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公开(公告)号：US12229974B2
公开(公告)日：2025-02-18
申请号：US18046404
申请日：2022-10-13
Applicant: 10x Genomics, Inc.
Inventor： Neil Ira Weisenfeld , Narek Dshkhunyan , Preyas Shah
Abstract: Systems and methods for spatial analysis of analytes are provided. A data structure is obtained comprising an image, as an array of pixel values, of a sample on a substrate having a identifier, fiducial markers and a set of capture spots. The pixel values are used to identify derived fiducial spots. The substrate identifier identifies a template having reference positions for reference fiducial spots and a corresponding coordinate system. The derived fiducial spots are aligned with the reference fiducial spots using an alignment algorithm to obtain a transformation between the derived and reference fiducial spots. The transformation and the template corresponding coordinate system are used to register the image to the set of capture spots. The registered image is then analyzed in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.
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Patent Agency Ranking
公开(公告)号：US11501440B2
公开(公告)日：2022-11-15
申请号：US16951843
申请日：2020-11-18
Applicant: 10X Genomics, Inc.
Inventor： Neil Ira Weisenfeld , Narek Dshkhunyan , Preyas Shah
Abstract: Systems and methods for spatial analysis of analytes are provided. A data structure is obtained comprising an image, as an array of pixel values, of a sample on a substrate having a identifier, fiducial markers and a set of capture spots. The pixel values are used to identify derived fiducial spots. The substrate identifier identifies a template having reference positions for reference fiducial spots and a corresponding coordinate system. The derived fiducial spots are aligned with the reference fiducial spots using an alignment algorithm to obtain a transformation between the derived and reference fiducial spots. The transformation and the template corresponding coordinate system are used to register the image to the set of capture spots. The registered image is then analyzed in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.
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公开(公告)号：US20210158522A1
公开(公告)日：2021-05-27
申请号：US16951843
申请日：2020-11-18
Applicant: 10X Genomics, Inc.
Inventor： Neil Ira Weisenfeld , Narek Dshkhunyan , Preyas Shah
Abstract: Systems and methods for spatial analysis of analytes are provided. A data structure is obtained comprising an image, as an array of pixel values, of a sample on a substrate having a identifier, fiducial markers and a set of capture spots. The pixel values are used to identify derived fiducial spots. The substrate identifier identifies a template having reference positions for reference fiducial spots and a corresponding coordinate system. The derived fiducial spots are aligned with the reference fiducial spots using an alignment algorithm to obtain a transformation between the derived and reference fiducial spots. The transformation and the template corresponding coordinate system are used to register the image to the set of capture spots. The registered image is then analyzed in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.
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公开(公告)号：US20210155982A1
公开(公告)日：2021-05-27
申请号：US16951864
申请日：2020-11-18
Applicant: 10X Genomics, Inc.
Inventor： Yifeng Yin , Zachary Bent , Stephen Williams , Ian Fiddes , Jeffrey Clark Mellen , Jasper Staab , Kevin J. Wu , Neil Ira Weisenfeld , Florian Baumgartner , Brynn Claypoole , Preyas Shah , Narek Dshkhunyan , Erik Leonard Henrik Borgstrom , Benjamin McCreath
IPC: C12Q1/6869 , C12Q1/6837 , G06T7/194 , G06T7/13 , G06T7/00 , G06N5/00
Abstract: Systems and methods for spatial analysis of analytes include placing a sample on a substrate having fiducial markers and capture spots. Then, an image of the sample is acquired and sequence reads are obtained from the capture spots. Each capture probe plurality in a set of capture probe pluralities is (i) at a different capture spot, (ii) directly or indirectly associates with analytes from the sample and (iii) has a unique spatial barcode. The sequencing reads serve to detect the analytes. Sequencing reads include a spatial barcode of the corresponding capture probe plurality. Spatial barcodes localize reads to corresponding capture spots, thereby dividing them into subsets, each subset for a respective capture spot. Fiducial markers facilitate a composite representation comprising (i) the image aligned to the capture spots and (ii) a representation of each subset of sequence reads at respective positions within the image mapping to the corresponding capture spots.
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公开(公告)号：US20230162381A1
公开(公告)日：2023-05-25
申请号：US18046404
申请日：2022-10-13
Applicant: 10x Genomics, Inc.
Inventor： Neil Ira Weisenfeld , Narek Dshkhunyan , Preyas Shah
CPC classification number: G06T7/33 , G06T7/136 , G16B25/00 , G06T3/0075 , G06T3/608 , G06T7/0014 , G06F18/22 , G06V20/695 , G06T2207/10056 , G06T2207/30072
Abstract: Systems and methods for spatial analysis of analytes are provided. A data structure is obtained comprising an image, as an array of pixel values, of a sample on a substrate having a identifier, fiducial markers and a set of capture spots. The pixel values are used to identify derived fiducial spots. The substrate identifier identifies a template having reference positions for reference fiducial spots and a corresponding coordinate system. The derived fiducial spots are aligned with the reference fiducial spots using an alignment algorithm to obtain a transformation between the derived and reference fiducial spots. The transformation and the template corresponding coordinate system are used to register the image to the set of capture spots. The registered image is then analyzed in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.
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公开(公告)号：US20220028492A1
公开(公告)日：2022-01-27
申请号：US17384407
申请日：2021-07-23
Applicant: 10x Genomics, Inc.
Inventor： Narek Dshkhunyan
Abstract: Methods and systems for removing aggregates from a dataset can be provided. For example, method for removing aggregates can comprise: receiving a first dataset comprising a plurality of sequence reads; grouping the plurality of sequence reads into bins, wherein each bin comprises sequence reads that share a common barcode sequence; identifying a subset of barcode sequences from the bins as aggregates by tracking correction events of sequence reads; removing the subset of barcode sequences from the first dataset to obtain a second dataset of sequence reads.
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