公开(公告)号：US12201985B2

公开(公告)日：2025-01-21

申请号：US18103625

申请日：2023-01-31

Applicant: ILLUMINA, INC.

Inventor： Merek Siu ,  Ali Agah ,  Stanley Hong ,  Tarun Khurana ,  Aathavan Karunakaran ,  Craig Ciesla ,  Amirali Kia

IPC: B01L3/00 ,  C12Q1/6869 ,  G11C13/02 ,  G11C13/04 ,  G16B50/30 ,  G16B30/10

Abstract: 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.

公开(公告)号：US11933728B2

公开(公告)日：2024-03-19

申请号：US18154405

申请日：2023-01-13

Applicant: ILLUMINA, INC. ,  ILLUMINA CAMBRIDGE LIMITED

Inventor： Gary Skinner ,  Geraint Evans ,  Stanley Hong

IPC: G06V10/10 ,  B01L3/00 ,  G01N21/05 ,  G01N21/64 ,  G02B21/06 ,  G02B21/16 ,  G02B21/36 ,  G02B27/42

CPC classification number: G01N21/6452 ,  B01L3/5085 ,  G01N21/05 ,  G02B21/06 ,  G02B21/16 ,  G02B21/365 ,  G02B27/425 ,  G06V10/10 ,  B01L2300/0654 ,  B01L2300/0663 ,  B01L2300/0893 ,  B01L2300/0896

Abstract: 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.

公开(公告)号：US20230321651A1

公开(公告)日：2023-10-12

申请号：US18202461

申请日：2023-05-26

Applicant: ILLUMINA, INC.

Inventor： Ali Agah ,  Aathavan Karunakaran ,  Tarun Khurana ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

IPC: B01L3/00 ,  G11C13/02 ,  B01J19/00

CPC classification number: B01L3/502715 ,  B01L3/502707 ,  B01L3/502738 ,  G11C13/02 ,  B01J19/0046 ,  C12Q1/6874

Abstract: 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.

公开(公告)号：US20230296516A1

公开(公告)日：2023-09-21

申请号：US18111298

申请日：2023-02-17

Applicant: Illumina, Inc. ,  Illumina Software, Inc.

Inventor： Anindita Dutta ,  Michael Gallaspy ,  Jeffrey Gau ,  Stanley Hong ,  Aathavan Karunakaran ,  Simon Prince ,  Merek Siu ,  Yina Wang ,  Rishi Verma

IPC: G01N21/64 ,  G06N3/08

CPC classification number: G01N21/6456 ,  G06N3/08

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.

公开(公告)号：US11691146B2

公开(公告)日：2023-07-04

申请号：US17898663

申请日：2022-08-30

Applicant: ILLUMINA, INC.

Inventor： Ali Agah ,  Aathavan Karunakaran ,  Tarun Khurana ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

IPC: B01L3/00 ,  G11C13/02 ,  B01J19/00 ,  C12Q1/6874 ,  C12N15/09

CPC classification number: B01L3/502715 ,  B01J19/0046 ,  B01L3/502707 ,  B01L3/502738 ,  G11C13/02 ,  B01J2219/00711 ,  B01J2219/00713 ,  B01J2219/00722 ,  B01L2200/026 ,  B01L2300/0645 ,  B01L2300/0816 ,  B01L2300/0867 ,  B01L2400/0487 ,  B01L2400/0622 ,  B01L2400/0655 ,  B01L2400/08 ,  C12N15/09 ,  C12Q1/6874

Abstract: 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.

公开(公告)号：US20230143682A1

公开(公告)日：2023-05-11

申请号：US17981206

申请日：2022-11-04

Applicant: ILLUMINA, INC.

Inventor： Danilo Condello ,  Dakota Watson ,  Andrew Carson ,  Vincent Hsieh ,  Steven Boege ,  Changqin Ding ,  Stanley Hong

IPC: G02B27/09 ,  G02B26/10 ,  G01N21/64

CPC classification number: G02B27/0927 ,  G02B26/101 ,  G02B27/0916 ,  G02B27/0955 ,  G02B27/0994 ,  G01N21/6428 ,  G01N21/6456 ,  G01N2021/6439

Abstract: Apparatus and methods for controlling heating of an objective in a linescanning sequencing system to improve resolution are disclosed. In accordance with a first implementation, an apparatus includes or comprises a beam source for providing input radiation and a beam shaping group including or comprising one or more optical elements positioned to receive the input radiation from the beam source, and to perform beam shaping on the input radiation to form a shaped beam. The apparatus further including or comprising an objective positioned to receive the shaped beam and to transform the shaped beam into a probe beam and configured to provide the probe beam to a focal plane of the objective for optically probing a sample. The beam shaping group is configured to adjust one or more properties of the shaped beam over time to generally uniformly heat the objective over a region of incidence for the shaped beam.

公开(公告)号：US20220410154A1

公开(公告)日：2022-12-29

申请号：US17898663

申请日：2022-08-30

Applicant: ILLUMINA, INC.

Inventor： Ali Agah ,  Aathavan Karunakaran ,  Tarun Khurana ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

IPC: B01L3/00 ,  G11C13/02 ,  B01J19/00

Abstract: 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.

公开(公告)号：US20220317100A1

公开(公告)日：2022-10-06

申请号：US17846538

申请日：2022-06-22

Applicant: ILLUMINA, INC.

Inventor： Tarun Khurana ,  Ali Agah ,  Aathavan Karunakaran ,  Stanley Hong ,  Merek Siu ,  Arvin Emadi ,  Craig Ciesla

IPC: G01N30/74 ,  C12Q1/6874

Abstract: 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.

公开(公告)号：US20220150394A1

公开(公告)日：2022-05-12

申请号：US17513042

申请日：2021-10-28

Applicant: ILLUMINA, INC. ,  ILLUMINA CAMBRIDGE LIMITED

Inventor： Geraint Evans ,  Stanley Hong ,  Merek Siu ,  Shaoping Lu ,  John Moon

IPC: H04N5/235 ,  H04N5/225 ,  G06K9/00 ,  G02B21/00

Abstract: 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.

公开(公告)号：US12062419B2

公开(公告)日：2024-08-13

申请号：US17683426

申请日：2022-03-01

Applicant: ILLUMINA, INC.

Inventor： Craig Ciesla ,  Ali Agah ,  Stanley Hong ,  Tarun Khurana ,  Aathavan Karunakaran ,  Arvin Emadi ,  Merek Siu

IPC: G16B50/30 ,  B01L3/00 ,  G11C13/02 ,  G16B30/10 ,  C12Q1/6874

CPC classification number: G16B50/30 ,  B01L3/5027 ,  G11C13/02 ,  G16B30/10 ,  C12Q1/6874

Abstract: 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.