Illumina Corporation

Cidra Corporation

Other

Joseph Francis Pinto

John A Moon

Tracy Helen Fung

Alan D Kersey

James R Dunphy

James S Sirkis

Tarun Kumar Khurana

Wenyi Feng

Poorya Sabounchi

Bernard Hirschbein

Randall Smith

Paul S Szczepanek

John Gerhardt Earney

Martin A Putnam

Michael A Davis

Robert Ezra Langlois

Hongji Ren

Xiuyu Cai

Bo Lu

Thomas A Baker

Austin Corbett

M Shane Bowen

Jay Walter Dawson

David Fournier

Dajun Yuan

Simon Prince

Michael S Graige

Bala Murali K Venkatesan

Arthur Pitera

Peter Clarke Newman

Robert N Brucato

Charles Winston

Christian Victor O'Keefe

Bala Murali Venkatesan

Dakota Watson

Ralph W Jones

Christopher Chestnut

Timothy J Bailey

James C Dunphy

Trevor Wayne MacDougall

Stanley S Hong

Yu Hsuan Chen

Geraint Wyn Evans

Anindita Dutta

David R Fournier

Rui Jiang

Jerin J Russell

John R Troll

Minfu Lu

Jeffrey Gau

Yina Wang

Freddie Falero, Jr

Francesco Birritta

Duane J Rodriguez

James Sirkis

Carol J Pinto

Yu Chen

Ralph Jones

There is set forth herein a light energy exciter that can include one or more light sources. A light energy exciter can emit excitation light directed toward a detector surface that can support biological or chemical samples.

Light energy fluorescence excitation

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

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

Light detection devices and related methods are provided. The devices may comprise a reaction structure for containing a reaction solution with a relatively high or low pH and a plurality of reaction sites that generate light emissions. The devices may comprise a device base comprising a plurality of light sensors, device circuitry coupled to the light sensors, and a plurality of light guides that block excitation light but permit the light emissions to pass to a light sensor. The device base may also include a shield layer extending about each light guide between each light guide and the device circuitry, and a protection layer that is chemically inert with respect to the reaction solution extending about each light guide between each light guide and the shield layer. The protection layer prevents reaction solution that passes through the reaction structure and the light guide from interacting with the device circuitry.

Light detection devices with protective liner and methods related to same

There is set forth herein a device comprising structure defining a detector surface configured for supporting biological or chemical substances, and a sensor array comprising light sensors and circuitry to transmit data signals using photons detected by the light sensors. The device can include one or more features for reducing fluorescence range noise in a detection band of the sensor array.

Detector with reduced fluorescence range noise

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

An inspection apparatus is provided that comprises an optical target including a solid host material and a fluorescing material embedded in the solid host material. The solid host material has a predetermined phonon energy HOST. The fluorescing material exhibits a select ground energy level and a target excitation (TE) energy level separated from the ground energy level by a first energy gap corresponding to a fluorescence emission wavelength of interest. The fluorescing material has a next lower lying (NLL) energy level relative to the TE energy level. The NLL energy level is spaced a second energy gap FMbelow the TE energy level, wherein a ratio of the FM/HOSTis three or more.

Solid inspection apparatus and method of use

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Solana Beach, CA, United States of America

Joseph Francis Pinto