Patents by Inventor Stanley S. Hong
Stanley S. Hong has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11977213Abstract: An imaging system may include a sample stage comprising a surface to support a sample container, the sample container including a sample having a plurality of sample locations; an optical stage to image the sample at the plurality of sample locations; one or more actuators physically coupled to at least one of the sample stage and the optical stage to move the sample stage relative to the optical stage to focus the optical stage onto a current sample location of the plurality of sample locations; a first light source to illuminate the current sample location; a second light source to project a pair of spots on a next sample location of the plurality of sample locations; and a controller to determine, based on an image of the pair of spots projected on the next sample location, a focus setting for the next sample location.Type: GrantFiled: June 4, 2021Date of Patent: May 7, 2024Assignee: ILLUMINA, INC.Inventors: Ashkan Arianpour, John Bailey, Dustin Blair, Xiangling (Steve) Chen, Stanley S. Hong, Simon Prince, Merek C. Siu, Chunhong (Allen) Zhou, Danilo Condello
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Patent number: 11675175Abstract: The disclosure provides for structured illumination microscopy (SIM) imaging systems. In one set of implementations, a SIM imaging system may be implemented as a multi-arm SIM imaging system, whereby each arm of the system includes a light emitter and a beam splitter (e.g., a transmissive diffraction grating) having a specific, fixed orientation with respect to the system's optical axis. In a second set of implementations, a SIM imaging system may be implemented as a multiple beam splitter slide SIM imaging system, where one linear motion stage is mounted with multiple beam splitters having a corresponding, fixed orientation with respect to the system's optical axis. In a third set of implementations, a SIM imaging system may be implemented as a pattern angle spatial selection SIM imaging system, whereby a fixed two-dimensional diffraction grating is used in combination with a spatial filter wheel to project one-dimensional fringe patterns on a sample.Type: GrantFiled: January 14, 2019Date of Patent: June 13, 2023Assignee: ILLUMINA, INC.Inventor: Stanley S. Hong
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Publication number: 20230149933Abstract: An array including a solid support having a plurality of contours along its exterior surface. A first subset of contours is positioned along the exterior surface of the solid support to form a first pattern of features and a second subset of contours is positioned along the exterior surface to form a second pattern of features. The contours of the first subset are juxtaposed with the second subset along the exterior surface, whereby the first and second patterns form an interleaved pattern. The features of the first pattern occur at a first elevation z1 and the features of the second pattern occur at a second elevation z2. The features of the first pattern are configured to attach analytes at a different elevation relative to analytes attached to the features of the second pattern.Type: ApplicationFiled: January 13, 2023Publication date: May 18, 2023Inventors: M. Shane Bowen, Michael Graige, Stanley S. Hong, John A. Moon, Merek Siu
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Patent number: 11650156Abstract: 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.Type: GrantFiled: August 3, 2021Date of Patent: May 16, 2023Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Publication number: 20230137970Abstract: A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir, (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.Type: ApplicationFiled: December 29, 2022Publication date: May 4, 2023Inventors: Dale Buermann, John A. Moon, Bryan Crane, Mark Wang, Stanley S. Hong, Jason Harris, Matthew Hage, Mark J. Nibbe
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Patent number: 11604346Abstract: A system includes: a light source; first and second gratings; and at least one reflective component that in a first position forms a first light path originating at the light source and extending to the first grating and thereafter to a subsequent component in the system, and that in a second position forms a second light path originating at the light source and extending to the second grating and thereafter to the subsequent component.Type: GrantFiled: January 13, 2021Date of Patent: March 14, 2023Assignee: Illumina, Inc.Inventors: Stanley S. Hong, William McGuigan, Frank DeWitt, IV
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Patent number: 11565267Abstract: A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.Type: GrantFiled: January 6, 2020Date of Patent: January 31, 2023Assignee: Illumina, Inc.Inventors: Dale Buermann, John A. Moon, Bryan Crane, Mark Wang, Stanley S. Hong, Jason Harris, Matthew Hage, Mark J. Nibbe
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Patent number: 11525993Abstract: Implementations of the disclosure are directed to predicting structured illumination parameters for a particular point in time, space, and/or temperature using estimates of structured illumination parameters obtained from structured illumination images captured by a structured illumination system. Particular implementations are directed to predicting structured illumination frequency, phase, orientation, and/or modulation order parameters.Type: GrantFiled: August 6, 2021Date of Patent: December 13, 2022Assignee: ILLUMINA, INC.Inventors: Michael J. Carney, Stanley S. Hong, Robert Langlois, Hongji Ren, Kevin Wayne Bartig, Rico Otto, Olga Andreevna Souverneva
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Publication number: 20220334065Abstract: A system includes a plurality of modular subassemblies and a plate; wherein each modular subassembly comprises an enclosure and a plurality of optical components aligned to the enclosure, and each enclosure comprises a plurality of mounting structures; and wherein each modular subassembly is mechanically coupled to the plate by attachment of a mounting structure of the modular subassembly directly to a corresponding mounting structure located on the plate, such that by mechanically coupling each modular subassembly to the plate using the mounting structure of the modular subassembly and the corresponding mounting structure on the plate, adjacent modular subassemblies are aligned to each other upon such attachment, and wherein two of the modular subassemblies mechanically coupled to the plate are also attached to each other by mechanically coupling an alignment structure on one of the two modular subassemblies to a respective alignment structure on the other of the two modular subassemblies.Type: ApplicationFiled: July 5, 2022Publication date: October 20, 2022Inventors: Wenyi Feng, Simon Prince, Peter Clarke Newman, Dakota Watson, Stanley S. Hong, Marco A. Krumbuegel, Yinghua Sun, Andrew James Carson, Merek C. Siu
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Publication number: 20220331798Abstract: For example, a flowcell includes: a nanowell layer having a first set of nanowells and a second set of nanowells to receive a sample; a first linear waveguide associated with the first set of nanowells, and a second linear waveguide associated with the second set of nanowells; and a first grating for the first linear waveguide, and a second grating for the second linear waveguide, the first and second gratings providing differential coupling of first light and second light.Type: ApplicationFiled: June 30, 2022Publication date: October 20, 2022Inventors: Geraint Evans, Stanley S. Hong
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Publication number: 20220276169Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: ApplicationFiled: May 16, 2022Publication date: September 1, 2022Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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Patent number: 11406977Abstract: For example, a flowcell includes: a nanowell layer having a first set of nanowells and a second set of nanowells to receive a sample; a first linear waveguide associated with the first set of nanowells, and a second linear waveguide associated with the second set of nanowells; and a first grating for the first linear waveguide, and a second grating for the second linear waveguide, the first and second gratings providing differential coupling of first light and second light.Type: GrantFiled: May 19, 2020Date of Patent: August 9, 2022Assignees: ILLUMINA CAMBRIDGE LIMITED, ILLUMINA, INC.Inventors: Geraint Evans, Stanley S. Hong
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Patent number: 11408828Abstract: A system includes a plurality of modular subassemblies and a plate; wherein each modular subassembly comprises an enclosure and a plurality of optical components aligned to the enclosure, and each enclosure comprises a plurality of mounting structures; and wherein each modular subassembly is mechanically coupled to the plate by attachment of a mounting structure of the modular subassembly directly to a corresponding mounting structure located on the plate, such that by mechanically coupling each modular subassembly to the plate using the mounting structure of the modular subassembly and the corresponding mounting structure on the plate, adjacent modular subassemblies are aligned to each other upon such attachment, and wherein two of the modular subassemblies mechanically coupled to the plate are also attached to each other by mechanically coupling an alignment structure on one of the two modular subassemblies to a respective alignment structure on the other of the two modular subassemblies.Type: GrantFiled: June 18, 2020Date of Patent: August 9, 2022Assignee: ILLUMINA, INC.Inventors: Wenyi Feng, Simon Prince, Peter Clarke Newman, Dakota Watson, Stanley S. Hong, Marco A. Krumbuegel, Yinghua Sun, Andrew James Carson, Merek C. Siu
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Patent number: 11360027Abstract: A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.Type: GrantFiled: March 12, 2019Date of Patent: June 14, 2022Assignee: Illumina, Inc.Inventors: Yinghua Sun, Stanley S. Hong, Frederick Erie, Alex Nemiroski, M. Shane Bowen, Danilo Condello, Dietrich Dehlinger, Marco A. Krumbuegel, Anthony Lam, Aaron Liu, Bojan Obradovic, Mark Pratt
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Publication number: 20220105511Abstract: For example, a flowcell includes: a nanowell layer having a first set of nanowells and a second set of nanowells to receive a sample; a first linear waveguide associated with the first set of nanowells, and a second linear waveguide associated with the second set of nanowells; and a first grating for the first linear waveguide, and a second grating for the second linear waveguide, the first and second gratings providing differential coupling of first light and second light.Type: ApplicationFiled: May 19, 2020Publication date: April 7, 2022Applicants: ILLUMINA CAMBRIDGE LIMITED, ILLUMINA, INCInventors: Geraint Evans, Stanley S. Hong
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Publication number: 20220049292Abstract: In a first aspect, a method includes: providing a sample, the sample including a first nucleotide and a second nucleotide; contacting the sample with a first fluorescent dye and a second fluorescent dye, the first fluorescent dye emitting first emitted light within a first wavelength band responsive to a first excitation illumination light, the second fluorescent dye emitting second emitted light within a second wavelength band responsive to a second excitation illumination light; simultaneously collecting, using one or more image detectors, multiplexed fluorescent light comprising the first emitted light and the second emitted light, the first emitted light being a first color channel corresponding to the first wavelength band and the second emitted light being a second color channel corresponding to the second wavelength band; and identifying the first nucleotide based on the first wavelength band of the first color channel and the second nucleotide based on the second wavelength band of the second color chType: ApplicationFiled: March 2, 2020Publication date: February 17, 2022Inventors: Nikolai Romanov, Stanley S. Hong, Patrick McCauley, Xiaohai Liu, Danilo Condello, Merek Siu
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Patent number: 11226475Abstract: The disclosure provides for structured illumination microscopy (SIM) imaging systems. In one set of implementations, a SIM imaging system may be implemented as a multi-arm SIM imaging system, whereby each arm of the system includes a light emitter and a beam splitter (e.g., a transmissive diffraction grating) having a specific, fixed orientation with respect to the system's optical axis. In a second set of implementations, a SIM imaging system may be implemented as a multiple beam splitter slide SIM imaging system, where one linear motion stage is mounted with multiple beam splitters having a corresponding, fixed orientation with respect to the system's optical axis. In a third set of implementations, a SIM imaging system may be implemented as a pattern angle spatial selection SIM imaging system, whereby a fixed two-dimensional diffraction grating is used in combination with a spatial filter wheel to project one-dimensional fringe patterns on a sample.Type: GrantFiled: January 14, 2019Date of Patent: January 18, 2022Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Peter Clarke Newman, Danilo Condello, Shaoping Lu, Simon Prince, Merek C. Siu, Stanley S. Hong, Aaron Liu, Gary Mark Skinner, Geraint Wyn Evans
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Publication number: 20210363578Abstract: A method of sequencing a plurality of polynucleotides includes: attaching a single DNA template molecule to each of a plurality of attachment elements on a sample container, wherein the average distance between adjacent elements is less than Abbe's limit; applying a stochastic photo-switching chemistry to all of the molecules at the same time to cause the attached molecules to fluoresce in on and off events in up to four different colors by stochastic photo-switching; and imaging the on and off events in a color channel for each color in real-time as the on and off events are occurring for the attached molecules.Type: ApplicationFiled: August 5, 2021Publication date: November 25, 2021Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Publication number: 20210364772Abstract: 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.Type: ApplicationFiled: August 3, 2021Publication date: November 25, 2021Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Publication number: 20210364773Abstract: Implementations of the disclosure are directed to predicting structured illumination parameters for a particular point in time, space, and/or temperature using estimates of structured illumination parameters obtained from structured illumination images captured by a structured illumination system. Particular implementations are directed to predicting structured illumination frequency, phase, orientation, and/or modulation order parameters.Type: ApplicationFiled: August 6, 2021Publication date: November 25, 2021Inventors: Michael J. Carney, Stanley S. Hong, Robert Langlois, Hongji Ren, Kevin Wayne Bartig, Rico Otto, Olga Andreevna Souverneva