting the projected optical pattern relative to the biological sample comprises phase shifting the optical diffraction grating; and performing a third phase shift of the optical diffraction grating, projecting the optical diffraction grating pattern onto the biological sample and capturing at least a third image of the phase shifted optical diffraction grating pattern overlaid on the biological sample prior to reconstructing the high resolution image. ### Claim 9 A method of imaging a biological sample, comprising: directing light through an optical diffraction grating in a first phase and angle orientation; projecting an optical diffraction grating pattern generated by the light being directed through the optical diffraction grating onto the biological sample and capturing a first image of the optical diffraction grating pattern overlaid on the biological sample, the biological sample being contained in an asymmetrically patterned flowcell comprising a plurality of elongated nanowells, wherein each of the elongated nanowells is elliptically shaped or rectangularly shaped; phase shifting the optical diffraction grating, projecting the optical diffraction grating pattern onto the biological sample and capturing at least a second image of the phase shifted optical diffraction grating pattern overlaid on the biological sample; reorienting the optical diffraction grating to a second angle orientation, projecting the optical diffraction grating pattern onto the biological sample, and capturing a third image of the optical diffraction grating pattern overlaid on the biological sample; phase shifting the optical diffraction grating, projecting the optical diffraction grating pattern onto the biological sample and capturing at least a fourth image of the phase shifted optical diffraction grating pattern overlaid on the biological sample; and reconstructing a high resolution image representative of the biological sample based upon the first, the at least second, the third, and the at least fourth captured images. ### Claim 10 A system, comprising: a laser source emitting a light beam; an optical diffraction grating adapted to generate an optical diffraction grating pattern upon passage of the emitted light beam through the optical diffraction grating; a camera assembly adapted to capture a plurality of images of optical diffraction grating pattern overlaid on a biological sample, the plurality of images reflecting three phases of the optical diffraction grating relative to the biological sample, wherein the biological sample is located in a flowcell comprising a plurality of nanowells that are oriented in an asymmetrical array and wherein each of the plurality of nanowells are elliptically shaped or rectangularly shaped; and a processor adapted to reconstruct a high resolution image representative of the biological sample based on a combination of the plurality of images. ### Claim 11 (depends on 10) The system of claim 10, wherein each of the plurality of nanowells are oriented such that along a first axis of the flowcell, resolution is increased to resolve information representative of the biological sample. ### Claim 12 (depends on 11) The system of claim 11, wherein each of the plurality of nanowells are oriented such that along a second axis of the flowcell, resolution is not increased to resolve information representative of the biological sample. ### Claim 13 A system, comprising: a laser source emitting a light beam; an optical diffraction grating adapted to generate an optical diffraction grating pattern upon passage of the emitted light beam through the optical diffraction grating; a camera assembly adapted to capture a plurality of images of optical diffraction grating pattern overlaid on a biological sample, the plurality of images reflecting three phases of the optical diffraction grating relative to the biological sample, wherein the camera assembly comprises a time delay integration line scanning camera assembly; and a processor adapted to reconstruct a high resolution image representative of the biological sample based on a combination of the plurality of images. ### Claim 14 (depends on 13) The system of claim 13, wherein the biological sample is contained in a flowcell, different portions of which are overlaid with representations of the three phases of the optical diffraction grating simultaneously. ### Claim 15 (depends on 13) The system of claim 13, wherein the optical diffraction grating comprises three phase stepped elements, wherein each of the three phase stepped elements is adapted to generate an optical diffraction grating pattern upon passage of the emitted light beam through the phase stepped element, wherein the camera assembly is adapted to capture an image of an optical diffraction grating pattern generated by each of the three phase stepped elements overlaid on the biological sample. ### Claim 16 (depends on 15) The system of claim 15, wherein the camera assembly comprises three image sensors, each of the three image sensors adapted to capture the image of the optical diffraction grating pattern generated by a respective one of the phase stepped elements. ### Claim 17 A system, comprising: a laser source emitting a light beam; an optical diffraction grating adapted to generate an optical diffraction grating pattern upon passage of the emitted light beam through the optical diffraction grating; a camera assembly adapted to capture a plurality of images of optical diffraction grating pattern overlaid on a biological sample, the plurality of images reflecting three phases of the optical diffraction grating relative to the biological sample and two angular orientations of the optical diffraction grating relative to the biological sample, wherein the biological sample is located in a flowcell comprising a plurality of nanowells that are oriented in an asymmetrical array and wherein each of the plurality of nanowells are elliptically shaped or rectangularly shaped; and a processor adapted to reconstruct a high resolution image representative of the biological sample based on a combination of the plurality of images. ### Claim 18 (depends on 17) The system of claim 17, wherein each of the plurality of nanowells are oriented such that resolution is increased to resolve information representative of the biological sample along first and second axes of the flowcell.