Patents by Inventor Nitin Udpa

Nitin Udpa 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: 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
  • 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: 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: 20200208204
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
    Type: Application
    Filed: March 5, 2020
    Publication date: July 2, 2020
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa
  • Patent number: 10584374
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
    Type: Grant
    Filed: April 30, 2018
    Date of Patent: March 10, 2020
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa
  • Patent number: 10460140
    Abstract: A method for tracking an item that includes the steps of (a) providing an item having a solid polymer material; (b) irradiating the item to create a spatial pattern of optical modifications in the polymer material, wherein the spatial pattern of optical modifications includes a code that indicates information; and (c) detecting the pattern of optical modifications, thereby determining the information.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: October 29, 2019
    Assignee: ILLUMINA, INC.
    Inventors: Dustin Blair, Nitin Udpa, Linh Tran, Nicholas Scheidler
  • Publication number: 20180341798
    Abstract: A method for tracking an item that includes the steps of (a) providing an item having a solid polymer material; (b) irradiating the item to create a spatial pattern of optical modifications in the polymer material, wherein the spatial pattern of optical modifications includes a code that indicates information; and (c) detecting the pattern of optical modifications, thereby determining the information.
    Type: Application
    Filed: March 11, 2016
    Publication date: November 29, 2018
    Applicant: ILLUMINA, INC.
    Inventors: Dustin Blair, Nitin Udpa, Linh Tran, Nicholas Scheidler
  • Publication number: 20180245143
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
    Type: Application
    Filed: April 30, 2018
    Publication date: August 30, 2018
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa
  • Patent number: 9976174
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
    Type: Grant
    Filed: March 22, 2016
    Date of Patent: May 22, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa
  • Publication number: 20160281150
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon.
    Type: Application
    Filed: March 22, 2016
    Publication date: September 29, 2016
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa