10x Genomics, Inc.

Paul Ryvkin

Zachary Bent

Jessica Michele Terry

Tarjei Sigurd Mikkelsen

Elliott Meer

Niranjan Srinivas

Serge Saxonov

Christopher Hindson

John R Stuelpnagel

Katherine Pfeiffer

Andrew D Price

Josephine Harada

Christopher Joachim O'Keeffe

Phillip Belgrader

Geoffrey McDermott

Vijay Kumar Sreenivasa Gopalan

Solongo B Ziraldo

Alexander Y Wong

Mohammad Rahimi Lenji

Kevin J Wu

Jeffrey Clark Mellen

Daniel P Riordan

Benjamin J Hindson

Michael Schnall-Levin

Rajiv Bharadwaj

Michael Ybarra Lucero

Patrick Marks

Tobias Daniel Wheeler

Neil Ira Weisenfeld

Preyas Shah

Indira Wu

Dongyao Li

Stephane Claude Boutet

Sarah Taylor

Jason Underwood

David Jaffe

Xiaoyan Qian

Meghan Leigh Flanders Frey

Alex Gagnon

Geoffrey Mcdermott

Meghan Frey

Provided herein are methods for image segmentation. An image having a plurality of pixels arranged in a plurality of dimensions is obtained. The image is provided to a pretrained machine learning model and a plurality of amplitudes for each of the plurality of pixel is received from the model. Each of the plurality of amplitudes for each of the plurality of pixels corresponds to exactly one of the plurality of dimensions. At least one instance in the image is identified by: determining a first basin associated with the at least one instance, where the basin consists of a contiguous subset of the plurality of pixels having an amplitude with a magnitude not exceeding first threshold, determining a second subset of the plurality of pixels having an amplitude with a magnitude exceeding the first threshold, where the second subset of pixels bounds the first subset of pixels, and constructing the at least one instance by a flow of the second subset of pixels to the first subset of pixels according to the amplitudes thereof.

Systems and methods for image segmentation

In embodiments, a method includes reading a nuclear segmentation mask of an image including pixels arranged in two dimensions. The nuclear segmentation mask identifies cellular nuclei stained with a cellular nucleus stain. The method includes determining amplitudes for each pixel. Each amplitude corresponds to exactly one dimension of the two dimensions. The method includes constructing a graph having nodes and edges. Each node corresponds to a pixel. Nodes corresponding to neighboring pixels are connected by an edge. The method includes assigning a weight to each edge. Each edge's weight is based on amplitudes of pixels corresponding to nodes connected thereby. The method further includes, based on the graph, determining, for each cellular nuclei, a heat map corresponding to a predicted cell region associated with that cellular nucleus. The method further includes based on the heat maps of the cellular nuclei, determining a cellular segmentation mask comprising predicted cell regions.

Systems and methods for image segmentation using multiple stain indicators

Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original 'tagging' structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.

Systems and methods for differentially tagging nucleic acid molecules

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for 'tagging' analytes for characterization.

Methods and systems for processing polynucleotides

The present disclosure provides methods and systems for producing full-length sequencing information of transcriptomes from single cells or from the bulk. Random ligation and circularization of barcoded or non-barcoded complementary deoxyribonucleic molecules can be used to provide a circular template for amplification and subsequent sequencing.

Transcriptome sequencing through random ligation

A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

Systems and methods for visualizing a pattern in a dataset

Methods for screening clonotypes are provided. Data representing a plurality of cells from a single subject is obtained. The data represents a plurality of clonotypes. The data includes a plurality of contigs for each respective clonotype in the plurality of clonotypes. Each respective contig in the plurality of contigs comprises (i) an indication of chain type for the respective contig and (ii) a contig sequence of an mRNA of the respective cell. There is determined, using the data, for each respective clonotype in the plurality of clonotypes, a number of the plurality of cells that represent the respective clonotype. In some instances, more than one cell in the plurality of cells have the same clonotype in the plurality of clonotypes. In some instances, the plurality of clonotypes comprises 25 clonotypes and where the plurality of cells includes at least one cell for each clonotype in the plurality of clonotypes.

Systems and methods for clonotype screening

The present disclosure provides methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto. A barcode molecule coupled to a support may comprise a barcode sequence and a functional sequence. A barcode molecule may be generated using two or more ligation reactions in a combinatorial fashion. A support comprising two or more different barcode molecules may be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents.

Functionalized gel beads

Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original 'tagging' structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or 'barcode' moieties.

Systems and methods for nucleic acid processing using degenerate nucleotides

Provided are systems and methods for analyzing a single cell application or experiment. A set of control beads may be introduced to a biological sample and subjected to the single cell application. The control beads may be configured to mimic analytes in the biological sample, such as a cell or other analyte, and comprise one or more known sequences. The one or more known sequences may be identified to analyze the single cell application.

Systems and methods for quality control in single cell processing

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Growing community of inventors

San Jose, CA, United States of America

Paul Ryvkin