Abstract: A self-calibrating scanning system and method are used in the analysis of biomolecules on a microarray. The self-calibrating scanning system comprises an excitation light source, an optical portion, a detection portion and a calibration portion that includes a calibration apparatus and compensation portion. The calibration apparatus comprises a light source having a highly reproducible or calibrated light based on a preselected or reference light level. The calibration apparatus emits the calibrated light that is measured by the detection portion of the scanning equipment. If the detection components are stable, the components will measure a constant output value for the calibrated light over time. As a detection component changes with time, the output value will change for the same calibrated light. The method comprises the steps of initially calibrating the detection portion of the scanning system and subsequently calibrating the detection portion to compensate for sensitivity changes.

Abstract: A method and system for employing pixel-based, signal-intensity data contained within areas of a scanned image of a molecular array corresponding to features and feature backgrounds in order to determine whether or not the features or feature backgrounds have non-uniform signal intensities and are thus outlier features and outlier feature backgrounds. A calculated, estimated variance for the signal intensities within a feature or feature background is compared to a maximum allowable variance calculated for the feature or feature background based on a signal intensity variance model. When the experimental variance is less than or equal to the maximum allowable variance, the feature or feature background is considered to have acceptable signal-intensity uniformity. Otherwise, the feature or feature background is flagged as an outlier feature or outlier feature background.

Abstract: Methods for correcting systematic errors in the measured position of deposited features of a nucleic acid array on a substrate. Systematic errors are modeled by an algorithmic model based on measuring the positions (and possibly other properties) of a subset of the features, and a model is constructed for predicting deviations in feature position from an ideal grid. Deviations arising in the deposition process, the scanning process, or both may be corrected.

Abstract: System for large dynamic range light detection. In one aspect, the system includes a hybrid counting/integrating system for processing a signal from a photomultiplier tube. In another aspect, large dynamic range is achieved in a cascaded detector system utilizing at least one asymmetric beam splitter for delivering a larger fraction of incident light to one photomultiplier tube and for delivering a smaller fraction of the incident light to another photomultiplier tube.

Abstract: A laser generates a collimated laser beam which passes through a lens off-axis. The beam is focused at a focal plane on a substrate surface. A first position sensitive detector receives the laser beam reflected from the substrate surface through the lens to generate a first signal proportional to lateral beam offset. A beam splitter may be provided to direct a portion of the laser beam before passing through the lens toward a second position sensitive detector to generate a second signal proportional to laser beam pointing instability. Apparatus computes the difference between the first and second signals, the difference being a defocused error signal. It is preferred that the first position sensitive detector be located at a distance from the lens that is at least twice the lens focal length.

Abstract: A self-calibrating scanning system and method are used in the analysis of biomolecules on a microarray. The self-calibrating scanning system comprises an excitation light source, an optical portion, a detection portion and a calibration portion that includes a calibration apparatus and compensation portion. The calibration apparatus comprises a light source having a highly reproducible or calibrated light based on a preselected or reference light level. The calibration apparatus emits the calibrated light that is measured by the detection portion of the scanning equipment. If the detection components are stable, the components will measure a constant output value for the calibrated light over time. As a detection component changes with time, the output value will change for the same calibrated light. The method comprises the steps of initially calibrating the detection portion of the scanning system and subsequently calibrating the detection portion to compensate for sensitivity changes.

Abstract: A laser generates a collimated laser beam which passes through a lens off-axis. The beam is focused at a focal plane on a substrate surface. A first position sensitive detector receives the laser beam reflected from the substrate surface through the lens to generate a first signal proportional to lateral beam offset. A beam splitter may be provided to direct a portion of the laser beam before passing through the lens toward a second position sensitive detector to generate a second signal proportional to laser beam pointing instability. Apparatus computes the difference between the first and second signals, the difference being a defocused error signal. It is preferred that the first position sensitive detector be located at a distance from the lens that is at least twice the lens focal length.

Abstract: A method, apparatus, and computer program product for reading fluorescence signals from an array of chemical moieties (such as different sequence peptides or polynucleotides, for example different DNA sequences). In the method the spatial sequence of scanned locations need not be the same as the temporal sequence. For example, a later illuminated line may be spatially closer to an earlier illuminated line than is a temporally intervening illuminated line.

Abstract: A method and apparatus of interrogating an addressable array unit, which includes a substrate, a light reflecting layer on a front side of the substrate, and a plurality of features on a front side of the array. The method may include, for each of multiple features, illuminating the feature simultaneously with reflected and non-reflected interrogating light. A light emitted from respective features is detected. Either or both, constructive interference of interrogating light at the features, or constructive interference of light emitted from the features, can be obtained to allow lowering of light power from the source, enhanced signal, or reduced noise, or combinations of the foregoing. High depth discrimination may also be obtained without the need for a confocal detection system with conventional pinhole.

Abstract: Apparatus and method for scanning a surface. An optical system generates a light beam to illuminate a surface. A carrier supports the surface for reciprocating motion with respect to the light beam to form one axis of a raster. A propulsion system moves the carrier at a substantially constant speed and a position sensor provides an output signal representing the surface position with respect to the light beam. A control system responsive to the output signal modulates a sample period reciprocally to carrier speed to achieve substantially constant scan length per sample and to control data acquisition timing.

Abstract: A method, apparatus for executing the method, and computer program products for use in such an apparatus. The method includes scanning an interrogating light across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple array features. Signals from respective scanned sites emitted in response to the interrogating light are detected. The interrogating light power is altered for a first site on the array package during the array scan, based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined value absent the altering (which allows for protecting a detector against expected overly bright sites), or is altered during the array scan based on the detected interrogating light power (which allows for compensating for light source drift during an array scan).

Abstract: System for large dynamic range light detection. In one aspect, the system includes a hybrid counting/integrating system for processing a signal from a photomultiplier tube. In another aspect, large dynamic range is achieved in a cascaded detector system utilizing at least one asymmetric beam splitter for delivering a larger fraction of incident light to one photomultiplier tube and for delivering a smaller fraction of the incident light to another photomultiplier tube.

Abstract: A method, apparatus for executing the method, and computer program products for use in such an apparatus. The method includes scanning an interrogating light across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple array features. Signals from respective scanned sites emitted in response to the interrogating light are detected. The interrogating light power is altered for a first site on the array package during the array scan, based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined value absent the altering (which allows for protecting a detector against expected overly bright sites), or is altered during the array scan based on the detected interrogating light power (which allows for compensating for light source drift during an array scan).

Abstract: Apparatus and method for scanning a surface. An optical system generates a light beam to illuminate a surface. A carrier supports the surface for reciprocating motion with respect to the light beam to form one axis of a raster. A propulsion system moves the carrier at a substantially constant speed and a position sensor provides an output signal representing the surface position with respect to the light beam. A control system responsive to the output signal modulates a sample period reciprocally to carrier speed to achieve substantially constant scan length per sample and to control data acquisition timing.

Abstract: System for large dynamic range light detection. In one aspect, the system includes a hybrid counting/integrating system for processing a signal from a photomultiplier tube. In another aspect, large dynamic range is achieved in a cascaded detector system utilizing at least one asymmetric beam splitter for delivering a larger fraction of incident light to one photomultiplier tube and for delivering a smaller fraction of the incident light to another photomultiplier tube.

Abstract: Apparatus and method for scanning a surface. An optical system generates a light beam to illuminate a surface. A carrier supports the surface for reciprocating motion with respect to the light beam to form one axis of a raster. A propulsion system moves the carrier at a substantially constant speed and a position sensor provides an output signal representing the surface position with respect to the light beam. A control system responsive to the output signal modulates a sample period reciprocally to carrier speed to achieve substantially constant scan length per sample and to control data acquisition timing.

Abstract: A method and apparatus for reducing the crosstalk between two or more dye channels in a multiple frequency laser induced fluorescence scanner in which two laser beams and associated optics are employed for focusing the two laser beams on a plurality of spatially separated spots, and for collecting and measuring the resulting emission from the sample labeled with at least two dyes. Crosstalk of the dye emission is minimized as the separated spots provide for a more nearly diagonal transformation matrix between signal channels and dye channels.

Abstract: The system includes a confocal optical system to illuminate an object at an intended detection plane and to focus light from the object onto a pinhole. An opaque obstacle is disposed within the confocal optical system, the obstacle selected to suppress light originating outside the intended detection plane from passing through the pinhole. It is preferred that the obstacle size and location be selected to achieve a desired level of suppression. A design goal is a 100-fold reduction in background with a 10% or less loss of signal.

Abstract: A projection surface includes scattering microparticles that are in constant motion in relation to each other and to a source of laser radiation in a laser projection system. The microparticles reduce the formation of spots that normally occur when viewing the contents of images which are uniformly illuminated by means of laser projection and which are reflected off a projection surface. The microparticles are formed in a suspension fluid and move due to Brownian molecular motion. The fluid is warmed to further increase motion of the microparticles or a piezoelectric force or other mixing mechanism is used to cause turbulence that also increases motion and mixing of the microparticles.

Abstract: An optical homogenizer is disclosed which enables an optical system to obtain the benefits of a high quantum efficiency photon detector without suffering from its non-uniform response. The optical homogenizer has an input end for receiving light emitted from a light source and an output end that produces a relatively uniform distribution of light along a spatial dimension of the photon detector in response to the light source. The optical homogenizer ensures that the photon detector is uniformly illuminated from the output end regardless of where photons from the light source enter the input end.