10x Genomics, Inc.

Xiaoyan Qian

Toon Verheyen

Jorge Iván Hernández Neuta

Jessica Östlin

Paul Ryvkin

Neil Ira Weisenfeld

Malte Kühnemund

Preyas Shah

Dongyao Li

The present disclosure in some aspects relates to methods and compositions for accurately detecting and quantifying multiple analytes present in a biological sample. In some aspects, the methods and compositions provided herein address one or more issues associated with the stability and/or size of nucleic acid structures such as rolling circle amplification products in the biological sample.

Stabilization and/or compaction of nucleic acid molecules

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

The present disclosure relates in some aspects to methods and compositions for analysis of a target nucleic acid, such as in situ detection of a region of interest in a polynucleotide in a tissue sample. In some embodiments, provided herein are templated ligation probes (e.g., RNA-templated ligation probes) and selector probes for generation of a circularized ligated probe comprising an insertion sequence of a selector probe, wherein the circularized ligated probe is amplified in a rolling circle amplification reaction to generate a product that is detected in the sample.

Circularizable probes for in situ analysis

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Stockholm, Sweden

Xiaoyan Qian