Abstract: Provided herein methods, systems, and apparatus for high throughput sequencing, such as at an industrial scale. A sequencing system and/or apparatus may comprise one or more stations that can be operated in parallel and/or independent of one or more other stations.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: Assemblies for and methods of coupling a microtiter plate and receptacle for centrifugation of liquid from the microtiter plate to the receptacle are provided. In some embodiments, a coupling frame can be used. In other embodiments, the microtiter plate couples directly to the receptacle. In some embodiments, relative motion between the receptacle and the microtiter plate is limited in the x-y plane. In some embodiments, relative motion between the receptacle and the microtiter plate is limited in the x-z plane. In some embodiments, relative motion between the receptacle and the microtiter plate is limited in the y-z plane.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: A heating apparatus comprising a support base and a microplate having a first surface and an opposing second surface. The microplate is positioned adjacent the support base and comprises a plurality of wells formed in the first surface thereof. Each of the plurality of wells is sized to receive an assay therein. A sapphire crystalline transparent window is positioned adjacent the microplate opposing the support base. A heating device heats the transparent window in response to a control system.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: A method for calibrating temperature can include cycling temperatures of a set of wells, wherein each well of the set comprises a sample with a spectrally distinguishable species. The method can further include measuring a signal from the spectrally distinguishable species for each well at a temperature during a first temperature cycle, and calibrating the temperatures for measuring the signal from each well during subsequent temperature cycles.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: Methods, software, and apparatus for focusing an image in biological instrument are disclosed. Focusing elements are moved to various focus positions within a focus element travel range, and sample images are captured at the various focus positions. The sample images are resolved into subregions and an optimal focus position is determined based on the image intensity statistical dispersions within the identified subregions.

Abstract: Methods, software, and apparatus for focusing an image in biological instrument are disclosed. Focusing elements are moved to various focus positions within a focus element travel range, and sample images are captured at the various focus positions. The sample images are resolved into subregions and an optimal focus position is determined based on the image intensity statistical dispersions within the identified subregions.

Abstract: Software, methods, and systems for calibrating photometric devices are provided. These involve using a non-uniform test illumination field to approximate a photon transfer curve by calculating stable pixel values and statistical dispersions on a pixel-by-pixel basis.

Abstract: An optical inspection module is provided for detecting defects on a substrate having first and second opposite planar surfaces. The module includes a substrate holding position and first and second measurement instruments. The first instrument includes a first illumination path extending to the substrate holding position and having a grazing angle of incidence with the first surface, which illuminates substantially the entire first surface. A first optical element is oriented to collect non-specularly reflected light scattered by the first surface. A first photodetector has a plurality of pixels positioned within a focal plane of the first lens, which together form a field of view that covers substantially the entire first surface. The second instrument includes a sensor oriented for sensing a physical characteristic of the second surface when the substrate is held in the substrate holding position and the first surface is being illuminated.

Abstract: An optical inspection module is provided for detecting defects on a substrate having first and second opposite planar surfaces. The module includes a substrate holding position and first and second measurement instruments. The first instrument includes a first illumination path extending to the substrate holding position and having a grazing angle of incidence with the first surface, which illuminates substantially the entire first surface. A first optical element is oriented to collect non-specularly reflected light scattered by the first surface. A first photodetector has a plurality of pixels positioned within a focal plane of the first lens, which together form a field of view that covers substantially the entire first surface. The second instrument includes a sensor oriented for sensing a physical characteristic of the second surface when the substrate is held in the substrate holding position and the first surface is being illuminated.

Abstract: An optical inspection module and method are provided for detecting particles on a surface of a substrate. The module includes a substrate holding position, wherein the surface of the substrate defines an object plane at the substrate holding position. A light source illuminates substantially the entire substrate surface. A lens is oriented to collect light reflected from the light beam path by the substrate surface and has a lens plane. A photodetector array has a plurality of pixels defining an image plane within a focal plane of the lens. Each pixel corresponds to an area on the surface and the plurality of pixels together form a field of view that covers substantially the entire surface.

Abstract: An optical inspection module and method are provided for detecting particles on a surface of a substrate. The module includes a substrate holding position, wherein the surface of the substrate defines an object plane at the substrate holding position. A light source illuminates substantially the entire substrate surface. A lens is oriented to collect light reflected from the light beam path by the substrate surface and has a lens plane. A photodetector array has a plurality of pixels defining an image plane within a focal plane of the lens. Each pixel corresponds to an area on the surface and the plurality of pixels together form a field of view that covers substantially the entire surface.

Abstract: A method and apparatus that accurately marks a wafer at selected locations such as a defect location on the surface of a wafer such that a wafer analysis system (e.g., SEM or AFM) may rapidly find the defect. The apparatus contains a wafer platen for retaining a wafer in a substantially horizontal orientation and a marking assembly mounted above the wafer platen. The marking assembly further contains an optical microscope and a marking head. In operation, a user locates a defect using the optical microscope and places a pattern of fiducial marks at a predetermined distance from the defect, e.g., four marks in a diamond pattern circumscribing the defect.

Abstract: A method and apparatus for accurately transforming coordinates within a first coordinate system (e.g., a two-dimensional coordinate system associated with a substrate (or portion thereof)) into coordinates in a second coordinate system (e.g., a three-dimensional coordinate system of substrate (or portion thereof) tilted within a wafer analysis tool.

Abstract: An optical inspection module detects defects on an active surface of a substrate in an integrated process tool system. The optical inspection module includes an enclosure, a substrate holder, a light source, a light beam path, a lens and a photodetector array. The light source has a light beam port. The light beam path extends from the light beam port to the substrate holder and has a grazing angle of incidence with respect to the active surface of the substrate. The light beam path illuminates substantially the entire active surface. The lens is oriented to collect non-secularly reflected light scattered from the light beam path by any defects on the active surface. The photodetector array has a plurality of pixels which are positioned within a focal plane of the lens. Each pixel corresponds to an area on the active surface, and the plurality of pixels together form a field of view that covers substantially the entire active surface.