Abstract: An optical scanning system including a switchable light source, a detector, a substrate and a plurality of optical sensing sites, as well s methods and kits for use thereof are provided. The substrate is coupled to and in optical communication with the switchable light source and the detector. Additionally, the substrate includes a plurality of substantially parallel excitation waveguides, and a plurality of substantially parallel collection waveguides, the excitation waveguides and collection waveguides crossing to form a two-dimensional array of intersection regions where an excitation waveguide and a collection waveguide cross and provide optical communication with the intersection region at each crossing. The plurality of optical sensing sites are each in optical communication with an intersection region.

Abstract: A scanning sensor system 100, methods and kits for use thereof including a switchable light source 102, a detector 106, a substrate 104 and a plurality of optical sensing sites 112 are provided. Substrate 104 is coupled to and in optical communication with switchable light source 102 and detector 106. Additionally, substrate 104 includes a plurality of substantially parallel excitation waveguides 108, and a plurality of substantially parallel collection waveguides 110, the excitation waveguides 108 and collection waveguides 110 crossing to form a two-dimensional array and optical communication with intersection regions 114 at each crossing. The plurality of optical sensing sites 112 are each in optical communication with an intersection region 114.

Abstract: A scanning sensor system 100, methods and kits for use thereof including a switchable light source 102, a detector 106, a substrate 104 and a plurality of optical sensing sites 112 are provided. Substrate 104 is coupled to and in optical communication with switchable light source 102 and detector 106. Additionally, substrate 104 includes a plurality of substantially parallel excitation waveguides 108, and a plurality of substantially parallel collection waveguides 110, the excitation waveguides 108 and collection waveguides 110 crossing to form a two-dimensional array and optical communication with intersection regions 114 at each crossing. The plurality of optical sensing sites 112 are each in optical communication with an intersection region 114.

Abstract: The invention provides methods and devices for generating optical pulses in one or more waveguides using a spatially scanning light source. A detection system, methods of use thereof and kits for detecting a biologically active analyte molecule are also provided. The system includes a scanning light source, a substrate comprising a plurality of waveguides and a plurality of optical sensing sites in optical communication with one or more waveguide of the substrate, a detector that is coupled to and in optical communication with the substrate, and means for spatially translating a light beam emitted from said scanning light source such that the light beam is coupled to and in optical communication with the waveguides of the substrate at some point along its scanning path. The use of a scanning light sources allows the coupling of light into the waveguides of the substrate in a simple and cost-effective manner.

Abstract: A system and methods of sequencing a nucleic acid by detecting the identity of a fluorescent nucleotide analogue incorporated at the 3? end of a growing nucleic acid strand are provided.

Abstract: A scanning sensor system, methods of use and kits for detecting a biologically active analyte are provided. The scanning sensor system includes a light source, a detector, a substrate comprising a plurality of waveguides and a plurality of optical sensing sites in optical communication with one or more waveguide of the substrate, and at least one adapter configured to couple with the substrate and provide optical communication between the light source, the waveguides of the substrate, and the detector.

Abstract: A scanning sensor system 100, methods and kits for use thereof including a switchable light source 102, a detector 106, a substrate 104 and a plurality of optical sensing sites 112 are provided. Substrate 104 is coupled to and in optical communication with switchable light source 102 and detector 106. Additionally, substrate 104 includes a plurality of substantially parallel excitation waveguides 108, and a plurality of substantially parallel collection waveguides 110, the excitation waveguides 108 and collection waveguides 110 crossing to form a two-dimensional array and optical communication with intersection regions 114 at each crossing. The plurality of optical sensing sites 112 are each in optical communication with an intersection region 114.

Abstract: Methods and systems for eliminating extinguish losses in a hub ring network that includes Optical Add Drop Multiplexers (OADMs). The need for a wavelength extinguishing function is eliminated by ensuring that when a wavelength is added to the optical path at a certain node in the ring, the arriving traffic in the path before the addition does not contain that wavelength. The methods include using different wavelengths for the drop and the add operations, ensuring that a trough traffic does not include local ADD wavelengths which are subsequently combined with the through wavelengths, and bi-directional transmission on one or two separate fibers of identical dropped and added wavelengths. Systems include the use of simple, inexpensive, half or fully dynamic OADMs implementing the low-loss functionality.

Abstract: A system for switching optical energy from a plurality of input waveguides to a plurality of output waveguides, while balancing power in the output waveguides, and a method for its use. The system is based on an optical switch matrix that includes, for each input waveguide and for each output waveguide, one or more attenuators that divert an adjustable portion of the optical energy, that enters via that input waveguide, to that output waveguide. Preferably, each input waveguide is coupled to each output waveguide via a pair of 2×2 mach-Zehnder interferometers, a first of which has an idle input port and a second of which has an idle output port. The system also includes a feedback mechanism that taps fixed portions of the power in either the input waveguides or the output waveguides, and adjusts the attenuators accordingly.

Abstract: The optical power in a waveguide of an optical circuit is monitored by mounting an optical sensor, such as a photodiode, laterally apart from the waveguide but sufficiently close to the waveguide to detect light emerging laterally from the waveguide, and by receiving signals from the sensor that are representative of the optical power. In a DWDM circuit, a bandpass filter is placed between the waveguide and the sensor for monitoring only one of the wavelengths carried by the waveguide. To minimize crosstalk, the monitored portions of the waveguides are isolated from each other, for example by trenches or by optically absorptive barriers. Suitably calibrated processing of signals from several sensors that monitor several waveguides eliminates crosstalk.

Abstract: A system for switching optical energy from a plurality of input waveguides to a plurality of output waveguides, while balancing power in the output waveguides, and a method for its use. The system is based on an optical switch matrix that includes, for each input waveguide and for each output waveguide, one or more attenuators that divert an adjustable portion of the optical energy, that enters via that input waveguide, to that output waveguide. Preferably, each input waveguide is coupled to each output waveguide via a pair of 2×2 mach-Zehnder interferometers, a first of which has an idle input port and a second of which has an idle output port. The system also includes a feedback mechanism that taps fixed portions of the power in either the input waveguides or the output waveguides, and adjusts the attenuators accordingly.

Abstract: A system for switching optical energy from a plurality of input waveguides to a plurality of output waveguides, while balancing power in the output waveguides, and a method for its use. The system is based on an optical switch matrix that includes, for each input waveguide and for each output waveguide, one or more attenuators that divert an adjustable portion of the optical energy, that enters via that input waveguide, to that output waveguide. Preferably, each input waveguide is coupled to each output waveguide via a pair of 2×2 Mach-Zehnder interferometers, a first of which has an idle input port and a second of which has an idle output port. The system also includes a feedback mechanism that taps fixed portions of the power in either the input waveguides or the output waveguides, and adjusts the attenuators accordingly.

Abstract: A system for switching optical energy from a plurality of input waveguides to a plurality of output waveguides, while balancing power in the output waveguides, and a method for its use. The system is based on an optical switch matrix that includes, for each input waveguide and for each output waveguide, one or more attenuators that divert an adjustable portion of the optical energy, that enters via that input waveguide, to that output waveguide. Preferably, each input waveguide is coupled to each output waveguide via a pair of 2×2 mach-Zehnder interferometers, a first of which has an idle input port and a second of which has an idle output port. The system also includes a feedback mechanism that taps fixed portions of the power in either the input waveguides or the output waveguides, and adjusts the attenuators accordingly.

Abstract: An optical switch matrix connects N input waveguides to M output waveguides via M rows of switch sets. Each row of switch sets includes a first switch set that has one input port and two output ports, N−2 intermediate switch sets that have two input ports and two output ports, and a last switch set that has two input ports and one or two output ports. One output port of each first or intermediate switch set is optically coupled to an input port of a succeeding switch set in the same row, and the other output port is optically coupled to an input port of a respective switch set in a cyclically succeeding row, by intermediate waveguides that do not cross each other. The only exceptions are the intermediate waveguides that connect the last row to the first row. These intermediate waveguides may cross other waveguides.

Abstract: A method and apparatus for detecting a contaminant in a substrate. An array of anode elements is positioned in proximity to the substrate and is biased at a positive voltage relative to the substrate. The substrate is irradiated with photons having energies below an atomic ionization energy of the substrate, so as to ionize the contaminant to emit electrons. The emitted electrons are collected at one or more of the anode elements, thereby generating a current indicative of the presence of the contaminant in the semiconductor in proximity to the one or more of the anode elements.

Abstract: Apparatus for optical analysis of a sample, including an energy source, which generates a pulse of energy that is incident on the sample, causing the sample to emit radiation characteristic of the composition of the sample, and a detector assembly, which receives and analyzes the radiation emitted by the excited sample. An optical assembly conveys the emitted radiation from the sample to the detector assembly, the optical assembly including an optic proximal to the sample, on which optic the radiation is incident along a beam path thereof between the sample and the detector assembly. A moving mechanical element moves in synchronization with the pulse from the energy source so as to substantially prevent matter ejected from the sample responsive to the incident energy from accumulating on the optic.