Abstract: The present invention is directed to a novel method to multiplex long lifetime fluorescent dyes using time-resolved fluorescence (TRF) detection. A combination of spectral and temporal differences in fluorescence emission is used to enhance the ability to separate signals in an assay from multiple dyes. Multiplexed TRF detection apparatuses and systems configured for performing all or part of any of the methods disclosed herein are also provided, particularly apparatuses and systems incorporating cartridge-based multi-mode readers.

Abstract: System, including methods and apparatus, for sample processing. In exemplary embodiments, the system comprises a plurality of devices to perform a protocol on sample holders supporting samples, and also comprises a control system that coordinates operation of the plurality of devices, such that the protocol is performed automatically. Each device of at least two of the plurality of devices may have one or more status lights configured to display a plurality of different visual indicators each indicating a different status of the device. The at least two devices may utilize a same indicator scheme as one another for each different status indicated by the visual indicators. In some embodiments, the indicator scheme is user-configurable. In some embodiments, the one or more status lights of at least one device are provided by one or more recessed light-emitting strips.

Abstract: System, including methods and apparatus, for sample processing. In exemplary embodiments, the system comprises a plurality of devices to perform a protocol on sample holders supporting samples, and also comprises a control system that coordinates operation of the plurality of devices, such that the protocol is performed automatically. Each device of at least two of the plurality of devices may have one or more status lights configured to display a plurality of different visual indicators each indicating a different status of the device. The at least two devices may utilize a same indicator scheme as one another for each different status indicated by the visual indicators. In some embodiments, the indicator scheme is user-configurable. In some embodiments, the one or more status lights of at least one device are provided by one or more recessed light-emitting strips.

Abstract: The present invention is directed to a novel method to multiplex long lifetime fluorescent dyes using time-resolved fluorescence (TRF) detection. A combination of spectral and temporal differences in fluorescence emission is used to enhance the ability to separate signals in an assay from multiple dyes. Multiplexed TRF detection apparatuses and systems configured for performing all or part of any of the methods disclosed herein are also provided, particularly apparatuses and systems incorporating cartridge-based multi-mode readers.

Abstract: A system for determining a baseline measurement for a biological curve is provided. A derivation module determines a derivative response curve based on the biological response curve. A peak identification module searches the derivate response curve to identify a peak in the biological response curve. A leading baseline identification module searches the derivative response curve to identify a starting position of the peak and identifies a leading baseline in the biological response curve. The leading baseline is identified based at least in part on the starting position of the peak. A baseline determination module determines a baseline measurement for the biological response curve based at least in part on the leading baseline associated with the peak.

Abstract: Methods and apparatus, including computer program products, implementing and using techniques for collecting optical data pertaining to one or more characteristics of a sample. The apparatus has a light source, one or more illumination optical elements, a scanner, one or more collection optical elements, and a device forming an aperture that limits detection of light from the sample. The illumination optical elements direct a light beam from the light source onto the sample. The scanner scans the light beam across the sample. The collection optical elements collect light from the sample and transmit the collected light to a detector. None of the collection optical elements are included among the illumination optical elements. The device forming an aperture limits detection of light from the sample to light associated with a limited vertical depth within the sample, and is one of the collection optical elements.

Abstract: Methods and apparatus are described for detecting specific binding between first and second chemical entities. The first chemical entity in association with a first fluorophore is immobilized. The second chemical entity is allowed to bind with the immobilized first chemical entity. The second chemical entity is or becomes coupled to a second fluorophore, which forms a FRET pair with the first fluorophore. The bound chemical entities are exposed to radiation at an excitation frequency for either the first or the second fluorophore, and polarization anisotropy of a FRET fluorescent signal from the bound chemical entities is measured to detect specific binding between the first and second chemical entities.

Abstract: Methods and apparatus for performing scatterometry measurements of biological samples as described herein. A substrate having formed therein one or more sample wells is provided. Each sample well is configured to hold a sample solution containing objects that are to be characterized based on their light scattering properties. One or more sample solutions are dispensed into the sample wells. A specular reflection reducing element is applied to at least some of the sample solutions in the sample wells to decrease reflections of light into one or more detectors. A light beam is directed from a light source onto the objects in the sample wells. Light scattered by the objects in the sample wells is collected and transmitted to one or more detectors. The signal from the detectors is analyzed to detect the one or more characteristics of the one or more samples.

Abstract: Methods and apparatus, including computer program products, implementing and using techniques for collecting optical data pertaining to one or more characteristics of a sample. A light beam of a first frequency is scanned onto a sample surface using one or more illumination optical elements. Light of a second frequency is collected from a scan line on the sample surface using one or more collection optical elements. None of the one or more collection optical elements are included among the one or more illumination optical elements. The collected light is transmitted to a detector.

Abstract: Methods and apparatus are described for detecting specific binding between first and second chemical entities. The first chemical entity in association with a first fluorophore is immobilized. The second chemical entity is allowed to bind with the immobilized first chemical entity. The second chemical entity is or becomes coupled to a second fluorophore, which forms a FRET pair with the first fluorophore. The bound chemical entities are exposed to radiation at an excitation frequency for either the first or the second fluorophore, and polarization anisotropy of a FRET fluorescent signal from the bound chemical entities is measured to detect specific binding between the first and second chemical entities.

Abstract: Methods and apparatus, including computer program products, implementing and using techniques for collecting optical data pertaining to one or more characteristics of a sample. The apparatus has a light source, one or more illumination optical elements, a scanner, one or more collection optical elements, and a device forming an aperture that limits detection of light from the sample. The illumination optical elements direct a light beam from the light source onto the sample. The scanner scans the light beam across the sample. The collection optical elements collect light from the sample and transmit the collected light to a detector. None of the collection optical elements are included among the illumination optical elements. The device forming an aperture limits detection of light from the sample to light associated with a limited vertical depth within the sample, and is one of the collection optical elements.

Abstract: Methods, apparatus, and system, implementing and using techniques for detecting a presence of one or more target analytes in particular regions of interest of one or more samples. One or more samples including objects and one or more target analytes are provided. Some of the target analytes are labeled with a fluorophore and are bound to some of the objects in the samples. The samples are illuminated with fluorescence inducing light and fluorescent light is collected from one or more regions of the one or more samples. At least one anisotropy measurement of the samples is performed to identify regions of interest where one or more target analytes are bound to the objects. The collected fluorescent light from the regions of interest is analyzed to determine a presence of target analytes that are bound to the objects in the one or more samples.

Abstract: A sputter pallet loading and unloading device includes in one embodiment a spindle that rotates the pallet while an arm is engaged with the spring in the pallet to open and close the spring. In another embodiment, the spindle is located adjacent an air track that moves the disk substrate over a cushion of air to the loading area of the pallet. The air pressure under the disk substrate is increased to raise the disk substrate into the loading area. Once raised into the loading area, the spring is closed, e.g., by rotating the pallet in the opposite direction. The pallet and air-track are at a small angle to allow the substrate to slide into the correct position. The simplicity of operation leads to a reduced cost and a higher throughput for this device compared to a robotic loader.

Abstract: An air track includes a concave top surface with a plurality of air outlets or a flat surface with a notch and a plurality of air outlets. The body of the air track includes at least one air filter that runs along the length of at least a portion of the body. The air filter divides the body into a first plenum and a second plenum. The air track also includes a hood covering at least a portion of the top surface. The air track further includes a stopper assembly that arrests the motion of a disk. The stopper assembly includes a disk detector that senses the presence of the disk on the air track.

Abstract: A silicon nitride self-lubricating layer forms the upper surface of a data storage device, such as a rotating disk or a non-rotating memory device, e.g., a credit card-type memory device using a memory strip. The silicon nitride self-lubricating layer can replace the carbon protective overcoat and liquid lubricant used in conventional data storage devices. The silicon nitride self-lubrication layer provides the desired lubrication and protection between the slider and the data storage device. The silicon nitride layer also will not evaporate under high temperatures found in an optical data storage system. In addition, a data storage device may include a plastic polymer layer over which an iron oxide material is deposited. The use of a plastic polymer layer and iron oxide recording layer is particularly advantageous because a low temperature deposition process can be used with the iron oxide material.

Abstract: A system for processing a disk includes an end-effector having a plurality of fingers. The end-effector is mounted to a rotary actuator. The rotary actuator is mounted to a linear stage. The linear stage is positioned adjacent to an air track and a tank. The rotary actuator and the linear stage place the fingers into the inner diameter of a disk on the air track. The fingers grip the inner diameter of the disk. The rotary actuator and the liner stage then place the fingers holding the disk into the tank. The tank is filled with a processing liquid such as a lubrication solution to lubricate the disk.

Abstract: A washer includes driving and scrubbing rollers that press against the opposing surfaces of a substrate, which may be, e.g., a small form factor disk. The driving rollers and scrubbing rollers are approximately aligned along two different radii of the substrate that are separated by 180 degrees. The driving rollers rotate in opposite directions as do the scrubbing rollers. During the scrub cycle, the driving rollers cause the substrate to rotate, while the scrubbing rollers scrub the opposing surfaces of the substrate. Outside diameter rollers that are orthogonally positioned relative to the driving rollers and the scrubbing rollers, and which may be free spinning, contact the outside diameter of the substrate and hold the substrate in position during the scrub cycle. The substrate is loaded into the washer by lifting the substrate, via a lifting arm, to the driving and scrubbing rollers.

Abstract: A sputter pallet loading and unloading device includes in one embodiment a spindle that rotates the pallet while an arm is engaged with the spring in the pallet to open and close the spring. In another embodiment, the spindle is located adjacent an air track that moves the disk substrate over a cushion of air to the loading area of the pallet. The air pressure under the disk substrate is increased to raise the disk substrate into the loading area. Once raised into the loading area, the spring is closed, e.g., by rotating the pallet in the opposite direction. The pallet and air-track are at a small angle to allow the substrate to slide into the correct position. The simplicity of operation leads to a reduced cost and a higher throughput for this device compared to a robotic loader.

Abstract: An air track included a first body having a concave top surface with a plurality of air outlets or a flat surface with a notch and a plurality of air outlets. The body includes at least one air filter that runs along the length of at least a portion of the body. The air filter dividing the body into a first plenum and a second plenum. The air track also includes a hood covering at least a portion of the top surface. The air track further includes a stopper assembly that arrests the motion of a disk. The stopper assembly includes a disk detector that senses the presence of the disk on the air track.

Abstract: A washer includes driving and scrubbing rollers that press against the opposing surfaces of a substrate, which may be, e.g., a small form factor disk. The driving rollers and scrubbing rollers are approximately aligned along two different radii of the substrate that are separated by 180 degrees. The driving rollers rotate in opposite directions as do the scrubbing rollers. During the scrub cycle, the driving rollers cause the substrate to rotate, while the scrubbing rollers scrub the opposing surfaces of the substrate. Outside diameter rollers that are orthogonally positioned relative to the driving rollers and the scrubbing rollers, and which may be free spinning, contact the outside diameter of the substrate and hold the substrate in position during the scrub cycle. The substrate is loaded into the washer by lifting the substrate, via a lifting arm, to the driving and scrubbing rollers.