公开(公告)号：US20240378734A1

公开(公告)日：2024-11-14

申请号：US18692758

申请日：2022-09-16

Applicant: 10x Genomics, Inc.

Inventor： Olga Vorobyova ,  Brynn Claypoole ,  Dongyao Li ,  Neil Ira Weisenfeld ,  Didem Pelin Sarikaya ,  Peigeng Li ,  Guy Joseph ,  Eric Siegel ,  Naga Sudha Kodavatikanti

IPC: G06T7/33 ,  G06T7/13

Abstract: Systems and methods for overlaying image data for a biological sample on spatial analyte data are provided. A first image of the sample on a first substrate and a second image of the sample on the first substrate overlayed on a second substrate are obtained. The second substrate includes spatial fiducials and capture spots. At least one of the first substrate and the second substrate is transparent. A registration for the first image and the second image is determined, using a first pattern of the sample in the first image and a second pattern of the sample in the second image. The registration is used to overlay the first image onto a spatial dataset including spatial analyte data for the capture spots from the sample. A frame of reference of the spatial dataset is known with respect to the second image, based on the spatial fiducials of the second image.

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.

公开(公告)号：US12125260B2

公开(公告)日：2024-10-22

申请号：US18355963

申请日：2023-07-20

Applicant: 10X Genomics, Inc.

Inventor： Jeffrey Clark Mellen ,  Jasper Staab ,  Kevin J. Wu ,  Neil Ira Weisenfeld ,  Florian Baumgartner ,  Brynn Claypoole

IPC: G06V10/762 ,  G01N1/30 ,  G06T7/00 ,  G16B15/00

CPC classification number: G06V10/762 ,  G01N1/30 ,  G06T7/0012 ,  G16B15/00 ,  G01N2001/302 ,  G06T2207/30024

Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.

公开(公告)号：US11756286B2

公开(公告)日：2023-09-12

申请号：US18047620

申请日：2022-10-18

Applicant: 10X Genomics, Inc.

Inventor： Jeffrey Clark Mellen ,  Jasper Staab ,  Kevin J. Wu ,  Neil Ira Weisenfeld ,  Florian Baumgartner ,  Brynn Claypoole

IPC: G06V10/762 ,  G16B15/00 ,  G01N1/30 ,  G06T7/00

CPC classification number: G06V10/762 ,  G01N1/30 ,  G06T7/0012 ,  G16B15/00 ,  G01N2001/302 ,  G06T2207/30024

Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.

公开(公告)号：US11514575B2

公开(公告)日：2022-11-29

申请号：US17039935

申请日：2020-09-30

Applicant: 10X Genomics, Inc.

Inventor： Jeffrey Clark Mellen ,  Jasper Staab ,  Kevin J. Wu ,  Neil Ira Weisenfeld ,  Florian Baumgartner ,  Brynn Claypoole

IPC: G01N1/30 ,  G06T7/00 ,  G16B15/00

Abstract: A discrete attribute value dataset is obtained that is associated with a plurality of probe spots each assigned a different probe spot barcode. The dataset comprises spatial projections, each comprising images of a biological sample. Each image includes a corresponding plurality of discrete attribute values for the probe spots. Each such value is associated with a probe spot in the plurality of probes spots based on the probe spot barcodes. The dataset is clustered using the discrete attribute values, or dimension reduction components thereof, for a plurality of loci at each respective probe spot across the images of the projections thereby assigning each probe spot to a cluster in a plurality of clusters. Morphological patterns are identified from the spatial arrangement of the probe spots in the various clusters.