Abstract: Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyzes, cellular analyzes and other molecular analyzes.

Abstract: Methods and systems for monitoring a plurality of different optical signals from a single source of such signals, where each such different optical signal is spatially separated from other such signals and directed to different detectors or locations upon a single detector, which direction is generally accomplished through the use of a small number of optical components and/or manipulations.

Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.

Abstract: Mitigative and remedial approaches to reduction of autofluorescence background noise are applied in analytical systems that rely upon sensitive measurement of fluorescent signals from arrays of fluorescent signal sources. Such systems are for particular use in fluorescence based sequencing by incorporation systems that rely upon small numbers or individual fluorescent molecules in detecting incorporation of nucleotides in primer extension reactions. Systems and methods for analyzing highly multiplexed sample arrays using highly multiplexed, high-density optical systems to illuminate high-density sample arrays and/or provide detection and preferably confocal detection off signals emanating from such high-density arrays. Systems and methods are applied in a variety of different analytical operations, including analysis of biological and biochemical reactions, including nucleic acid synthesis and derivation of sequence information from such synthesis.

Abstract: Mitigative and remedial approaches to reduction of autofluorescence background noise are applied in analytical systems that rely upon sensitive measurement of fluorescent signals from arrays of fluorescent signal sources. Such systems are for particular use in fluorescence based sequencing by incorporation systems that rely upon small numbers or individual fluorescent molecules in detecting incorporation of nucleotides in primer extension reactions.

Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.

Abstract: Apparatus, systems and methods for use in analyzing discrete reactions at ultra high multiplex with reduced optical noise, and increased system flexibility. Apparatus include substrates having integrated optical components that increase multiplex capability by one or more of increasing density of reaction regions, improving transmission of light to or collection of light from discrete reactions regions. Integrated optical components include reflective optical elements which re-direct illumination light and light emitted from the discrete regions to more efficiently collect emitted light. Particularly preferred applications include single molecule reaction analysis, such as polymerase mediated template dependent nucleic acid synthesis and sequence determination.

Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.

Abstract: This invention provides substrates for use in various applications, including single-molecule analytical reactions. Methods for propagating optical energy within a substrate are provided. Devices comprising waveguide substrates and dielectric omnidirectional reflectors are provided. Waveguide substrates with improved uniformity of optical energy intensity across one or more waveguides and enhanced waveguide illumination efficiency within an analytic detection region of the arrays are provided.

Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.

Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.

Abstract: Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.

Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.

Abstract: Methods, systems and their components for monitoring fluorescent signals and particularly transient fluorescent signals from reaction mixtures of interest, which methods and systems employ modulated excitation light sources to reduce impacts of excessive illumination on the reaction components or the data obtained therefrom.

Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.

Abstract: Mitigative and remedial approaches to reduction of autofluorescence background noise are applied in analytical systems that rely upon sensitive measurement of fluorescent signals from arrays of fluorescent signal sources.

Abstract: Systems and methods for analyzing highly multiplexed sample arrays using highly multiplexed, high density optical systems to illuminate high density sample arrays and/or provide detection and preferably confocal detection off signals emanating from such high density arrays. Systems and methods are applied in a variety of different analytical operations, including analysis of biological and biochemical reactions, including nucleic acid synthesis and derivation of sequence information from such synthesis.

Abstract: An apparatus for suppressing optical power transients includes a variable optical attenuator receiving an input optical signal and outputting an output optical signal; an optical power sensing element coupled to the input optical signal and sensing a portion of the input optical signal; and a feedforward loop controller coupled to the variable optical attenuator and to the optical power sensing element; the feedforward control loop providing feedforward control of the variable optical attenuator to reduce optical power transients of the input optical signal and maintain a substantially constant output power based on the input optical power and a reference value; the variable optical attenuator having a default opaque state in which the input optical signal is substantially attenuated when power is not being supplied to said variable optical attenuator. Variations include feedback loop controllers and a combination feedback and feedforward loop controllers.

Abstract: Methods and systems for monitoring a plurality of different optical signals from a single source of such signals, where each such different optical signal is spatially separated from other such signals and directed to different detectors or locations upon a single detector, which direction is generally accomplished through the use of a small number of optical components and/or manipulations.

Abstract: An optical selector device is disclosed that includes a first arrayed waveguide grating (AWG) demultiplexing an input WDM signal and outputting demultiplexed signals on respective outputs; an array of optical shutters optically coupled to the outputs from the first AWG; a second AWG optically coupled to the array of optical shutters, the second AWG multiplexing optical signals output from the array to form a WDM signal; and a common optical shutter optically coupled to either of the first and second AWGs. The common optical shutter has a default state that is substantially opaque to the WDM signal. Additionally, the array of optical shutters may have a default state that is substantially transparent to the demultiplexed signals. A reconfigurable wavelength blocking device incorporating the optical selector device is also disclosed which additionally includes a controller that controls the optical shutter array to selectively block/pass designated wavelength channels or bands.