Patents by Inventor Ali Agah
Ali Agah 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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Publication number: 20230039010Abstract: A device for base calling is provided. The device includes a receptacle configured to hold a biosensor having a sample surface holding a plurality of clusters during a sequence of sampling events, an array of sensors sensing information from clusters disposed in corresponding pixel areas of the sample surface during the sampling events and generate sequences of pixel signals and a communication port configured to output the sequences of pixel signals. The device also includes a signal processor coupled to the communication port and configured to receive and process at least one pixel signal in the sequences of pixel signals that mixes light gathered from at least two clusters in a corresponding pixel area, and to base call each of the at least two clusters using the at least one pixel signal.Type: ApplicationFiled: October 20, 2022Publication date: February 9, 2023Applicant: ILLUMINA, INC.Inventors: Dietrich DEHLINGER, Ali AGAH, Tracy Helen FUNG, Emrah KOSTEM
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Patent number: 11561196Abstract: In one embodiment, a sample surface of a biosensor includes pixel areas and holds a plurality of clusters during a sequence of sampling events such that the clusters are distributed unevenly over the pixel areas. In another embodiment, a biosensor has a sample surface that includes pixel areas and an array of wells overlying the pixel areas, the biosensor including two wells and two clusters per pixel area. The two wells per pixel area include a dominant well and a subordinate well. The dominant well has a larger cross section over the pixel area than the subordinate well. In yet another embodiment, an illumination system is coupled to a biosensor that illuminates the pixel areas with different angles of illumination during a sequence of sampling events, including, for a sampling event, illuminating each of the wells with off-axis illumination to produce asymmetrically illuminated well regions in each of the wells.Type: GrantFiled: January 7, 2019Date of Patent: January 24, 2023Assignee: Illumina, Inc.Inventors: Dietrich Dehlinger, Ali Agah, Tracy Helen Fung, Emrah Kostem, Craig Hetherington
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Patent number: 11554370Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.Type: GrantFiled: April 7, 2022Date of Patent: January 17, 2023Assignee: Cellanome, Inc.Inventors: Tarun Kumar Khurana, Ali Agah, Yir-Shyuan Wu, Filiz Gorpe Yasar
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Publication number: 20230001413Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.Type: ApplicationFiled: August 26, 2022Publication date: January 5, 2023Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
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Publication number: 20220415731Abstract: Provided herein include various examples of an apparatus, a sensor system and examples of a method for manufacturing aspects of an apparatus, a sensor system. The apparatus may include a die. The apparatus may also include a substrate comprising a cavity. The die may be oriented in a portion of the cavity in the substrate, where the orientation defines a first space in the cavity adjacent to a first edge of the upper surface of the die and a second space in the cavity adjacent to the second edge of the upper surface of the die. The apparatus may further include fluidics fan-out regions comprising a first cured material deposited in the first space and the second space, a surface of the fluidics fan-out regions being contiguous with the upper surface of the die.Type: ApplicationFiled: August 18, 2022Publication date: December 29, 2022Inventors: Arvin Emadi, Arnaud Rival, Ali Agah, Tara Bozorg-Grayeli
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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: 20220367547Abstract: Disclosed in one example is an apparatus including a substrate, a sensor over the substrate including an active surface and a sensor bond pad, a molding layer over the substrate and covering sides of the sensor, the molding layer having a molding height relative to a top surface of the substrate that is greater than a height of the active surface of the sensor relative to the top surface of the substrate, and a lidding layer over the molding layer and over the active surface. The lidding layer and the molding layer form a space over the active surface of the sensor that defines a flow channel.Type: ApplicationFiled: May 25, 2022Publication date: November 17, 2022Inventors: Arvin Emadi, Arnaud Rival, Ali Agah
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Publication number: 20220352228Abstract: An image sensor structure including an image stack disposed over a device stack. The image stack includes a plurality of light detectors. A first optical filter stack is disposed over the image stack. The first optical filter stack includes a light guide layer. Light pipe cavities are disposed in the light guide layer. Each light pipe cavity is associated with a light detector. Each light pipe cavity has an aspect ratio that is greater than about 2.5 to about 1. A nanowell layer is disposed over the first optical filter stack. Nanowells are disposed in the nanowell layer. Each nanowell is associated with a light detector.Type: ApplicationFiled: September 29, 2020Publication date: November 3, 2022Applicant: ILLUMINA, INC.Inventors: Arvin EMADI, Ali AGAH, Xiuyu CAI, Craig Lee HETHERINGTON
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Publication number: 20220341837Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.Type: ApplicationFiled: July 11, 2022Publication date: October 27, 2022Applicant: Illumina, Inc.Inventors: Arnaud RIVAL, Ali AGAH, Tracy H. FUNG, Dietrich DEHLINGER, Poorya SABOUNCHI, Tarun KHURANA, Craig M. CIESLA, M. Shane BOWEN
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Patent number: 11476171Abstract: Provided herein include various examples of an apparatus, a sensor system and examples of a method for manufacturing aspects of an apparatus, a sensor system. The apparatus may include a die. The apparatus may also include a substrate comprising a cavity. The die may be oriented in a portion of the cavity in the substrate, where the orientation defines a first space in the cavity adjacent to a first edge of the upper surface of the die and a second space in the cavity adjacent to the second edge of the upper surface of the die. The apparatus may further include fluidics fan-out regions comprising a first cured material deposited in the first space and the second space, a surface of the fluidics fan-out regions being contiguous with the upper surface of the die.Type: GrantFiled: February 19, 2021Date of Patent: October 18, 2022Assignee: ILLUMINA, INC.Inventors: Arvin Emadi, Arnaud Rival, Ali Agah, Tara Bozorg-Grayeli
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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: 20220299470Abstract: A device for base calling is provided. The device includes a receptacle configured to hold a biosensor having a sample surface holding a plurality of clusters during a sequence of sampling events, an array of sensors sensing information from clusters disposed in corresponding pixel areas of the sample surface during the sampling events and generate sequences of pixel signals and a communication port configured to output the sequences of pixel signals. The device also includes a signal processor coupled to the communication port and configured to receive and process at least one pixel signal in the sequences of pixel signals that mixes light gathered from at least two clusters in a corresponding pixel area, and to base call each of the at least two clusters using the at least one pixel signal.Type: ApplicationFiled: June 2, 2022Publication date: September 22, 2022Applicant: ILLUMINA, INC.Inventors: Dietrich DEHLINGER, Ali AGAH, Tracy Helen FUNG, Emrah KOSTEM
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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: 20220226820Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.Type: ApplicationFiled: April 7, 2022Publication date: July 21, 2022Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
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Publication number: 20220219170Abstract: Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.Type: ApplicationFiled: February 10, 2022Publication date: July 14, 2022Inventors: Tarun Kumar KHURANA, Ali AGAH, Yir-Shyuan WU, Filiz Gorpe YASAR
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Patent number: 11387269Abstract: Disclosed in one example is an apparatus including a substrate, a sensor over the substrate including an active surface and a sensor bond pad, a molding layer over the substrate and covering sides of the sensor, the molding layer having a molding height relative to a top surface of the substrate that is greater than a height of the active surface of the sensor relative to the top surface of the substrate, and a lidding layer over the molding layer and over the active surface. The lidding layer and the molding layer form a space over the active surface of the sensor that defines a flow channel.Type: GrantFiled: May 20, 2020Date of Patent: July 12, 2022Assignee: ILLUMINA, INC.Inventors: Arvin Emadi, Arnaud Rival, Ali Agah
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Patent number: 11385162Abstract: Flow cells and corresponding methods are provided. The flow cells may include a support frame with top and back sides, and at least one cavity extending from the top side. The flow cells may include at least one light detection device with an active area disposed within the at least one cavity. The flow cells may include a support material disposed within the at least one cavity between the support frame and the periphery of the at least one light detection device coupling them together. The flow cells may include a lid extending over the at least one light detection device and coupled to the support frame about the periphery of the at least one light detection device. The lid and at least a top surface of the at least one light detection device form a flow channel therebetween.Type: GrantFiled: January 13, 2021Date of Patent: July 12, 2022Assignee: ILLUMINA, INC.Inventors: Arnaud Rival, Ali Agah, Tracy H. Fung, Dietrich Dehlinger, Poorya Sabounchi, Tarun Khurana, Craig M. Ciesla, M. Shane Bowen
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Publication number: 20220216191Abstract: Provided herein include various examples of a method for manufacturing aspects of an apparatus, a sensor system. The method may include obtaining a first carrier bonded to an upper surface of the silicon wafer. This wafer includes through silicon vias (TSVs) extended through openings in a passivation stack, with electrical contacts coupled to portions of the TSVs exposed through these openings. The method may include de-bonding the first carrier from the upper surface of the silicon wafer. The method may include dicing the silicon wafer into subsections comprising dies.Type: ApplicationFiled: September 26, 2020Publication date: July 7, 2022Applicant: ILLUMINA, INC.Inventors: Arvin EMADI, Jon ADAY, Ali AGAH, Arnaud RIVAL