Illumina Corporation

University of Arizona

Johnson and Johnson Vision Care, Inc.

Illumina Cambridge Limited

Optics 1, Inc.

Simon Prince

Danilo Condello

Stanley S Hong

Peter Clarke Newman

Merek C Siu

Wenyi Feng

Dakota Watson

Marco A Krumbuegel

Christophe Sigel

Steven J Boege

Chunhong Zhou

John O'Shaughnessy

Geraint Wyn Evans

Yinghua Sun

Andrew James Carson

Ashkan Arianpour

David E Hargis

Joseph Francis Pinto

Jeffrey Bendick

Robert Ezra Langlois

Dustin W Blair

Robert E Fischer

Hongji Ren

Matthew William Hage

Bo Lu

John Bailey

Shaoping Lu

Austin Corbett

Aaron Liu

Chunhong (Allen) Zhou

Greg Moeller

Xiangling (Steve) Chen

John O'shauhnessy

Russell J Edwards

Russell T Spaulding

Anindita Dutta

Frederick G Erie

Gary Mark Skinner

Gregory A Williby

John Edward Greivenkamp, Jr

William Butterfield

Paul Hudson

Vincent Hsieh

Jeffrey Gau

Yina Wang

Michael Sherwood

Syed Tariq Shafaat

Shawn Mulcahey

John C Hootman

Krysada Phounsiri

John Edward Greivenkamp

Chunhong (allen) Zhou

Xiangling (steve) Chen

Xiangling Chen

John Edward Greivenkamp Jr

A method for extending a depth of field of a nucleic acid sequencer may comprise optimization steps which are repeated one or more times, in which a result of passing light through an objective lens and a mask is compared with an ideal result, and any discrepancy is used to update the mask. Such a mask may be incorporated into a nucleic acid sequencer which adds fluorescent tags to nucleic acid sites and then detect light emitted from the fluorescent tags, thereby extending the sequencer's depth of field.

Apparatus and method for extended depth of field

An apparatus and method for imaging includes an imaging system formed of a movable objective stage proximal to a sample and positioned for providing an excitation beam onto and for capturing an emission from the sample. The movable objective stage includes an optical lens apparatus and a turn reflector optically coupled to the imaging optics, where at least one of the optical lens apparatus and the turn reflector are movable relative to one another for scanning the sample, and wherein the movement is achieved while maintaining a substantially fixed optical path length between the optical lens apparatus and a fixed plane in a fixed imaging optics stage.

Apparatus and methods for transmitting light

Apparatus and methods for transmitting light are disclosed. In an implementation, an apparatus includes a collimator at an input end positioned to receive an input beam from a fiber beam source and to produce a collimated beam. The apparatus further includes a beam shaping group having one or more optical elements and positioned to receive the collimated beam from the collimator and format the collimated beam into a shaped propagation beam having a substantially rectangular cross-section in a far field. The apparatus further includes an objective stage for optically probing a sample, such as a flow cell, using substantially rectangular cross-section sampling beam, where fluorescence from the sample is captured by a line sensor for detecting properties of the sample, such as chemical reactions therein.

Resolution of images used in processes such as sequencing by synthesis may be increased by structuring sites that would emit signals in the images to have different elevations. Differences in focus caused by these differences in elevation may be used to filter out background illumination, thereby providing an image in which in focus sites may be resolved even though the separation between any site and its nearest neighbor may be below the diffraction limit of the light that would be emitted.

Flow cell with enhanced well imaging resolution

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

A system includes a plurality of modular subassemblies and a plate; wherein each modular subassembly comprises an enclosure and a plurality of optical components aligned to the enclosure, and each enclosure comprises a plurality of mounting structures; and wherein each modular subassembly is mechanically coupled to the plate by attachment of a mounting structure of the modular subassembly directly to a corresponding mounting structure located on the plate, such that by mechanically coupling each modular subassembly to the plate using the mounting structure of the modular subassembly and the corresponding mounting structure on the plate, adjacent modular subassemblies are aligned to each other upon such attachment, and wherein two of the modular subassemblies mechanically coupled to the plate are also attached to each other by mechanically coupling an alignment structure on one of the two modular subassemblies to a respective alignment structure on the other of the two modular subassemblies.

Modular optical analytic systems and methods

An imaging system may include a sample stage comprising a surface to support a sample container, the sample container including a sample having a plurality of sample locations; an optical stage to image the sample at the plurality of sample locations; one or more actuators physically coupled to at least one of the sample stage and the optical stage to move the sample stage relative to the optical stage to focus the optical stage onto a current sample location of the plurality of sample locations; a first light source to illuminate the current sample location; a second light source to project a pair of spots on a next sample location of the plurality of sample locations; and a controller to determine, based on an image of the pair of spots projected on the next sample location, a focus setting for the next sample location.

Predictive focus tracking apparatus and methods

A method comprises: directing, using an objective and a first reflective surface, first autofocus light toward a sensor, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing, using the objective and a second reflective surface, emission light toward the sensor, the emission light originating from a sample at the substrate.

Autofocus functionality in optical sample analysis

The disclosure provides for structured illumination microscopy (SIM) imaging systems. In one set of implementations, a SIM imaging system may be implemented as a multi-arm SIM imaging system, whereby each arm of the system includes a light emitter and a beam splitter (e.g., a transmissive diffraction grating) having a specific, fixed orientation with respect to the system's optical axis. In a second set of implementations, a SIM imaging system may be implemented as a multiple beam splitter slide SIM imaging system, where one linear motion stage is mounted with multiple beam splitters having a corresponding, fixed orientation with respect to the system's optical axis. In a third set of implementations, a SIM imaging system may be implemented as a pattern angle spatial selection SIM imaging system, whereby a fixed two-dimensional diffraction grating is used in combination with a spatial filter wheel to project one-dimensional fringe patterns on a sample.

Dual optical grating slide structured illumination imaging

Systems and methods disclosed herein include an imaging system that may include a laser diode source; an objective lens positioned to direct a focus tracking beam from the light source onto a location in a sample container and to receive the focus tracking beam reflected from the sample; and an image sensor that may include a plurality of pixel locations to receive focus tracking beam that is reflected off of the location in the sample container, where the reflected focus tracking beam may create a spot on the image sensor. Some examples may further include a laser diode light source that may be operated at a power level that is above a power level for operation at an Amplified Spontaneous Emission ('ASE') mode, but below a power level for single mode operation.

Systems and methods for improved focus tracking using a hybrid mode light source

An imaging system including a light source; a first focusing lens positioned to focus a beam from the light source to a beam waist at a predetermined location along an optical path of the beam in the imaging system; a beam splitter positioned relative to the first focusing lens to receive the beam from the first focusing lens and to create first and second beams; a second focusing lens positioned to receive the first and second beams output by the beam splitter, to focus the received first and second beams to a spot sized dimensioned to fall within a sample to be image, and further positioned to receive first and second beams reflected from the sample; an image sensor positioned to receive the light beams reflected from the sample; and a roof prism positioned in the optical path between the second focusing lens and the image sensor.

Systems and methods for improved focus tracking using a light source configuration

Systems and methods disclosed herein include an optical blocking structure that may include a frame defining an aperture, first and second elongate structural members each comprising first and second ends such that the first and second elongate structural members may be connected at their first ends to opposite sides of the aperture, and further such that the first and second elongate structural members may extend from the frame parallel to and in the same direction as one another; and an optically opaque blocking member positioned to extend between the respective second ends of the first and second blocking members.

Systems and methods for improved focus tracking using blocking structures

Growing community of inventors

San Diego, CA, United States of America

Simon Prince