Patents by Inventor Simon Prince

Simon Prince 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).

  • Patent number: 11977213
    Abstract: 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: Grant
    Filed: June 4, 2021
    Date of Patent: May 7, 2024
    Assignee: 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
  • Publication number: 20240027349
    Abstract: A method comprises: directing, using an objective and a first reflective surface, first autofocus light toward a sensor, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing, using the objective and a second reflective surface, emission light toward the sensor, the emission light originating from a sample at the substrate.
    Type: Application
    Filed: October 4, 2023
    Publication date: January 25, 2024
    Inventors: Simon Prince, Danilo Condello, Vincent Hsieh, Krysada Phounsiri, John O’Shaughnessy
  • Publication number: 20230407386
    Abstract: Defocus is introduced during sequencing by synthesis by tilt of a flow cell and by variations in flatness of the flow cell. Effects of the defocus are reduced, and base calling quality is improved using techniques relating to dependence of base calling on flow cell tilt. For example, the flow cell surface height is measured throughout the flow cell. A focal height of an imager having a sensor for the sequencing is set, optionally adaptively, one or more times during the sequencing. Each image captured by the sensor is partitioned, e.g., based on differences between focal height and the measured flow cell surface height across areas of the sensor. Filters, e.g., related to defocus correction, are selected based at least in part on the difference between the focal height and the measured flow cell surface height at a particular area of the image being corrected for defocus.
    Type: Application
    Filed: June 9, 2023
    Publication date: December 21, 2023
    Applicants: Illumina, Inc., Illumina Software, Inc.
    Inventors: Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Simon Prince
  • Publication number: 20230393379
    Abstract: A method is used to generate a distortion model for a structured illumination microscopy (SIM) optical system. A sliding window is moved in relation to a plurality of images to define a plurality of sub-tiles. Each sub-tile represents a portion of the corresponding image. Parameters are estimated for each sub-tiles. The parameters include two or more parameters selected from the group consisting of modulation, angle, spacing, phase offset, and phase deviation. A full width at half maximum (FWHM) value associated with each sub-tile is estimated. A distortion model is estimated, based at least in part on a combination of the estimated parameters and FWHM values stored in the predetermined format and an estimated center window parameter. A two-dimensional image may be generated, based at least in part on the estimated distortion model. The two-dimensional image may include representations indicating where distortions occur in the optical system.
    Type: Application
    Filed: August 21, 2023
    Publication date: December 7, 2023
    Inventors: Robert Langlois, Bo Lu, Hongji Ren, Joseph Pinto, Simon Prince, Austin Corbett
  • Patent number: 11815458
    Abstract: A method comprises: directing, using an objective and a first reflective surface, first autofocus light toward a sensor, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing, using the objective and a second reflective surface, emission light toward the sensor, the emission light originating from a sample at the substrate.
    Type: Grant
    Filed: December 22, 2020
    Date of Patent: November 14, 2023
    Assignee: Illumina, Inc.
    Inventors: Simon Prince, Danilo Condello, Vincent Hsieh, Krysada Phounsiri, John O'Shaughnessy
  • Patent number: 11768364
    Abstract: A method is used to generate a distortion model for a structured illumination microscopy (SIM) optical system. A sliding window is moved in relation to a plurality of images to define a plurality of sub-tiles. Each sub-tile represents a portion of the corresponding image. Parameters are estimated for each sub-tiles. The parameters include two or more parameters selected from the group consisting of modulation, angle, spacing, phase offset, and phase deviation. A full width at half maximum (FWHM) value associated with each sub-tile is estimated. A distortion model is estimated, based at least in part on a combination of the estimated parameters and FWHM values stored in the predetermined format and an estimated center window parameter. A two-dimensional image may be generated, based at least in part on the estimated distortion model. The two-dimensional image may include representations indicating where distortions occur in the optical system.
    Type: Grant
    Filed: December 3, 2020
    Date of Patent: September 26, 2023
    Assignee: ILLUMINA, INC.
    Inventors: Robert Langlois, Bo Lu, Hongji Ren, Joseph Pinto, Simon Prince, Austin Corbett
  • Publication number: 20230296516
    Abstract: Artificial intelligence driven signal enhancement of sequencing images enables enhanced sequencing by synthesis that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken at unreduced and reduced power levels used to excite fluorescence during sequencing by synthesis is used to train a neural network to enable the neural network to recover enhanced images, as if taken at the unreduced power level, from unenhanced images taken at the reduced power level.
    Type: Application
    Filed: February 17, 2023
    Publication date: September 21, 2023
    Applicants: Illumina, Inc., Illumina Software, Inc.
    Inventors: Anindita Dutta, Michael Gallaspy, Jeffrey Gau, Stanley Hong, Aathavan Karunakaran, Simon Prince, Merek Siu, Yina Wang, Rishi Verma
  • Publication number: 20230260096
    Abstract: Artificial intelligence driven enhancement of motion blurred sequencing images enables enhanced sequencing that determines a sequence of bases in genetic material with any one or more of: improved performance, improved accuracy, and/or reduced cost. A training set of images taken after unreduced and reduced movement settling times during sequencing is used to train a neural network to enable the neural network to recover enhanced images, as if taken after the unreduced movement settling time, from unenhanced images taken after the reduced movement settling time.
    Type: Application
    Filed: February 17, 2023
    Publication date: August 17, 2023
    Applicants: Illumina, Inc., Illumina Software, Inc.
    Inventors: Simon Prince, Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Yina Wang, Rishi Verma
  • Publication number: 20230108792
    Abstract: An apparatus and method for imaging includes an imaging system formed of a movable objective stage proximal to a sample and positioned for providing an excitation beam onto and for capturing an emission from the sample. The movable objective stage includes an optical lens apparatus and a turn reflector optically coupled to the imaging optics, where at least one of the optical lens apparatus and the turn reflector are movable relative to one another for scanning the sample, and wherein the movement is achieved while maintaining a substantially fixed optical path length between the optical lens apparatus and a fixed plane in a fixed imaging optics stage.
    Type: Application
    Filed: September 30, 2022
    Publication date: April 6, 2023
    Inventors: Steven Boege, Simon Prince, Peter Newman, Matthew Hage, Geraint Evans
  • Publication number: 20230070459
    Abstract: Resolution of images used in processes such as sequencing by synthesis may be increased by structuring sites that would emit signals in the images to have different elevations. Differences in focus caused by these differences in elevation may be used to filter out background illumination, thereby providing an image in which in focus sites may be resolved even though the separation between any site and its nearest neighbor may be below the diffraction limit of the light that would be emitted.
    Type: Application
    Filed: August 30, 2022
    Publication date: March 9, 2023
    Inventor: Simon Prince
  • Publication number: 20220334065
    Abstract: 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: Application
    Filed: July 5, 2022
    Publication date: October 20, 2022
    Inventors: Wenyi Feng, Simon Prince, Peter Clarke Newman, Dakota Watson, Stanley S. Hong, Marco A. Krumbuegel, Yinghua Sun, Andrew James Carson, Merek C. Siu
  • Publication number: 20220326156
    Abstract: A system for analysis of a sample at a substrate comprises: a light source to generate first light; and a spatial light modulator to form second light from the first light, wherein the substrate includes at least one sensor to detect an emission emitted based on the second light, wherein at the substrate the second light forms a shape selected based on the at least one sensor, wherein the second light illuminates an area of the substrate corresponding to the shape.
    Type: Application
    Filed: April 6, 2022
    Publication date: October 13, 2022
    Inventors: Simon Prince, Krysada Phounsiri, Wenyi FENG
  • Publication number: 20220308354
    Abstract: Apparatus and methods for transmitting light are disclosed. In an implementation, an apparatus includes a collimator at an input end positioned to receive an input beam from a fiber beam source and to produce a collimated beam. The apparatus further includes a beam shaping group having one or more optical elements and positioned to receive the collimated beam from the collimator and format the collimated beam into a shaped propagation beam having a substantially rectangular cross-section in a far field. The apparatus further includes an objective stage for optically probing a sample, such as a flow cell, using substantially rectangular cross-section sampling beam, where fluorescence from the sample is captured by a line sensor for detecting properties of the sample, such as chemical reactions therein.
    Type: Application
    Filed: March 25, 2022
    Publication date: September 29, 2022
    Inventors: Steven Boege, Simon Prince, Danilo Condello
  • Patent number: 11408828
    Abstract: 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: Grant
    Filed: June 18, 2020
    Date of Patent: August 9, 2022
    Assignee: 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
  • Patent number: 11226475
    Abstract: 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: Grant
    Filed: January 14, 2019
    Date of Patent: January 18, 2022
    Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Peter Clarke Newman, Danilo Condello, Shaoping Lu, Simon Prince, Merek C. Siu, Stanley S. Hong, Aaron Liu, Gary Mark Skinner, Geraint Wyn Evans
  • Patent number: 11190706
    Abstract: Systems and methods disclosed herein include an imaging system that may include a laser diode source; an objective lens positioned to direct a focus tracking beam from the light source onto a location in a sample container and to receive the focus tracking beam reflected from the sample; and an image sensor that may include a plurality of pixel locations to receive focus tracking beam that is reflected off of the location in the sample container, where the reflected focus tracking beam may create a spot on the image sensor. Some examples may further include a laser diode light source that may be operated at a power level that is above a power level for operation at an Amplified Spontaneous Emission (“ASE”) mode, but below a power level for single mode operation.
    Type: Grant
    Filed: April 27, 2020
    Date of Patent: November 30, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Danilo Condello, Simon Prince, David Hargis, Jeffrey Bendick, Christophe Sigel
  • Patent number: 11143856
    Abstract: An imaging system including a light source; a first focusing lens positioned to focus a beam from the light source to a beam waist at a predetermined location along an optical path of the beam in the imaging system; a beam splitter positioned relative to the first focusing lens to receive the beam from the first focusing lens and to create first and second beams; a second focusing lens positioned to receive the first and second beams output by the beam splitter, to focus the received first and second beams to a spot sized dimensioned to fall within a sample to be image, and further positioned to receive first and second beams reflected from the sample; an image sensor positioned to receive the light beams reflected from the sample; and a roof prism positioned in the optical path between the second focusing lens and the image sensor.
    Type: Grant
    Filed: August 16, 2019
    Date of Patent: October 12, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Danilo Condello, Simon Prince, John O'Shaughnessy, Christophe Sigel, Ashkan Arianpour
  • Publication number: 20210294083
    Abstract: 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: Application
    Filed: June 4, 2021
    Publication date: September 23, 2021
    Inventors: Ashkan Arianpour, John Bailey, Dustin Blair, Xiangling (Steve) Chen, Stanley S. Hong, Simon Prince, Merek C. Siu, Chunhong (Allen) Zhou, Danilo Condello
  • Patent number: 11125988
    Abstract: Systems and methods disclosed herein include an optical blocking structure that may include a frame defining an aperture, first and second elongate structural members each comprising first and second ends such that the first and second elongate structural members may be connected at their first ends to opposite sides of the aperture, and further such that the first and second elongate structural members may extend from the frame parallel to and in the same direction as one another; and an optically opaque blocking member positioned to extend between the respective second ends of the first and second blocking members.
    Type: Grant
    Filed: March 6, 2018
    Date of Patent: September 21, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Danilo Condello, Simon Prince, David Hargis, John O'Shaughnessy, William Butterfield, Jeffrey Bendick, Peter Clarke Newman
  • Patent number: 11054624
    Abstract: 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: Grant
    Filed: December 22, 2017
    Date of Patent: July 6, 2021
    Assignee: 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