Abstract: 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.

Abstract: A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.

Abstract: 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.

Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include features and materials that are provided on or in the support of a patterned array and that return at least a portion of incident light by reflection. The fiducial markers may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the patterned array.

Abstract: Fiducial markers are provided on a patterned array of the type that may be used for molecular analysis, such as sequencing. The fiducial markers may have configurations and layouts that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducial markers may include non-rectilinear layouts that may provide for more robust location of both the fiducial markers and sites of the patterned array.

Abstract: 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.

Abstract: 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.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: 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.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.

Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include a non-closed shape that may encode information, allow for bubbles to escape during manufacture, and provide additional advantages over closed shape fiducials.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include features and materials that are provided on or in the support of the array and that return at least a portion of incident light by reflection. The fiducials may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the array.

Abstract: Embodiments for registering features in a repeating pattern are described. These embodiments can include providing an object having a repeating pattern of features and a fiducial. These embodiment can also include obtaining a target image of the object, where the target image includes the repeating pattern of features and the fiducial. These embodiment can also include comparing the fiducial in the target image to reference data, where the reference data includes xy coordinates for a virtual fiducial. These embodiment can also include determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.

Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an “always on” type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.

Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations and layouts that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include offset layouts that may be useful in detecting the fiducials in different types and approaches in imaging, and that may help to distinguish regions of the array from one another in image data.

Abstract: Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations and layouts that that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include non-rectilinear layouts that may provide for more robust location of both the fiducials and sites of the array.

Abstract: Presented herein are techniques for indexing of nucleic acid, e.g., for use in conjunction with sequencing. The techniques include generating indexed nucleic acid fragments from an individual sample, whereby the index sequence incorporated into each index site of the nucleic acid fragment is selected from a plurality of distinguishable of index sequences and such that the population of generated nucleic acid fragments represents each index sequence from the plurality. In this manner, the generated indexed nucleic acid fragments from a single sample are indexed with a diverse mix of index sequences that reduce misassignment due to index read errors associated with low sequence diversity.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.