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    Automated feature extraction processes and systems
    1.
    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。

    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。

    Methods and systems for facilitating analysis of feature extraction outputs
    6.
    发明申请
    Methods and systems for facilitating analysis of feature extraction outputs 审中-公开
    用于促进特征提取输出分析的方法和系统

    公开(公告)号：US20070255512A1

    公开(公告)日：2007-11-01

    申请号：US11413643

    申请日：2006-04-28

    申请人： Glenda Delenstarr ,  Charles Troup ,  John Corson ,  Andrew Payne ,  David Gordon

    发明人： Glenda Delenstarr ,  Charles Troup ,  John Corson ,  Andrew Payne ,  David Gordon

    IPC分类号： G06F19/00 ,  G06F17/40

    CPC分类号： G16B50/00 ,  G16B25/00

    摘要： Methods, systems and computer readable media for facilitating analysis of feature extraction outputs across multiple extractions. A feature extraction output of an extraction resulting from feature extraction of an array is inputted, and global statistics and array processing parameters are extracted from the feature extraction output. A table/file is populated with the extracted global statistics and array processing parameters of the extraction. The inputting, extracting and populating steps are repeated for at least one additional feature extraction output of another extraction, so that the table/file includes global statistics that can be readily cross-compared over multiple extractions with reference to a single table or file. Methods, systems and computer readable media are provided for setting threshold values for metrics that global statistics are provided for. An evaluation metric may be set by a user, based upon the threshold values set for the metrics. A metric set including the metrics and optionally one or more thresholds and optionally an evaluation metric may be stored and/or applied to additional global statistics for those metrics to evaluate the quality of one or more extractions. A set of reports are provided for facilitating analysis of feature extraction outputs across multiple extractions. A diagnostic tool is provided for identifying and diagnosing potential problems in feature extraction outputs.

    摘要翻译： 方法，系统和计算机可读介质，用于促进跨多次提取的特征提取输出的分析。 输入从阵列的特征提取产生的提取的特征提取输出，并从特征提取输出中提取全局统计和阵列处理参数。 用提取的全局统计数据和数组处理参数填充表/文件。 针对另一个提取的至少一个附加特征提取输出重复输入，提取和填充步骤，使得表/文件包括参考单个表或文件可以容易地通过多次提取进行交叉比较的全局统计。 提供了方法，系统和计算机可读介质，用于为为全球统计提供的度量设置阈值。 评估度量可以由用户基于针对度量设置的阈值来设置。 可以将包括指标和可选的一个或多个阈值以及可选的评估度量的度量值存储和/或应用于这些度量的附加全局统计量，以评估一个或多个提取的质量。 提供了一组报告，以便于跨多次提取的特征提取输出分析。 提供诊断工具用于识别和诊断特征提取输出中的潜在问题。

    Methods and systems for detrending signal intensity data from chemical arrays
    7.
    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。

    Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners
    8.
    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。

    Method and system for automated focus-distance determination for molecular array scanners
    9.
    发明申请
    Method and system for automated focus-distance determination for molecular array scanners 审中-公开
    分子阵列扫描仪的自动聚焦距离测定方法和系统

    公开(公告)号：US20050067583A1

    公开(公告)日：2005-03-31

    申请号：US10910562

    申请日：2004-08-02

    申请人： John Corson ,  Stanley Woods ,  Russell Parker ,  Xiangyang Zhou ,  Bo Curry

    发明人： John Corson ,  Stanley Woods ,  Russell Parker ,  Xiangyang Zhou ,  Bo Curry

    IPC分类号： G01N21/64

    CPC分类号： G01N21/6452 ,  G01N21/6458 ,  G01N2021/6463

    摘要： An automated method and system for determining an optimal focus distance for scanning a molecular array by a molecular array scanner. Blocks of rows of a reference array are 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 a peak-height-based, or window-based, focus-finding routine that selects an optimal focus-distance for data scans.

    摘要翻译： 一种用于通过分子阵列扫描仪确定用于扫描分子阵列的最佳聚焦距离的自动化方法和系统。 参考阵列的行的块自动地从阶段相对较远的距离光收集介质（诸如光纤或z位置）扫描，以产生提供z位置和测量的信号强度之间的功能关系的数据。 然后通过基于峰值高度或基于窗口的聚焦寻找程序处理数据，该程序为数据扫描选择最佳聚焦距离。

    Chemical arrays on a common carrier
    10.
    发明申请
    Chemical arrays on a common carrier 审中-公开
    化学阵列在共同载体上

    公开(公告)号：US20050026299A1

    公开(公告)日：2005-02-03

    申请号：US10786557

    申请日：2004-02-24

    申请人： Arindam Bhattacharjee ,  John Corson ,  J. Mitchell ,  George Tsai

    发明人： Arindam Bhattacharjee ,  John Corson ,  J. Mitchell ,  George Tsai

    IPC分类号： G01N21/25 ,  G01N21/00

    CPC分类号： G01N21/253 ,  G01N2021/6439 ,  G01N2021/6482

    摘要： A set of chemical arrays held together by a common carrier with one or more arrays of the set having been previously exposed to a sample. In one embodiment the common carrier optionally includes an indication of locations along which the carrier should be separated so as to separate the set of chemical arrays into multiple sub-sets each with one or more arrays. A method of use may include separating the set of chemical arrays into multiple sub-sets each with one or more arrays.

    摘要翻译： 一组化学阵列由共同的载体与一组或多组先前暴露于样品的阵列保持在一起。 在一个实施例中，公共载体可选地包括载体应该被分离的位置的指示，以便将该组化学阵列分成具有一个或多个阵列的多个子组。 一种使用的方法可以包括将该组化学阵列分成具有一个或多个阵列的多个子组。