Abstract: Optical system for reading structurally distinct microbeads. The microbeads are encoded and provide output light signals onto a Fourier plane when illuminated by an incident light. The system includes an input light source configured to illuminate the structurally distinct microbeads thereby providing the output light signals. The output light signals are configured to be projected onto the Fourier plane in a readable manner. The system also includes a reading device that is positioned to detect the output light signals from the Fourier plane. The input light source and the reading device are configured to automatically illuminate the microbeads and detect the output light signals in a predetermined manner. The system also includes a processor configured to perform Fourier plane analysis of the output light signals to determine corresponding codes of the microbeads.

Abstract: A fluidic device including an inorganic solid support attached to an organic solid support by a bonding layer, wherein the inorganic solid support has a rigid structure and wherein the bonding layer includes a material that absorbs radiation at a wavelength that is transmitted by the inorganic solid support or the organic solid support; and a channel formed by the inorganic solid support and the organic solid support, wherein the bonding layer that attaches the inorganic solid support to the organic solid support provides a seal against liquid flow. Methods for making fluidic devices, such as this, are also provided.

Abstract: Compositions and methods for diagnosing, treating and/or preventing cancers characterized by CDH17 overexpression based on the detection of CDH17 or the use of CDH17 as a target for therapeutic intervention or prophylactic intervention are provided. Methods for diagnosing and/or monitoring liver cancers using the expressing of CDH17 involve detecting and/or quantitating the CDH17 protein or encoding nucleic acids (DNA or RNA) in a biological sample such as urine from the subject. Methods for treating liver cancers using CDH17 as a target and of sensitizing cells with aberrant expression of CDH17 have also been developed. The methods include suppression or knockdown of the expression of CDH17 by administering an effective amount of a CDH17 inhibitor.

Abstract: A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates.

Abstract: A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 ?m.

Abstract: A plurality of isolated microvessels including a plurality of encoded microvessels each having a microbody and a reservoir core. The microbody is configured to separate a biological or chemical substance in the reservoir core from an ambient environment surrounding the microbody. The microbody includes a transparent material that at least partially surrounds the reservoir core and facilitates detection of an optical characteristic of the substance within the reservoir core. The microbody of each microvessel includes an identifiable code that distinguishes individual microvessels of the plurality of encoded microvessels from each other. The plurality of isolated microvessels also includes a plurality of compartments each configured to separate individual microvessels of the plurality of encoded microvessels from each other.

Abstract: Methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.

Abstract: A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates.

Abstract: A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.

Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

Abstract: A method and apparatus for reading a microbead having a code thereon is provided wherein the code is projected on and read from a Fourier plane. The microbead may be 1-1000 microns (um) or smaller in feature size. The code is projected on the Fourier plane by scattering input light off the microbead. The scattered light from the microbead is directed through an optical arrangement having a transform lens for projecting the code on the Fourier plane, and read on the Fourier plane using a charge coupled device (CCD) or other similar device.

Abstract: A plurality of isolated microvessels including a plurality of encoded microvessels each having a microbody and a reservoir core. The microbody is configured to separate a biological or chemical substance in the reservoir core from an ambient environment surrounding the microbody. The microbody includes a transparent material that at least partially surrounds the reservoir core and facilitates detection of an optical characteristic of the substance within the reservoir core. The microbody of each microvessel includes an identifiable code that distinguishes individual microvessels of the plurality of encoded microvessels from each other. The plurality of isolated microvessels also includes a plurality of compartments each configured to separate individual microvessels of the plurality of encoded microvessels from each other.

Abstract: An encoded microparticle including an optical substrate including a material that permits light to propagate therethrough. The optical substrate has an elongated body that extends in a direction along a central axis. The optical substrate includes an outer region that extends about the central axis. The encoded microparticle also includes an optically detectable code that is disposed within the optical substrate and extends along the central axis. The outer region surrounds the optically detectable code about the central axis. The optically detectable code is readable when the light propagates through the outer region and is at least one of reflected or filtered by the optically detectable code. Said at least one of reflected or filtered light propagates through the outer region to be detected for reading the optically detectable code.

Abstract: An optical system for reading encoded microbeads. The microbeads provide output light signals onto a Fourier plane when illuminated by an incident light. The system includes an input light source that is configured to illuminate the microbeads thereby providing the output light signals. The output light signals are configured to be projected onto the Fourier plane in a readable manner. The system also includes a reading device that is positioned to detect the output light signals from the Fourier plane. The system also includes a processor that is configured to perform Fourier plane analysis of the optical light signals to determine corresponding codes of the microbeads.

Abstract: A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed.

Abstract: A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.

Abstract: Method of detecting surface features of a microarray. The method includes providing a microarray to an optical scanner, wherein the microarray includes a surface having features. The method also includes carrying out a scanning process using the optical scanner, wherein the scanning process includes: (i) acquiring images of sequential regions on the surface, wherein a defocus spread is applied to the optical scanner during the acquiring, (ii) determining a focus score for the images, (iii) adjusting the optical scanner to a different defocus spread based on the focus score, and (iv) repeating (i) through (iii) at the different defocus spread, thereby acquiring images of further sequential regions on the surface. The method also includes analyzing the images to distinguish different target molecules at the features of the microarray. The images that are analyzed were acquired at the defocus spread and at the different defocus spread during the scanning process.