Neil Ira Weisenfeld

20230081613, Mar 16, 2023

Oct 18, 2022

18/047620

- Pleasanton CA, US
Jasper STAAB - Honolulu HI, US
Kevin J. WU - San Francisco CA, US
Neil Ira WEISENFELD - Lynnfield MA, US
Florian BAUMGARTNER - , US
Brynn CLAYPOOLE - San Francisco CA, US

G06T 7/00
G16B 15/00
G01N 1/30

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.

20210155982, May 27, 2021

Nov 18, 2020

16/951864

- Pleasanton CA, US
Zachary Bent - Pleasanton CA, US
Stephen Williams - Dublin CA, US
Ian Fiddes - San Francisco CA, US
Jeffrey Clark Mellen - Martinez CA, US
Jasper Staab - Honolulu HI, US
Kevin J. Wu - San Francisco CA, US
Neil Ira Weisenfeld - Lynnfield MA, US
Florian Baumgartner - Stockholm, SE
Brynn Claypoole - Pleasanton CA, US
Preyas Shah - Pleasanton CA, US
Erik Leonard Henrik Borgstrom - Stockholm, SE
Benjamin McCreath - Pleasanton CA, US

C12Q 1/6869
C12Q 1/6837
G06T 7/194
G06T 7/13
G06T 7/00
G06N 5/00

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.

20210097684, Apr 1, 2021

Sep 30, 2020

17/039935

- Pleasanton CA, US
Jasper STAAB - Honolulu HI, US
Kevin J. WU - San Francisco CA, US
Neil Ira WEISENFELD - Lynnfield MA, US
Florian BAUMGARTNER - Stockholm, SE
Brynn CLAYPOOLE - San Francisco CA, US

G06T 7/00
G16B 15/00
G01N 1/30

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.

20170235876, Aug 17, 2017

Aug 19, 2016

15/242256

- Pleasanton CA, US
Patrick Marks - San Francisco CA, US
Neil Weisenfeld - North Reading MA, US

G06F 19/22

Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.