Patents by Inventor John S. Vieceli

John S. Vieceli 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).

  • Patent number: 11455487
    Abstract: The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. The technology disclosed accesses a section of an image output by a biosensor, where the section of the image includes a plurality of pixels depicting intensity emission values from a plurality of clusters within the biosensor and from locations within the biosensor that are adjacent to the plurality of clusters. The plurality of clusters includes a target cluster. The section of the image is convolved with a convolution kernel, to generate a feature map comprising a plurality of features having a corresponding plurality of feature values. A weighted feature value is assigned to the target cluster, where the weighted feature value is based on one or more features values of the plurality of feature values of the feature map. The weighted feature value assigned to the target cluster is processed, to base call the target cluster.
    Type: Grant
    Filed: October 26, 2021
    Date of Patent: September 27, 2022
    Assignee: Illumina Software, Inc.
    Inventors: Abde Ali Hunaid Kagalwalla, Eric Jon Ojard, Rami Mehio, Gavin Derek Parnaby, Nitin Udpa, Bo Lu, John S. Vieceli
  • Publication number: 20220300772
    Abstract: The technology disclosed corrects inter-cluster intensity profile variation for improved base calling on a cluster-by-cluster basis. The technology disclosed accesses current intensity data and historic intensity data of a target cluster, where the current intensity data is for a current sequencing cycle and the historic intensity data is for one or more preceding sequencing cycles. A first accumulated intensity correction parameter is determined by accumulating distribution intensities measured for the target cluster at the current and preceding sequencing cycles. A second accumulated intensity correction parameter is determined by accumulating intensity errors measured for the target cluster at the current and preceding sequencing cycles. Based on the first and second accumulated intensity correction parameters, next intensity data for a next sequencing cycle is corrected to generate corrected next intensity data, which is used to base call the target cluster at the next sequencing cycle.
    Type: Application
    Filed: May 24, 2022
    Publication date: September 22, 2022
    Applicant: ILLUMINA, INC.
    Inventors: Eric Jon Ojard, Abde Ali Hunaid Kagalwalla, Rami Mehio, Nitin Udpa, Gavin Derek Parnaby, John S. Vieceli
  • Patent number: 11427868
    Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include a non-closed shape that may encode information, allow for bubbles to escape during manufacture, and provide additional advantages over closed shape fiducials.
    Type: Grant
    Filed: January 31, 2018
    Date of Patent: August 30, 2022
    Assignee: Illumina, Inc.
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
  • Patent number: 11361194
    Abstract: The technology disclosed generates variation correction coefficients on a cluster-by-cluster basis to correct inter-cluster intensity profile variation for improved base calling. An amplification coefficient corrects scale variation. Channel-specific offset coefficients correct shift variation along respective intensity channels. The variation correction coefficients for a target cluster are generated based on combining analysis of historic intensity data generated for the target cluster at preceding sequencing cycles of a sequencing run with analysis of current intensity data generated for the target cluster at a current sequencing cycle of the sequencing run. The variation correction coefficients are then used to correct next intensity data generated for the target cluster at a next sequencing cycle of the sequencing run. The corrected next intensity data is then used to base call the target cluster at the next sequencing cycle.
    Type: Grant
    Filed: October 25, 2021
    Date of Patent: June 14, 2022
    Assignee: ILLUMINA, INC.
    Inventors: Eric Jon Ojard, Abde Ali Hunaid Kagalwalla, Rami Mehio, Nitin Udpa, Gavin Derek Parnaby, John S. Vieceli
  • Publication number: 20220129711
    Abstract: The technology disclosed generates variation correction coefficients on a cluster-by-cluster basis to correct inter-cluster intensity profile variation for improved base calling. An amplification coefficient corrects scale variation. Channel-specific offset coefficients correct shift variation along respective intensity channels. The variation correction coefficients for a target cluster are generated based on combining analysis of historic intensity data generated for the target cluster at preceding sequencing cycles of a sequencing run with analysis of current intensity data generated for the target cluster at a current sequencing cycle of the sequencing run. The variation correction coefficients are then used to correct next intensity data generated for the target cluster at a next sequencing cycle of the sequencing run. The corrected next intensity data is then used to base call the target cluster at the next sequencing cycle.
    Type: Application
    Filed: October 25, 2021
    Publication date: April 28, 2022
    Applicant: ILLUMINA, INC.
    Inventors: Eric Jon OJARD, Abde Ali Hunaid KAGALWALLA, Rami MEHIO, Nitin UDPA, Gavin Derek PARNABY, John S. VIECELI
  • Patent number: 11308640
    Abstract: A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.
    Type: Grant
    Filed: December 6, 2019
    Date of Patent: April 19, 2022
    Assignee: ILLUMINA, INC.
    Inventors: John S. Vieceli, Stephen Tanner, John A. Moon, M. Shane Bowen
  • Publication number: 20220067418
    Abstract: The technology disclosed relates to equalizer-based intensity correction for base calling. In particular, the technology disclosed relates to accessing an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters, selecting a lookup table that contains pixel coefficients that are configured to increase a signal-to-noise ratio, applying the pixel coefficients to intensity values of the pixels in the image to produce an output, and base calling the target cluster based on the output.
    Type: Application
    Filed: November 9, 2021
    Publication date: March 3, 2022
    Applicant: ILLUMINA, INC.
    Inventors: Eric Jon OJARD, Rami MEHIO, Gavin Derek PARNABY, Nitin UDPA, John S. VIECELI
  • Patent number: 11262307
    Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include features and materials that are provided on or in the support of a patterned array and that return at least a portion of incident light by reflection. The fiducial markers may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the patterned array.
    Type: Grant
    Filed: January 31, 2018
    Date of Patent: March 1, 2022
    Assignee: Illumina, Inc.
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
  • Patent number: 11249025
    Abstract: Fiducial markers are provided on a patterned array of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations and layouts that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include non-rectilinear layouts that may provide for more robust location of both the fiducial markers and sites of the patterned array.
    Type: Grant
    Filed: January 31, 2018
    Date of Patent: February 15, 2022
    Assignee: Illumina, Inc.
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
  • Patent number: 11188778
    Abstract: The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. In particular, the technology disclosed accesses an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters. The pixels include a center pixel that contains a center of the target cluster. Each pixel in the pixels is divisible into a plurality of subpixels. Depending upon a particular subpixel, in a plurality of subpixels of the center pixel, which contains the center of the target cluster, the technology disclosed selects, from a bank of subpixel lookup tables, a subpixel lookup table that corresponds to the particular subpixel. The selected subpixel lookup table contains pixel coefficients that are configured to maximizes a signal-to-noise ratio. The technology disclosed element-wise multiplies the pixel coefficients with the pixels and determines a weighted sum.
    Type: Grant
    Filed: May 4, 2021
    Date of Patent: November 30, 2021
    Assignee: Illumina, Inc.
    Inventors: Eric Jon Ojard, Rami Mehio, Gavin Derek Parnaby, Nitin Udpa, John S. Vieceli
  • Publication number: 20210350163
    Abstract: The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. In particular, the technology disclosed accesses an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters. The pixels include a center pixel that contains a center of the target cluster. Each pixel in the pixels is divisible into a plurality of subpixels. Depending upon a particular subpixel, in a plurality of subpixels of the center pixel, which contains the center of the target cluster, the technology disclosed selects, from a bank of subpixel lookup tables, a subpixel lookup table that corresponds to the particular subpixel. The selected subpixel lookup table contains pixel coefficients that are configured to maximizes a signal-to-noise ratio. The technology disclosed element-wise multiplies the pixel coefficients with the pixels and determines a weighted sum.
    Type: Application
    Filed: May 4, 2021
    Publication date: November 11, 2021
    Applicant: Illumina, Inc.
    Inventors: Eric Jon OJARD, Rami MEHIO, Gavin Derek PARNABY, Nitin UDPA, John S. VIECELI
  • Publication number: 20210310065
    Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
    Type: Application
    Filed: June 15, 2021
    Publication date: October 7, 2021
    Inventors: Paul Belitz, Stephen Tanner, John S. Vieceli, Xiaoyu Chen
  • Publication number: 20210265015
    Abstract: A system for analysis of base call sensor output has memory accessible by the runtime program storing tile data including sensor data for a tile from sensing cycles of a base calling operation. A neural network processor having access to the memory is configured to execute runs of a neural network using trained parameters to produce classification data for sensing cycles. A run of the neural network operates on a sequence of N arrays of tile data from respective sensing cycles of N sensing cycles, including a subject cycle, to produce the classification data for the subject cycle. Data flow logic moves tile data and the trained parameters from the memory to the neural network processor for runs of the neural network using input units including data for spatially aligned patches of the N arrays from respective sensing cycles of N sensing cycles.
    Type: Application
    Filed: February 15, 2021
    Publication date: August 26, 2021
    Applicant: Illumina, Inc.
    Inventors: Gavin Derek PARNABY, Mark David HAHM, Andrew Christopher DU PREEZ, Jason Edward COSKY, John S. VIECELI, Andrew Dodge HEIBERG, Gery VESSERE
  • Publication number: 20200377938
    Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
    Type: Application
    Filed: June 12, 2020
    Publication date: December 3, 2020
    Applicant: Illumina, Inc.
    Inventors: Paul Belitz, Stephen Tanner, John S. Vieceli, Xiaoyu Chen
  • Publication number: 20200250851
    Abstract: A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.
    Type: Application
    Filed: December 6, 2019
    Publication date: August 6, 2020
    Inventors: John S. Vieceli, Stephen Tanner, John A. Moon, M. Shane Bowen
  • Publication number: 20200248252
    Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include a non-closed shape that may encode information, allow for bubbles to escape during manufacture, and provide additional advantages over closed shape fiducials.
    Type: Application
    Filed: January 31, 2018
    Publication date: August 6, 2020
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
  • Patent number: 10689696
    Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
    Type: Grant
    Filed: December 3, 2014
    Date of Patent: June 23, 2020
    Assignee: ILLUMINA, INC.
    Inventors: Paul Belitz, Stephen Tanner, John S. Vieceli, Xiaoyu Chen
  • Publication number: 20200064266
    Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include features and materials that are provided on or in the support of the array and that return at least a portion of incident light by reflection. The fiducials may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the array.
    Type: Application
    Filed: January 31, 2018
    Publication date: February 27, 2020
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner
  • Patent number: 10540783
    Abstract: Embodiments for registering features in a repeating pattern are described. These embodiments can include providing an object having a repeating pattern of features and a fiducial. These embodiment can also include obtaining a target image of the object, where the target image includes the repeating pattern of features and the fiducial. These embodiment can also include comparing the fiducial in the target image to reference data, where the reference data includes xy coordinates for a virtual fiducial. These embodiment can also include determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.
    Type: Grant
    Filed: October 31, 2014
    Date of Patent: January 21, 2020
    Assignee: ILLUMINA, INC.
    Inventors: John S. Vieceli, Stephen Tanner, John A. Moon, M. Shane Bowen
  • Publication number: 20200009525
    Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an “always on” type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.
    Type: Application
    Filed: January 31, 2018
    Publication date: January 9, 2020
    Inventors: John S. Vieceli, Alex Nemiroski, Paul Belitz, Robert Langlois, M. Shane Bowen, Danny Yuan Chan, Bala Murali K. Venkatesan, Hui Han, Kevan Samiee, Stephen Tanner