Patents by Inventor Merek Siu
Merek Siu 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: 11867672Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.Type: GrantFiled: February 9, 2023Date of Patent: January 9, 2024Assignee: ILLUMINA, INC.Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Publication number: 20230407386Abstract: 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: ApplicationFiled: June 9, 2023Publication date: December 21, 2023Applicants: Illumina, Inc., Illumina Software, Inc.Inventors: Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Simon Prince
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Publication number: 20230321651Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.Type: ApplicationFiled: May 26, 2023Publication date: October 12, 2023Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Publication number: 20230296516Abstract: 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: ApplicationFiled: February 17, 2023Publication date: September 21, 2023Applicants: Illumina, Inc., Illumina Software, Inc.Inventors: Anindita Dutta, Michael Gallaspy, Jeffrey Gau, Stanley Hong, Aathavan Karunakaran, Simon Prince, Merek Siu, Yina Wang, Rishi Verma
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Publication number: 20230285974Abstract: Devices, systems, and methods for non-volatile storage include a well activation device operable to modify one or more wells from a plurality of wells of a flow cell to provide a set of readable wells. Readable wells are configured to allow exposure of a well to substances from nucleotide sequencing fluids, and prevent exposure to other substances and fluids, such as nucleotide synthesizing fluids. The well activation device may also modify wells to provide a set of writeable wells. This set of wells is configured to allow exposure to the nucleotide synthesizing fluids and substances; and prevent exposure to the nucleotide sequencing fluids and substances. There may also be provisions made for risk mitigation for data errors such as generating commands to write specified data to a nucleotide sequence associated with a particular location in a storage device, reading the nucleotide sequence and performing a comparison.Type: ApplicationFiled: January 31, 2023Publication date: September 14, 2023Inventors: Merek Siu, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Craig Ciesla, Amirali Kia
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Publication number: 20230260096Abstract: 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: ApplicationFiled: February 17, 2023Publication date: August 17, 2023Applicants: Illumina, Inc., Illumina Software, Inc.Inventors: Simon Prince, Stanley Hong, Michael Gallaspy, Merek Siu, Jeffrey Gau, Anindita Dutta, Aathavan Karunakaran, Yina Wang, Rishi Verma
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Publication number: 20230228984Abstract: Some implementations of the disclosure relate to an imaging system, including: a sample holder to support a sample container having multiple sample locations; an optical stage having; an assembly comprising one or more actuators physically coupled to the sample holder to tilt the sample holder relative to the optical stage during imaging of the multiple sample locations to focus the optical stage onto a current sample location; a first light source to project a first pair of spots on the sample container; and a controller to control, based on a sample tilt determined from a first separation measurement of the first pair of spots from one or more images taken by an image sensor at one or more of the sample locations, the one or more actuators to tilt the sample holder along a first direction of the imaging or a second direction substantially perpendicular to the first direction.Type: ApplicationFiled: January 17, 2023Publication date: July 20, 2023Inventors: Dakota Watson, Merek Siu, Dustin Blair, Danilo Condello, John Earney, Paul Sangiorgio
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Patent number: 11691146Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.Type: GrantFiled: August 30, 2022Date of Patent: July 4, 2023Assignee: ILLUMINA, INC.Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Publication number: 20230184725Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.Type: ApplicationFiled: February 9, 2023Publication date: June 15, 2023Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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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: 11604175Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.Type: GrantFiled: June 22, 2022Date of Patent: March 14, 2023Assignee: ILLUMINA, INC.Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Patent number: 11590505Abstract: Devices, systems, and methods for non-volatile storage include a well activation device operable to modify one or more wells from a plurality of wells of a flow cell to provide a set of readable wells. Readable wells are configured to allow exposure of a well to substances from nucleotide sequencing fluids, and prevent exposure to other substances and fluids, such as nucleotide synthesizing fluids. The well activation device may also modify wells to provide a set of writeable wells. This set of wells is configured to allow exposure to the nucleotide synthesizing fluids and substances; and prevent exposure to the nucleotide sequencing fluids and substances. There may also be provisions made for risk mitigation for data errors such as generating commands to write specified data to a nucleotide sequence associated with a particular location in a storage device, reading the nucleotide sequence and performing a comparison.Type: GrantFiled: May 26, 2020Date of Patent: February 28, 2023Assignee: ILLUMINA, INC.Inventors: Merek Siu, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Craig Ciesla, Amirali Kia
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Publication number: 20220410154Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.Type: ApplicationFiled: August 30, 2022Publication date: December 29, 2022Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Publication number: 20220317100Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.Type: ApplicationFiled: June 22, 2022Publication date: October 6, 2022Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Patent number: 11453003Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.Type: GrantFiled: December 14, 2021Date of Patent: September 27, 2022Assignee: ILLUMINA, INC.Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Publication number: 20220254452Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.Type: ApplicationFiled: March 1, 2022Publication date: August 11, 2022Inventors: Craig Ciesla, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Arvin Emadi, Merek Siu
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Patent number: 11402358Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an imaging assembly, and one or more barrier features. The flow cell body defines one or more flow channels and a plurality of wells defined as recesses in the floor of each flow channel. Each well is fluidically coupled with the corresponding flow channel. The flow cell body further defines interstitial surfaces between adjacent wells. Each well defines a corresponding depth. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are to effect writing of polynucleotides in the wells. The imaging assembly is to capture images of polynucleotides written in the wells. The one or more barrier features are positioned in the wells, between the wells, or above the wells. The one or more barrier features contain reactions in each well, reduce diffusion between the wells, or reduce optical cross-talk between the wells.Type: GrantFiled: September 20, 2021Date of Patent: August 2, 2022Assignee: ILLUMINA, INC.Inventors: Tarun Khurana, Ali Agah, Aathavan Karunakaran, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Publication number: 20220150394Abstract: A method is used to generate an analysis image of a moving sample based on one or more exposures. An illumination source illuminates a field of view of a camera for one or more pulses while the sample moves through the field of view. The distance moved by the sample during each of these one or more pulses may be less than the size of one pixel in an image captured by the camera.Type: ApplicationFiled: October 28, 2021Publication date: May 12, 2022Inventors: Geraint Evans, Stanley Hong, Merek Siu, Shaoping Lu, John Moon
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Publication number: 20220097060Abstract: An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.Type: ApplicationFiled: December 14, 2021Publication date: March 31, 2022Inventors: Ali Agah, Aathavan Karunakaran, Tarun Khurana, Stanley Hong, Merek Siu, Arvin Emadi, Craig Ciesla
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Patent number: 11282588Abstract: A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.Type: GrantFiled: May 26, 2020Date of Patent: March 22, 2022Assignee: ILLUMINA, INC.Inventors: Craig Ciesla, Ali Agah, Stanley Hong, Tarun Khurana, Aathavan Karunakaran, Arvin Emadi, Merek Siu