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    Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners
    1.
    发明申请
    Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners 失效
    生物聚合物阵列基板厚度相关的生物聚合物阵列扫描仪的自动聚焦距离测定方法

    公开(公告)号：US20050153349A1

    公开(公告)日：2005-07-14

    申请号：US11022302

    申请日：2004-12-23

    申请人： Jayati Ghosh ,  John Corson ,  Debra Sillman

    发明人： Jayati Ghosh ,  John Corson ,  Debra Sillman

    IPC分类号： G01N21/27 ,  G01N21/64 ,  G02B21/24 ,  C12Q1/68 ,  G01N33/48 ,  G01N33/50 ,  G06F19/00

    CPC分类号： G01N21/6452 ,  G01N21/274 ,  G01N21/276 ,  G02B21/241 ,  G02B21/244

    摘要： A method and system for determining a biopolymer array substrate thickness dependent optimal focus distance for scanning a molecular array by a molecular array scanner are provided. A reference substrate is automatically scanned at successively greater distances of the stage from a light gathering medium, such as an optical fiber, or z-positions, to produce data providing a functional relationship between z-position and measured signal intensities. The data is then processed by an array substrate thickness dependent focus-finding routine that selects an optimal focus-distance for data scans which is optimized for the thickness of the reference substrate. Also provided are methods of determining the thickness of a biopolymer array substrate using a position sensitive device (PSD) component of a biopolymer array scanner. Further methods include determining the thickness of said biopolymeric array and automatically selecting an optimal focus distance using the determined thickness and a calibration function on thickness versus optimal focus distance. The subject invention finds use in a variety of different applications, including both genomic and proteomic applications.

    摘要翻译： 提供了一种用于通过分子阵列扫描器来确定用于扫描分子阵列的生物聚合物阵列基底厚度相关的最佳聚焦距离的方法和系统。 参考基板在从阶段的连续更远的距离处自动扫描，例如光纤或z位置，以产生提供z位置和测量信号强度之间的功能关系的数据。 然后通过阵列基板厚度相关的聚焦寻找程序来处理数据，该程序为针对参考基板的厚度优化的数据扫描选择最佳聚焦距离。 还提供了使用生物聚合物阵列扫描仪的位置敏感装置（PSD）组分确定生物聚合物阵列基底的厚度的方法。 其他方法包括确定所述生物聚合物阵列的厚度并使用所确定的厚度和厚度与最佳聚焦距离之间的校准函数自动选择最佳聚焦距离。 本发明可用于各种不同的应用，包括基因组和蛋白质组学应用。

    Scanning parameterization for biopolymeric array scanner
    2.
    发明申请
    Scanning parameterization for biopolymeric array scanner 审中-公开
    生物聚合物阵列扫描仪的扫描参数化

    公开(公告)号：US20060006237A1

    公开(公告)日：2006-01-12

    申请号：US11174296

    申请日：2005-07-01

    申请人： Debra Sillman ,  Xiangyang Zhou ,  Chetan Jadhaw ,  Herbert Cattell ,  Jayati Ghosh

    发明人： Debra Sillman ,  Xiangyang Zhou ,  Chetan Jadhaw ,  Herbert Cattell ,  Jayati Ghosh

    IPC分类号： G06F17/00

    CPC分类号： G01N21/6452 ,  G01N33/52 ,  G01N33/582 ,  G01N33/68 ,  G01N2201/0484

    摘要： Methods for programming an array scanner to scan a plurality of biopolymer arrays are provided. In the subject methods, individual scanning parameters for at least two different arrays of the plurality of arrays to be scanned are selected and input into the array scanner prior to scanning the plurality arrays. The programmed scanner then scans the plurality of arrays according to the pre-selected scanning parameters Also provided are scanners programmed according to the subject methods, as well as computer programming that provides for programming of scanners according to the subject methods. The subject methods and compositions find use in a variety of different applications, including both genomics and proteomics applications.

    摘要翻译： 提供了对阵列扫描器进行编程以扫描多个生物聚合物阵列的方法。 在主题方法中，在扫描多个阵列之前，选择要扫描的多个阵列的至少两个不同阵列的各个扫描参数并将其输入阵列扫描器。 编程的扫描仪然后根据预先选择的扫描参数扫描多个阵列。还提供了根据主题方法编程的扫描器以及根据主题方法提供对扫描仪的编程的计算机编程。 主题方法和组合物可用于各种不同的应用，包括基因组学和蛋白质组学应用。

    Methods and systems for detrending signal intensity data from chemical arrays
    3.
    发明申请
    Methods and systems for detrending signal intensity data from chemical arrays 有权
    从化学阵列中去除信号强度数据的方法和系统

    公开(公告)号：US20080004824A1

    公开(公告)日：2008-01-03

    申请号：US11479269

    申请日：2006-06-30

    申请人： John Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

    发明人： John Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

    IPC分类号： G06F17/10 ,  G06F19/00 ,  G06F17/40

    CPC分类号： G06F19/20

    摘要： Methods, systems and computer readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface fitted to calculate a surface approximation. The surface approximation is normalized and used to de-trend the signal intensity values from the features.

    摘要翻译： 用于从化学阵列上的特征消除信号强度值趋势的方法，系统和计算机可读介质。 来自阵列中特征的输入信号值进行表面拟合，以计算表面近似值。 表面近似被归一化并用于从特征中消除信号强度值。

    System and methods for characterization of chemical arrays for quality control
    5.
    发明申请
    System and methods for characterization of chemical arrays for quality control 有权
    用于表征化学阵列以进行质量控制的系统和方法

    公开(公告)号：US20070027637A1

    公开(公告)日：2007-02-01

    申请号：US11192680

    申请日：2005-07-29

    申请人： Glenda Delenstarr ,  Jayati Ghosh ,  John Corson

    发明人： Glenda Delenstarr ,  Jayati Ghosh ,  John Corson

    IPC分类号： G01N31/00 ,  G06F19/00

    CPC分类号： G06F19/20 ,  Y10T436/25

    摘要： Systems, methods and computer readable media for characterizing a chemical array. At least one metric indicative of accuracy of location of features on the chemical array by a feature extraction process used to extract signals from features of the chemical array may be generated, as well as additional metrics adapted to identify errors caused by a particular process used in generating the signals on the array. A quality control report may be generated to contain at least one metric indicative of accuracy of location and said at least one additional metric. Customized quality control reports may be generated by providing for user selection of at least one metric adapted to identify errors caused by a particular process used in generating signals on a chemical array, from plurality of metrics, and including such selections in the quality control report generated. Systems, methods and computer readable media are provided for characterizing a chemical array by generating metrics adapted to identify errors caused by a particular process used in generating the signals on the array, generating a quality control report containing at least one of the metrics, and outputting the quality control report.

    摘要翻译： 用于表征化学阵列的系统，方法和计算机可读介质。 可以产生指示化学阵列上的特征位置精度的至少一个度量，其特征提取过程用于从化学阵列的特征提取信号，以及适于识别由特定方法使用的特定过程引起的错误的附加度量 在阵列上产生信号。 可以生成质量控制报告以包含指示位置的精确度和所述至少一个附加度量的至少一个度量。 定制的质量控制报告可以通过提供用户选择适于识别由用于从多个度量生成化学阵列上的信号的特定过程引起的错误的至少一个度量，并且在生成的质量控制报告中包括这样的选择 。 提供了系统，方法和计算机可读介质，用于通过产生适于识别由用于产生阵列上的信号的特定过程引起的错误的度量来表征化学阵列，生成包含度量的至少一个的质量控制报告，以及输出 质量控制报告。

    Automated feature extraction processes and systems
    8.
    发明申请
    Automated feature extraction processes and systems 审中-公开
    自动特征提取过程和系统

    公开(公告)号：US20060056671A1

    公开(公告)日：2006-03-16

    申请号：US10941501

    申请日：2004-09-15

    申请人： Jayati Ghosh ,  Christian Le Cocq. ,  Xiangyang Zhou ,  John Corson ,  Glenda Delenstarr ,  Charles Troup

    发明人： Jayati Ghosh ,  Christian Le Cocq. ,  Xiangyang Zhou ,  John Corson ,  Glenda Delenstarr ,  Charles Troup

    IPC分类号： G06K9/00 ,  G06K9/46 ,  C12M1/34

    CPC分类号： G06T7/00 ,  G06T2207/30072 ,  G16B25/00

    摘要： Methods, systems and computer readable media for automatically feature extracting array images in batch mode. At least two images to be feature extracted are loaded into a batch project, and the system automatically and sequentially feature extracts the images in the batch project. At least one of the images may be feature extracted based upon a different grid template or protocol than at least one other of the images. Methods, systems and computer readable media are provided to automatically feature extract a single array image having an identifier indicating that it is a multipack, multiple array image. A system provided for feature extracting array images in batch mode includes a user interface with a feature enabling a user to select images to be loaded into a batch project; and based upon the loaded images in the batch project, the system may automatically assign a grid template to each image loaded into the batch project. Further, the system may automatically assign a protocol to each image loaded into the batch project.

    摘要翻译： 方法，系统和计算机可读介质，用于以批处理模式自动特征提取阵列图像。 要将特征提取的至少两个图像加载到批处理项目中，并且系统自动并顺序地特征提取批处理项目中的图像。 可以基于与至少另一个图像不同的网格模板或协议来提取图像中的至少一个。 提供方法，系统和计算机可读介质以自动特征提取具有指示其是多包多重阵列图像的标识符的单个阵列图像。 提供用于以批处理模式提取阵列图像的特征的系统包括具有使得用户能够选择要加载到批处理项目中的图像的特征的用户界面; 并且基于批处理项目中加载的图像，系统可以自动将网格模板分配给加载到批处理项目中的每个图像。 此外，系统可以自动将协议分配给加载到批处理项目中的每个图像。

    Methods and systems for detrending signal intensity data from chemical arrays
    9.
    发明申请
    Methods and systems for detrending signal intensity data from chemical arrays 有权
    从化学阵列中去除信号强度数据的方法和系统

    公开(公告)号：US20090012732A1

    公开(公告)日：2009-01-08

    申请号：US12231517

    申请日：2008-09-02

    申请人： John Frederick Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

    发明人： John Frederick Corson ,  Jayati Ghosh ,  Svetlana Shchegrova

    IPC分类号： G06F17/10

    CPC分类号： G06F19/20

    摘要： Methods, systems and computer readable media for removing trends in signal intensity values from features on a chemical array. Inputted signal values from features on the array are surface fitted to calculate a surface approximation. The surface approximation is normalized and used to de-trend the signal intensity values from the features.

    摘要翻译： 用于从化学阵列上的特征消除信号强度值趋势的方法，系统和计算机可读介质。 来自阵列中特征的输入信号值进行表面拟合，以计算表面近似值。 表面近似被归一化并用于从特征中消除信号强度值。