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    Scanning parameterization for biopolymeric array scanner
    1.
    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。

    Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners
    2.
    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。

    System and methods for automated processing of multiple chemical arrays
    3.
    发明授权
    System and methods for automated processing of multiple chemical arrays 有权
    用于自动处理多个化学阵列的系统和方法

    公开(公告)号：US07877213B2

    公开(公告)日：2011-01-25

    申请号：US11233560

    申请日：2005-09-22

    申请人： Jayati Ghosh ,  Charles D. Troup ,  Xiangyang Zhou

    发明人： Jayati Ghosh ,  Charles D. Troup ,  Xiangyang Zhou

    IPC分类号： G01N33/48

    CPC分类号： G06F19/20

    摘要： A system and method of operating a data processing system to provide feature extraction from an image obtained from a plurality of chemical arrays is disclosed. The method includes bifurcating processing of the image by performing image processing and post-processing. The image processing includes processing parts of the image, each part corresponding to a different one of the arrays, in an automated batch process, to produce image-processed outputs that are different from the image and contain information extracted from the image. The post-processing includes processing the image-processed outputs according to different post-processing protocols with respect to different ones of those parts of the image corresponding to at least two of the arrays, to produce post-processed outputs. The method includes outputting at least one of the image-processed outputs and/or at least one of the post-processed outputs.

    摘要翻译： 公开了一种操作数据处理系统以从从多个化学阵列获得的图像中提取特征提取的系统和方法。 该方法包括通过执行图像处理和后处理来对图像进行分岔处理。 图像处理包括在自动批处理过程中处理图像的每个部分对应于不同的阵列的部分，以产生不同于图像的图像处理的输出并且包含从图像提取的信息。 后处理包括根据不同的后处理协议对相应于至少两个阵列的图像的那些部分中的不同的部分处理图像处理的输出，以产生后处理的输出。 该方法包括输出图像处理输出和/或至少一个后处理输出中的至少一个。

    Automated Processing of chemical arrays and systems therefore
    5.
    发明申请
    Automated Processing of chemical arrays and systems therefore 审中-公开
    因此化学阵列和系统的自动化处理

    公开(公告)号：US20060064246A1

    公开(公告)日：2006-03-23

    申请号：US10946142

    申请日：2004-09-20

    申请人： Scott Medberry ,  Xiangyang Zhou ,  Jayati Ghosh

    发明人： Scott Medberry ,  Xiangyang Zhou ,  Jayati Ghosh

    IPC分类号： G06F19/00

    CPC分类号： G16B25/00

    摘要： Methods, systems and computer readable media for automatically generating information from chemical arrays. A plurality of image files representative pf features contained on a plurality of substrates, respectively, may be automatically and sequentially generated. Automatic and sequential feature extraction of the image files may be carried out, wherein automatic feature extracting of a first of the automatically generated image files is begun immediately after completion of the generation of that image file while a next substrate is being processed for automatic generation of a next image file therefrom. Methods, systems and computer readable media are provided for automatically generating information from chemical arrays, to include identifying an entity selected from the group consisting of data structures, directories, subdirectories and drives into which image files created from reading the chemical arrays are to be stored; polling the entity for the presence of a next new image file not identified in a most recent previous polling of the entity; automatically feature extracting the next new image file; outputting results from the step of automatically feature extracting the next new image file; iterating the step of polling the entity until a next new image is identified or until a predetermined time or predetermined number of polls have been reached; and repeating the steps of automatically feature extracting, outputting results and iterating polling when a next new image file is identified prior to passage. of the predetermined time or completion of the predetermined number of polls with an iteration.

    摘要翻译： 用于从化学阵列自动生成信息的方法，系统和计算机可读介质。 分别包含在多个基板上的表示pf特征的多个图像文件可以被自动并顺序地生成。 可以执行图像文件的自动和顺序特征提取，其中自动生成的图像文件中的第一个的自动特征提取在完成该图像文件的生成之后立即开始，而下一个基板正在被处理以自动生成 下一个图像文件。 提供了用于从化学阵列自动生成信息的方法，系统和计算机可读介质，以包括识别从由数据结构，目录，子目录和驱动器组成的组中选择的实体，其中通过读取化学阵列创建的图像文件将被存储在该组中 ; 轮询该实体以存在在该实体的最近一次轮询中未被识别的下一新的图像文件; 自动提取下一张新图像文件; 从自动特征提取下一个新图像文件的步骤输出结果; 迭代轮询实体的步骤，直到识别出下一个新图像，或者直到达到预定时间或预定次数的轮询; 并且在通过之前识别下一个新的图像文件时，重复自动特征提取，输出结果和迭代轮询的步骤。 的预定时间或预定次数的轮询的完成。

    Scanning parameterization for biopolymeric array scanner
    7.
    发明授权
    Scanning parameterization for biopolymeric array scanner 失效
    生物聚合物阵列扫描仪的扫描参数化

    公开(公告)号：US06913200B2

    公开(公告)日：2005-07-05

    申请号：US10301471

    申请日：2002-11-20

    申请人： Debra Ann Sillman ,  Xiangyang Zhou ,  Chetan D Jadhaw ,  Herbert F. Cattell ,  Jayati Ghosh

    发明人： Debra Ann Sillman ,  Xiangyang Zhou ,  Chetan D Jadhaw ,  Herbert F. Cattell ,  Jayati Ghosh

    IPC分类号： G01N21/64 ,  G01N33/52 ,  G01N33/58 ,  G01N33/68 ,  G06F17/00 ,  G06F7/10 ,  G06F19/00

    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 parametersAlso 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。还提供根据主题方法编程的扫描仪，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。

    System and methods for automated processing of multiple chemical arrays
    8.
    发明申请
    System and methods for automated processing of multiple chemical arrays 有权
    用于自动处理多个化学阵列的系统和方法

    公开(公告)号：US20070174007A1

    公开(公告)日：2007-07-26

    申请号：US11233560

    申请日：2005-09-22

    申请人： Jayati Ghosh ,  Charles Troup ,  Xiangyang Zhou

    发明人： Jayati Ghosh ,  Charles Troup ,  Xiangyang Zhou

    IPC分类号： G06F19/00

    CPC分类号： G06F19/20

    摘要： Methods, systems and computer readable media for bifurcating automated feature extraction processing of chemical arrays. A plurality of arrays may be image-processed sequentially, and then, outputs resulting from the image processing of at least two of the plurality of the arrays may be post-processed in an automated batch process to obtain processed outputs. In another aspect, a plurality of arrays may be image-processed in an automated batch process, and then outputs resulting from the image processing may be post-processed according to different post-processing protocols with respect to at least two of the plurality of the arrays. In another aspect, an array may be image-processed, and then an output of the image processing may be post-processed in an automated batch process, where at least two different post-processing protocols are assigned to the output of image processing, so that processed outputs are outputted for each of the processing protocols. In still another aspect, methods, systems and computer readable media perform inter-array analysis. A first array is image-processed with a first image processing protocol to obtain a first output, a second array is image-processed with a second image processing protocol to obtain a second output, and the first and second outputs of the image processing of the first and second arrays are post-processed together in an automated batch process to obtain processed outputs. In another aspect, methods, systems and computer readable media are provided for feature extraction processing multiple arrays contained on a single substrate. The multiple arrays are image-processed in an automated batch process, and then outputs of individual arrays, resulting from-image processing of the multiple arrays, are post-processed according to at least one post-processing protocol.

    摘要翻译： 用于分叉化学阵列自动特征提取处理的方法，系统和计算机可读介质。 可以顺次对多个阵列进行图像处理，然后，可以在自动分批处理中对由多个阵列中的至少两个的图像处理产生的输出进行后处理，以获得经处理的输出。 在另一方面，多个阵列可以在自动批处理过程中被图像处理，然后可以根据不同的后处理协议对图像处理产生的输出进行后处理，关于多个 阵列 在另一方面，阵列可以被图像处理，然后图像处理的输出可以在自动批处理过程中进行后处理，其中至少两个不同的后处理协议被分配给图像处理的输出，因此 为每个处理协议输出处理后的输出。 在另一方面，方法，系统和计算机可读介质执行阵列间分析。 利用第一图像处理协议对第一阵列进行图像处理以获得第一输出，利用第二图像处理协议对第二阵列进行图像处理以获得第二输出，并且所述第一和第二输出的图像处理 第一和第二阵列在自动分批过程中一起进行后处理以获得经处理的输出。 在另一方面，提供方法，系统和计算机可读介质用于特征提取处理包含在单个基板上的多个阵列。 多个阵列在自动批处理过程中进行图像处理，然后根据至少一个后处理协议对多个阵列的图像处理产生的各个阵列的输出进行后处理。

    Classification of pixels in a microarray image based on pixel intensities and a preview mode facilitated by pixel-intensity-based pixel classification
    9.
    发明申请
    Classification of pixels in a microarray image based on pixel intensities and a preview mode facilitated by pixel-intensity-based pixel classification 审中-公开
    基于像素强度的微阵列图像中的像素的分类以及基于像素强度的像素分类促进的预览模式

    公开(公告)号：US20060083428A1

    公开(公告)日：2006-04-20

    申请号：US10763645

    申请日：2004-01-22

    申请人： Jayati Ghosh ,  Xiangyang Zhou

    发明人： Jayati Ghosh ,  Xiangyang Zhou

    IPC分类号： G06K9/34 ,  G06K9/00

    CPC分类号： G06K9/38 ,  B60R13/10 ,  G06T7/0012 ,  G06T7/11 ,  G06T7/194 ,  G06T2207/10064 ,  G06T2207/30072 ,  G16B25/00

    摘要： One disclosed embodiment is a method based on an iteratively employed Bayesian-probability-based pixel classification, used to refine an initial feature mask that specifies those pixels in a region of interest, including and surrounding a feature in the scanned image of a microarray, that together compose a pixel-based image of the feature within the region of interest. In a described embodiment, a feature mask is prepared using only the pixel-based intensity data for a region of interest, a putative position and size of the feature within the region of interest, and mathematical models of the probability distribution of background-pixel and feature-pixel signal noise and mathematical models of the probabilities of finding feature pixels and background pixels at various distances from the putative feature position. In a described embodiment, preparation of a feature mask allows a feature-extraction system to display feature sizes and locations to a user prior to undertaking the computationally intensive and time-consuming task of feature-signal extraction from the pixel-based intensity data obtained by scanning a microarray.

    摘要翻译： 一个公开的实施例是基于迭代采用的基于贝叶斯概率的像素分类的方法，用于细化初始特征掩模，该初始特征掩模指定感兴趣区域中的那些像素，包括并围绕微阵列的扫描图像中的特征， 一起组成了该区域内的特征的基于像素的图像。 在所描述的实施例中，仅使用感兴趣区域中的特征区域的推定位置和尺寸的像素强度数据，以及背景像素的概率分布的数学模型和 特征像素信号噪声和从假定特征位置不同距离处寻找特征像素和背景像素的概率的数学模型。 在所描述的实施例中，特征掩模的准备允许特征提取系统在从基于像素的强度数据进行的计算密集和耗时的特征信号提取任务之前向用户显示特征尺寸和位置， 扫描微阵列

    Automated feature extraction processes and systems
    10.
    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。