	US 11,989,265 B2
	Intensity extraction from oligonucleotide clusters for base calling
Abde Ali Hunaid Kagalwalla, San Diego, CA (US); Eric Jon Ojard, San Francisco, CA (US); Rami Mehio, San Diego, CA (US); Gavin Derek Parnaby, Laguna Niguel, CA (US); Nitin Udpa, San Diego, CA (US); Bo Lu, San Diego, CA (US); and John S. Vieceli, Encinitas, CA (US)
Assigned to Illumina, Inc., San Diego, CA (US)
Filed by Illumina, Inc., San Diego, CA (US)
Filed on Sep. 2, 2022, as Appl. No. 17/902,630.
Application 17/902,630 is a continuation of application No. 17/511,483, filed on Oct. 26, 2021, granted, now 11,455,487.
Claims priority of provisional application 63/223,408, filed on Jul. 19, 2021.
Prior Publication US 2023/0015945 A1, Jan. 19, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. G06F 18/23213 (2023.01); G06F 18/20 (2023.01); G06V 10/56 (2022.01)

CPC G06F 18/23213 (2023.01) [G06F 18/285 (2023.01); G06V 10/56 (2022.01)]

30 Claims

1. A computer-implemented method of base calling, the computer-implemented method including:

accessing, from an image of clusters of oligonucleotides output by a sensor, a particular section from a plurality of sections of the image, the particular section of the image including at least one pixel depicting intensity emission values from a target cluster of oligonucleotides and neighboring clusters of oligonucleotides located across the sensor;

convolving the particular section of the image with a corresponding convolution kernel in a plurality of convolution kernels, to generate a feature map comprising a plurality of feature values;

assigning a corresponding feature value to the target cluster of oligonucleotides based on feature values in the plurality of feature values adjoining a center of the target cluster of oligonucleotides; and

processing the corresponding feature value assigned to the target cluster of oligonucleotides, to base call by determining a nucleotide base for the target cluster of oligonucleotides.