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公开(公告)号：US20240220584A1
公开(公告)日：2024-07-04
申请号：US18501904
申请日：2023-11-03
申请人： Illumina, Inc.
发明人： Eric Jon OJARD , Abde Ali Hunaid KAGALWALLA , Rami MEHIO , Nitin UDPA , Gavin Derek PARNABY , John S. VIECELI
IPC分类号： G06F18/2411 , G06F18/2135 , G06T7/187 , G06V10/50
CPC分类号： G06F18/2411 , G06F18/21355 , G06T7/187 , G06V10/507
摘要： The technology disclosed corrects inter-cluster intensity profile variation for improved base calling on a cluster-by-cluster basis. The technology disclosed accesses current intensity data and historic intensity data of a target cluster, where the current intensity data is for a current sequencing cycle and the historic intensity data is for one or more preceding sequencing cycles. A first accumulated intensity correction parameter is determined by accumulating distribution intensities measured for the target cluster at the current and preceding sequencing cycles. A second accumulated intensity correction parameter is determined by accumulating intensity errors measured for the target cluster at the current and preceding sequencing cycles. Based on the first and second accumulated intensity correction parameters, next intensity data for a next sequencing cycle is corrected to generate corrected next intensity data, which is used to base call the target cluster at the next sequencing cycle.
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公开(公告)号：US20230259588A1
公开(公告)日：2023-08-17
申请号：US18154603
申请日：2023-01-13
申请人： Illumina, Inc.
发明人： Eric Jon OJARD , Abde Ali Hunaid KAGALWALLA , Rami MEHIO , Nitin UDPA , Gavin Derek PARNABY , John S. VIECELI
IPC分类号： G06F18/2411 , G06T7/187 , G06V10/50 , G06F18/2135
CPC分类号： G06F18/2411 , G06T7/187 , G06V10/507 , G06F18/21355
摘要： The technology disclosed corrects inter-cluster intensity profile variation for improved base calling on a cluster-by-cluster basis. The technology disclosed accesses current intensity data and historic intensity data of a target cluster, where the current intensity data is for a current sequencing cycle and the historic intensity data is for one or more preceding sequencing cycles. A first accumulated intensity correction parameter is determined by accumulating distribution intensities measured for the target cluster at the current and preceding sequencing cycles. A second accumulated intensity correction parameter is determined by accumulating intensity errors measured for the target cluster at the current and preceding sequencing cycles. Based on the first and second accumulated intensity correction parameters, next intensity data for a next sequencing cycle is corrected to generate corrected next intensity data, which is used to base call the target cluster at the next sequencing cycle.
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公开(公告)号：US20210265015A1
公开(公告)日：2021-08-26
申请号：US17176147
申请日：2021-02-15
申请人： Illumina, Inc.
发明人： Gavin Derek PARNABY , Mark David HAHM , Andrew Christopher DU PREEZ , Jason Edward COSKY , John S. VIECELI , Andrew Dodge HEIBERG , Gery VESSERE
摘要： A system for analysis of base call sensor output has memory accessible by the runtime program storing tile data including sensor data for a tile from sensing cycles of a base calling operation. A neural network processor having access to the memory is configured to execute runs of a neural network using trained parameters to produce classification data for sensing cycles. A run of the neural network operates on a sequence of N arrays of tile data from respective sensing cycles of N sensing cycles, including a subject cycle, to produce the classification data for the subject cycle. Data flow logic moves tile data and the trained parameters from the memory to the neural network processor for runs of the neural network using input units including data for spatially aligned patches of the N arrays from respective sensing cycles of N sensing cycles.
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公开(公告)号：US20230385991A1
公开(公告)日：2023-11-30
申请号：US18313973
申请日：2023-05-08
申请人： Illumina, Inc.
发明人： Eric Jon OJARD , Rami MEHIO , Gavin Derek PARNABY , Nitin UDPA , John S. VIECELI
IPC分类号： G06T5/00 , G16B40/20 , G16B40/10 , G06V10/762 , G06V20/69
CPC分类号： G06T5/002 , G16B40/20 , G16B40/10 , G06V10/762 , G06V20/698
摘要： The technology disclosed relates to equalizer-based intensity correction for base calling. In particular, the technology disclosed relates to accessing an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters, selecting a lookup table that contains pixel coefficients that are configured to increase a signal-to-noise ratio, applying the pixel coefficients to intensity values of the pixels in the image to produce an output, and base calling the target cluster based on the output.
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公开(公告)号：US20220067418A1
公开(公告)日：2022-03-03
申请号：US17522864
申请日：2021-11-09
申请人： ILLUMINA, INC.
发明人： Eric Jon OJARD , Rami MEHIO , Gavin Derek PARNABY , Nitin UDPA , John S. VIECELI
摘要： The technology disclosed relates to equalizer-based intensity correction for base calling. In particular, the technology disclosed relates to accessing an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters, selecting a lookup table that contains pixel coefficients that are configured to increase a signal-to-noise ratio, applying the pixel coefficients to intensity values of the pixels in the image to produce an output, and base calling the target cluster based on the output.
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公开(公告)号：US20230029970A1
公开(公告)日：2023-02-02
申请号：US17839387
申请日：2022-06-13
IPC分类号： G16B30/00 , C12Q1/6869
摘要： A method of generating base calls by a base caller is disclosed. The method includes receiving a plurality of sensor data from a flow cell, wherein the plurality of sensor data is within a first range and identifying a second range, such that at least a threshold percentage of the plurality of sensor data are within the second range. At least a subset of the plurality of sensor data, that are within the second range, are mapped to a third range, thereby generating a plurality of normalized sensor data. The plurality of normalized sensor data is processed in a base caller, to call, for the plurality of normalized sensor data, one or more corresponding bases.
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公开(公告)号：US20220129711A1
公开(公告)日：2022-04-28
申请号：US17510285
申请日：2021-10-25
申请人： ILLUMINA, INC.
发明人： Eric Jon OJARD , Abde Ali Hunaid KAGALWALLA , Rami MEHIO , Nitin UDPA , Gavin Derek PARNABY , John S. VIECELI
摘要： The technology disclosed generates variation correction coefficients on a cluster-by-cluster basis to correct inter-cluster intensity profile variation for improved base calling. An amplification coefficient corrects scale variation. Channel-specific offset coefficients correct shift variation along respective intensity channels. The variation correction coefficients for a target cluster are generated based on combining analysis of historic intensity data generated for the target cluster at preceding sequencing cycles of a sequencing run with analysis of current intensity data generated for the target cluster at a current sequencing cycle of the sequencing run. The variation correction coefficients are then used to correct next intensity data generated for the target cluster at a next sequencing cycle of the sequencing run. The corrected next intensity data is then used to base call the target cluster at the next sequencing cycle.
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公开(公告)号：US20210350163A1
公开(公告)日：2021-11-11
申请号：US17308035
申请日：2021-05-04
申请人： Illumina, Inc.
发明人： Eric Jon OJARD , Rami MEHIO , Gavin Derek PARNABY , Nitin UDPA , John S. VIECELI
摘要： The technology disclosed attenuates spatial crosstalk from sequencing images for base calling. In particular, the technology disclosed accesses an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters. The pixels include a center pixel that contains a center of the target cluster. Each pixel in the pixels is divisible into a plurality of subpixels. Depending upon a particular subpixel, in a plurality of subpixels of the center pixel, which contains the center of the target cluster, the technology disclosed selects, from a bank of subpixel lookup tables, a subpixel lookup table that corresponds to the particular subpixel. The selected subpixel lookup table contains pixel coefficients that are configured to maximizes a signal-to-noise ratio. The technology disclosed element-wise multiplies the pixel coefficients with the pixels and determines a weighted sum.
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