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    CALIBRATION SEQUENCES FOR NUCELOTIDE SEQUENCING
    1.
    发明公开
    CALIBRATION SEQUENCES FOR NUCELOTIDE SEQUENCING 审中-公开

    公开(公告)号：US20230410944A1

    公开(公告)日：2023-12-21

    申请号：US18174468

    申请日：2023-02-24

    申请人： Illumina, Inc. ,  Illumina Software, Inc.

    发明人： John S. Vieceli ,  Bo Lu ,  Jeffrey S. Fisher

    IPC分类号： G16B30/00 ,  G16B35/00

    CPC分类号： G16B30/00 ,  G16B35/00

    摘要： This disclosure describes methods, non-transitory computer readable media, and systems that can introduce short calibration sequences into a sequencing device and run calibration cycles to adjust or otherwise determine a sequencing parameter corresponding to the sequencing device. For instance, the disclosed systems can detect a flow cell (or other sample-nucleotide slide) with calibration sequences incorporated into samples' library fragments or into a surface of the sample-nucleotide slide. By running one or more calibration cycles to incorporate nucleobases on oligonucleotides corresponding to calibration sequences and capture corresponding images for calibration sequences—separate from genomic sequencing cycles for sample genomic sequences—the disclosed systems can determine a sequencing parameter corresponding to the sequencing device.

    Intensity extraction from oligonucleotide clusters for base calling
    2.
    发明授权
    Intensity extraction from oligonucleotide clusters for base calling 有权

    公开(公告)号：US11989265B2

    公开(公告)日：2024-05-21

    申请号：US17902630

    申请日：2022-09-02

    申请人： Illumina, Inc.

    发明人： Abde Ali Hunaid Kagalwalla ,  Eric Jon Ojard ,  Rami Mehio ,  Gavin Derek Parnaby ,  Nitin Udpa ,  Bo Lu ,  John S. Vieceli

    IPC分类号： G06F18/23213 ,  G06F18/20 ,  G06V10/56

    CPC分类号： G06F18/23213 ,  G06F18/285 ,  G06V10/56

    摘要： The technology disclosed extracts intensities from sequencing images for base calling target clusters and attenuates spatial crosstalk from neighboring clusters. The technology disclosed accesses a particular section from a plurality of sections of an image output by a sensor, the particular section of the image including at least one pixel depicting intensity emission values from a target cluster and neighboring clusters located across the sensor, and convolves the particular section of the image with a corresponding convolution kernel in a plurality of convolution kernels, to generate a feature map comprising a plurality of feature values. The technology disclosed further assigns a corresponding feature value to the target cluster based on feature values in the plurality of feature values adjoining a center of the target cluster, and processes the corresponding feature value assigned to the target cluster, to base call the target cluster.

    Apparatus and method of estimating values from images
    5.
    发明授权
    Apparatus and method of estimating values from images 有权

    公开(公告)号：US11768364B2

    公开(公告)日：2023-09-26

    申请号：US17110409

    申请日：2020-12-03

    申请人： ILLUMINA, INC.

    发明人： Robert Langlois ,  Bo Lu ,  Hongji Ren ,  Joseph Pinto ,  Simon Prince ,  Austin Corbett

    IPC分类号： G06T7/00 ,  G02B21/36 ,  G02B21/14

    CPC分类号： G02B21/367 ,  G02B21/14 ,  G06T7/0012 ,  G06T2207/10056 ,  G06T2207/30024

    摘要： 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.

    FIDUCIALS FOR USE IN REGISTRATION OF A PATTERNED SURFACE
    6.
    发明申请
    FIDUCIALS FOR USE IN REGISTRATION OF A PATTERNED SURFACE 有权

    公开(公告)号：US20220414853A1

    公开(公告)日：2022-12-29

    申请号：US17845519

    申请日：2022-06-21

    申请人： ILLUMINA, INC. ,  ILLUMINA SOFTWARE, INC.

    发明人： John S. Vieceli ,  Hui Han ,  Robert Langlois ,  Bo Lu

    IPC分类号： G06T7/00 ,  G01N15/14 ,  G06T3/00 ,  G06T7/30

    摘要： Registration of a patterned flow cell may utilize fiducials comprising sets or groupings of features (e.g., sites, sample wells, nanowells) having known locations and in which the placement of the features is not in accordance with a periodic pattern or is otherwise distinguishable from the periodic pattern of sites present in non-fiducial regions of the flow cell substrate. In certain embodiments the positioning of the sites that are part of the fiducial represent a break or discontinuity in the periodic pattern of sites that are otherwise present on the surface of a patterned flow cell.

    Increased calculation efficiency for structured illumination microscopy
    7.
    发明授权
    Increased calculation efficiency for structured illumination microscopy 有权

    公开(公告)号：US11340437B2

    公开(公告)日：2022-05-24

    申请号：US17075694

    申请日：2020-10-21

    申请人： Illumina, Inc.

    发明人： Robert Ezra Langlois ,  Andrew James Young ,  Andrew Dodge Heiberg ,  Bo Lu

    IPC分类号： G02B21/00 ,  G02B27/60 ,  G01N21/64 ,  G06T3/40 ,  G02B21/14 ,  G06T5/50

    摘要： The technology disclosed relates to structured illumination microscopy (SIM). In particular, the technology disclosed relates to capturing and processing, in real time, numerous image tiles across a large image plane, dividing them into subtiles, efficiently processing the subtiles, and producing enhanced resolution images from the subtiles. The enhanced resolution images can be combined into enhanced images and can be used in subsequent analysis steps. The technology disclosed includes logic to reduce computing resources required to produce an enhanced resolution image from structured illumination of a target. A method is described for producing an enhanced resolution image from images of a target captured under structured illumination. This method applies one or more transformations to non-redundant data and then recovers redundant data from the non-redundant data after the transformations.

    APPARATUS AND METHOD OF PROVIDING PARAMETER ESTIMATION
    8.
    发明申请
    APPARATUS AND METHOD OF PROVIDING PARAMETER ESTIMATION 有权

    公开(公告)号：US20220113532A1

    公开(公告)日：2022-04-14

    申请号：US17558829

    申请日：2021-12-22

    申请人： ILLUMINA, INC.

    发明人： Austin Corbett ,  Bo Lu ,  Robert Langlois ,  Joseph Pinto ,  Yu Chen ,  Peter Newman ,  Hongji Ren

    IPC分类号： G02B21/36 ,  G06T7/80 ,  G02B26/06 ,  G06T7/00 ,  H04N5/225

    摘要： 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.