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公开(公告)号：US20210271074A1
公开(公告)日：2021-09-02
申请号：US17302418
申请日：2021-05-03
Applicant: Illumina, Inc.
Inventor： Darren Robert Segale , John Moon , Hongji Ren
Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.
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公开(公告)号：US10227636B2
公开(公告)日：2019-03-12
申请号：US15009272
申请日：2016-01-28
Applicant: Illumina, Inc.
Inventor： Darren Robert Segale , John A. Moon , Hongji Ren
IPC: G01B11/24 , C12Q1/6818 , G01N21/64 , G02B21/24 , H04N5/232 , C12Q1/6874 , G01B9/02
Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.
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公开(公告)号：US20160304940A1
公开(公告)日：2016-10-20
申请号：US15009272
申请日：2016-01-28
Applicant: Illumina, Inc.
Inventor： Darren Robert Segale , John A. Moon , Hongji Ren
CPC classification number: C12Q1/6818 , C12Q1/6874 , G01B9/02063 , G01B11/24 , G01N21/6428 , G01N21/6458 , G02B21/244 , H04N5/23212
Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.
Abstract translation: 一种用于扫描微阵列的方法，包括（a）向光学扫描仪提供微阵列，其中所述微阵列包括具有不同靶分子特征的表面; （b）在x或y方向上扫描表面以从表面的顺序区域获取来自特征的光学信号，其中通过重复（i）将光学扫描器和表面之间的聚焦设置实时地动态地控制， 预定的焦点偏移，从而在聚焦设置中引入误差，以及（ii）调整聚焦设置以减少焦点设置中的误差，从而以不同的焦点度从不同的区域获取光信号，使得区域的子集 被扫描引起的焦点错误; 和（c）分析以不同焦点获得的光学信号以识别不同的目标分子。
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公开(公告)号：US20230393379A1
公开(公告)日：2023-12-07
申请号：US18236088
申请日：2023-08-21
Applicant: ILLUMINA, INC.
Inventor： Robert Langlois , Bo Lu , Hongji Ren , Joseph Pinto , Simon Prince , Austin Corbett
CPC classification number: G02B21/367 , G02B21/14 , G06T7/0012 , G06T2207/10056 , G06T2207/30024
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.
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公开(公告)号：US11702694B2
公开(公告)日：2023-07-18
申请号：US17188109
申请日：2021-03-01
Applicant: Illumina, Inc.
Inventor： Wayne N. George , Andrew A. Brown , Daniel Bratton , Hongji Ren , Ryan Christopher Smith
IPC: C12Q1/6874 , B05D3/06 , C09D133/26 , C09D135/00 , C12Q1/6806
CPC classification number: C12Q1/6874 , B05D3/06 , B05D3/065 , C09D133/26 , C09D135/00 , C12Q1/6806 , Y10T428/24802 , Y10T428/24917 , Y10T428/24926 , Y10T428/2998 , Y10T428/31536 , Y10T428/31935
Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.
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Patent Agency Ranking
公开(公告)号：US11243390B2
公开(公告)日：2022-02-08
申请号：US17110406
申请日：2020-12-03
Applicant: ILLUMINA, INC.
Inventor： Austin Corbett , Bo Lu , Robert Langlois , Joseph Pinto , Yu Chen , Peter Newman , Hongji Ren
Abstract: A method is used to generate a report presenting parameter values corresponding to a structured illumination microscopy (SIM) optical system. The parameter values are based at least in part on the performed modulation calculation corresponding to an image set captured with the SIM optical system. A minimum FWHM slice is identified, based at least in part on an average FWHM value across the images in the first image set. Parameter estimation is performed on the identified minimum FWHM slice. Best in-focus parameters are identified based at least in part on the performed estimation. A phase estimate is performed for each image in the set. A modulation calculation is performed based at least in part on the identified best in-focus parameters. The report is based at least in part on the performed modulation calculation.
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公开(公告)号：US10831012B2
公开(公告)日：2020-11-10
申请号：US16447729
申请日：2019-06-20
Applicant: ILLUMINA, INC.
Inventor： Michael J. Carney , Stanley S. Hong , Robert Langlois , Hongji Ren , Kevin Wayne Bartig , Rico Otto , Olga Andreevna Souverneva
Abstract: 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.
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公开(公告)号：US20190153519A1
公开(公告)日：2019-05-23
申请号：US16251859
申请日：2019-01-18
Applicant: Illumina, Inc.
Inventor： Darren Robert Segale , John Moon , Hongji Ren
IPC: C12Q1/6818 , G01N21/64 , C12Q1/6874 , G01B11/24 , H04N5/232 , G02B21/24
Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.
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公开(公告)号：US10266891B2
公开(公告)日：2019-04-23
申请号：US15680561
申请日：2017-08-18
Applicant: Illumina, Inc.
Inventor： Wayne N. George , Andrew A. Brown , Daniel Bratton , Hongji Ren , Ryan C. Smith
IPC: C12Q1/68 , C12Q1/6874 , B05D3/06 , C09D133/26 , C09D135/00 , C12Q1/6806
Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.
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公开(公告)号：US20250052999A1
公开(公告)日：2025-02-13
申请号：US18921425
申请日：2024-10-21
Applicant: Illumina, Inc.
Inventor： Darren Robert Segale , John Moon , Hongji Ren
IPC: G02B26/12 , C12Q1/6818 , C12Q1/6874 , G01B9/02055 , G01B11/24 , G01N15/1434 , G01N21/64 , G02B7/38 , G02B21/24 , G02B26/10 , H04N23/67
Abstract: A method for scanning a microarray, including (a) providing a microarray to an optical scanner, wherein the microarray includes a surface having features having different target molecules; (b) scanning the surface in the x or y direction to acquire optical signals from the features at sequential regions of the surface, wherein the focus setting between the optical scanner and the surface is dynamically controlled in real time by repeatedly (i) adding a predetermined focal offset, thereby introducing an error in the focus setting, and (ii) adjusting the focus setting to reduce the error in the focus setting, thereby acquiring the optical signals from different regions at different degrees of focus such that a subset of the regions that are scanned have an introduced focus error; and (c) analyzing the optical signals that are obtained at the different degrees of focus to identify the different target molecules.
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