Illumina Corporation

Emd Millipore Corporation

Merck Patent Gmbh

Robert Ezra Langlois

Paul Belitz

Bo Lu

Hongji Ren

M Shane Bowen

John S Vieceli

Stephen Tanner

Alex Nemiroski

Hui Han

Kevan Samiee

Bala Murali K Venkatesan

Danny Yuan Chan

Joseph Francis Pinto

Austin Corbett

Andrew Dodge Heiberg

Andrew James Young

Stanley S Hong

Michael J Carney

James J Vigna

Joseph William Muldoon

Rico Otto

John Cieciuch

Kevin Wayne Bartig

Olga Andreevna Souverneva

Peter Clarke Newman

Simon Prince

James Vigna

Yu Hsuan Chen

Thomas Coton

Olivier Flick

Christine Crequy

Yu Chen

Memory efficient methods determine corrected color values from image data acquired by a nucleic acid sequencer during a base calling cycle. Such methods may: (a) obtain an image of a substrate (e.g., a portion of a flow cell) including a plurality of sites where nucleic acid bases are read; (b) measure color values of the plurality of sites from the image of the substrate; (c) store the color values in a processor buffer of the sequencer's one or more processors; (d) retrieve partially phase-corrected color values of the plurality of sites, where the partially phase-corrected color values were stored in the sequencer's memory during an immediately preceding base calling cycle; (e) determine a prephasing correction; and (f) determine the corrected color values. In various implementations, these operations are all performed during a single base calling cycle. In certain embodiments, the methods additionally include using the corrected color values to make base calls for the plurality of sites. Sequencers may be designed or configured to implement such methods.

Phasing correction

A method is used to generate a distortion model for a structured illumination microscopy (SIM) optical system. A sliding window is moved in relation to a plurality of images to define a plurality of sub-tiles. Each sub-tile represents a portion of the corresponding image. Parameters are estimated for each sub-tiles. The parameters include two or more parameters selected from the group consisting of modulation, angle, spacing, phase offset, and phase deviation. A full width at half maximum (FWHM) value associated with each sub-tile is estimated. A distortion model is estimated, based at least in part on a combination of the estimated parameters and FWHM values stored in the predetermined format and an estimated center window parameter. A two-dimensional image may be generated, based at least in part on the estimated distortion model. The two-dimensional image may include representations indicating where distortions occur in the optical system.

Apparatus and method of estimating values from images

Techniques are described for dynamically correcting image distortion during imaging of a patterned sample having repeating spots. Different sets of image distortion correction coefficients may be calculated for different regions of a sample during a first imaging cycle of a multicycle imaging run and subsequently applied in real time to image data generated during subsequent cycles. In one implementation, image distortion correction coefficients may be calculated for an image of a patterned sample having repeated spots by: estimating an affine transform of the image; sharpening the image; and iteratively searching for an optimal set of distortion correction coefficients for the sharpened image, where iteratively searching for the optimal set of distortion correction coefficients for the sharpened image includes calculating a mean chastity for spot locations in the image, and where the estimated affine transform is applied during each iteration of the search.

Optical distortion correction for imaged samples

The disclosure herein relates to a flow path comprising half clampshaving an interior surface surrounding a flexible tubingconnection with a barb adapter, when assembled may be placed within a clamshell reduce or prevent deformation of the flexible tubing.

Tubing connectors

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.

System and method with fiducials responding to multiple excitation frequencies

A method is used to generate a report presenting parameter values corresponding to a structured illumination microscopy (SIM) optical system. The parameter values are based at least in part on the performed modulation calculation corresponding to an image set captured with the SIM optical system. A minimum FWHM slice is identified, based at least in part on an average FWHM value across the images in the first image set. Parameter estimation is performed on the identified minimum FWHM slice. Best in-focus parameters are identified based at least in part on the performed estimation. A phase estimate is performed for each image in the set. A modulation calculation is performed based at least in part on the identified best in-focus parameters. The report is based at least in part on the performed modulation calculation.

Apparatus and method of providing parameter estimation

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.

System and method with fiducials having offset layouts

The technology disclosed relates to structured illumination microscopy (SIM). In particular, the technology disclosed relates to capturing and processing, in real time, numerous image tiles across a large image plane, dividing them into subtiles, efficiently processing the subtiles, and producing enhanced resolution images from the subtiles. The enhanced resolution images can be combined into enhanced images and can be used in subsequent analysis steps.

Systems and methods for structured illumination microscopy

The technology disclosed present systems and methods to produce an enhanced resolution image from images of a target using structured illumination microscopy (SIM). The method includes transforming at least three images of the target captured by a sensor in a spatial domain into a Fourier domain to produce at least three frequency domain matrices that each include first blocks of complex coefficients and redundant second blocks of complex coefficients that are conjugates to the first blocks. The method includes reducing computing resources required to produce the enhanced resolution image by using first blocks of complex coefficients to produce at least three phase-separated half-matrices in the Fourier domain. The method includes performing one or more intermediate transformation on the phase-separated half-matrices to produce realigned shifted half-matrices. The method includes calculating complex coefficients of second blocks in the Fourier domain to produce full matrices from half-matrices.

Using non-redundant components to increase calculation efficiency for structured illumination microscopy

Implementations of the disclosure are directed to predicting structured illumination parameters for a particular point in time, space, and/or temperature using estimates of structured illumination parameters obtained from structured illumination images captured by a structured illumination system. Particular implementations are directed to predicting structured illumination frequency, phase, orientation, and/or modulation order parameters.

Predicting structured illumination parameters

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.

System and method with fiducials of non-closed shapes

Growing community of inventors

San Diego, CA, United States of America

Robert Ezra Langlois