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: 11150455Abstract: 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: January 22, 2019Date of Patent: October 19, 2021Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Publication number: 20210294083Abstract: 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: ApplicationFiled: June 4, 2021Publication date: September 23, 2021Inventors: 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: 11119302Abstract: 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: November 5, 2020Date of Patent: September 14, 2021Assignee: 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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Patent number: 11111533Abstract: 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: GrantFiled: March 6, 2019Date of Patent: September 7, 2021Assignees: ILLUMINA CAMBRIDGE LIMITED, ILLUMINA, INC.Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Patent number: 11112591Abstract: 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: January 22, 2019Date of Patent: September 7, 2021Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong
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Patent number: 11054624Abstract: An imaging system may include a sample stage comprising a surface to support a sample container, the sample container having a plurality of sample locations; an optical stage having an objective lens, the optical stage being positionable relative to the sample stage to image samples at the sample locations; an actuator 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; and a drive circuit to determine a focus setting for a next sample location and to provide a drive signal to the actuator before the optical stage is positioned to image a sample at the next sample location, wherein at least one parameter of the drive signal is determined using a difference between a focus setting for the current sample location and the determined focus setting for the next sample location.Type: GrantFiled: December 22, 2017Date of Patent: July 6, 2021Assignee: 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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Publication number: 20210132365Abstract: 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: ApplicationFiled: January 13, 2021Publication date: May 6, 2021Inventors: Stanley S. Hong, William McGuigan, Frank DeWitt, IV
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Patent number: 10996453Abstract: 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: May 4, 2021Assignee: ILLUMINA, INC.Inventors: Peter Clarke Newman, Danilo Condello, Shaoping Lu, Simon Prince, Merek C. Siu, Stanley S. Hong, Aaron Liu
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Publication number: 20210055535Abstract: 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: November 5, 2020Publication date: February 25, 2021Inventors: Michael J. Carney, Stanley S. Hong, Robert Langlois, Hongji Ren, Kevin Wayne Bartig, Rico Otto, Olga Andreevna Souverneva
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Patent number: 10901230Abstract: Example super-resolution microscopy systems are described herein that are configured for relatively high throughput. The disclosed microscopy systems can be to generate an array of sub-diffraction activated areas for imaging. The microscopy systems can be to utilize imaging techniques that employ time delay integration to build up super-resolution images over time. The disclosed microscopy systems can utilize long-lived fluorophores in conjunction with wide field and patterned illumination to generate super-resolution images of a sample with relatively high throughput.Type: GrantFiled: June 20, 2017Date of Patent: January 26, 2021Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong, John A. Moon, M. Shane Bowen, Jonathan Mark Boutell, Jason Richard Betley
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Patent number: 10901202Abstract: 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: September 17, 2019Date of Patent: January 26, 2021Assignee: ILLUMINA, INC.Inventors: Stanley S. Hong, William McGuigan, Frank DeWitt, IV
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Patent number: 10831012Abstract: 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: June 20, 2019Date of Patent: November 10, 2020Assignee: 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: 20200319115Abstract: 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: June 18, 2020Publication date: October 8, 2020Inventors: 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: 10774371Abstract: Imaging systems including an objective lens and a line generation module are described herein. The objective lens may focus a first light beam emitted by the line generation module and a second light beam emitted by the line generation module at a focal point external to a sample so as to adjust line width. Line width may be increased to lower overall power density of a light beam on a surface of the sample such that the power density of the light beam on the surface of the sample is below a photosaturation threshold of a dye on the sample.Type: GrantFiled: March 6, 2018Date of Patent: September 15, 2020Assignee: ILLUMINA, INC.Inventors: Yinghua Sun, Stanley S. Hong, Marco A. Krumbuegel, Peter Clarke Newman, Simon Prince, Dakota Watson, Wenyi Feng, Andrew James Carson, Frederick Erie
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Patent number: 10732122Abstract: A system for biological sample analysis includes a plurality of modular subassemblies and a precision mounting plate, wherein each modular subassembly includes an enclosure and a plurality of optical components pre-aligned to the enclosure, and the enclosure includes a plurality of precision mounting structures, and each modular subassembly is mechanically coupled to the precision mounting plate, such that each precision mounting structure from a modular subassembly attaches directly to a corresponding precision mounting structure located on the precision mounting plate or an adjacent modular subassembly to optimize optomechanical tolerance.Type: GrantFiled: December 19, 2017Date of Patent: August 4, 2020Assignee: 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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Publication number: 20200218052Abstract: 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: ApplicationFiled: January 14, 2019Publication date: July 9, 2020Inventor: Stanley S. Hong
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Publication number: 20200218050Abstract: 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: ApplicationFiled: January 14, 2019Publication date: July 9, 2020Inventors: Peter Clarke Newman, Danilo Condello, Shaoping Lu, Simon Prince, Merek C. Siu, Stanley S. Hong, Aaron Liu
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Publication number: 20200192071Abstract: 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: ApplicationFiled: January 14, 2019Publication date: June 18, 2020Inventors: 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: 20200139375Abstract: 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: January 6, 2020Publication date: May 7, 2020Inventors: Dale Buermann, John A. Moon, Bryan Crane, Mark Wang, Stanley S. Hong, Jason Harris, Matthew Hage, Mark J. Nibbe
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Publication number: 20200103639Abstract: 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: January 22, 2019Publication date: April 2, 2020Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong