公开(公告)号：US06835938B2

公开(公告)日：2004-12-28

申请号：US10210855

申请日：2002-07-31

申请人： Jayati Ghosh ,  John F. Corson ,  Debra A. Sillman

发明人： Jayati Ghosh ,  John F. Corson ,  Debra A. Sillman

IPC分类号： G01N2164

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 disclosed. Also disclosed 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： 公开了一种用于通过分子阵列扫描器确定用于扫描分子阵列的生物聚合物阵列基底厚度相关最佳聚焦距离的方法和系统。 还公开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。

公开(公告)号：US07361906B2

公开(公告)日：2008-04-22

申请号：US11022302

申请日：2004-12-23

申请人： Jayati Ghosh ,  John F. Corson ,  Debra A. Sillman

发明人： Jayati Ghosh ,  John F. Corson ,  Debra A. Sillman

IPC分类号： G01N21/64

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。

公开(公告)号：US06914229B2

公开(公告)日：2005-07-05

申请号：US10086658

申请日：2002-02-28

申请人： John F. Corson ,  Debra A. Sillman ,  Jayati Ghosh ,  Kenneth L. Staton

发明人： John F. Corson ,  Debra A. Sillman ,  Jayati Ghosh ,  Kenneth L. Staton

IPC分类号： G01N21/27 ,  G01N21/64 ,  H01J40/14

CPC分类号： G01N21/6452 ,  G01N21/6428 ,  G01N2021/6421

摘要： A method and system for preventing signal clipping in a molecular array scanner by adding an offset signal to the signal generated by the photodetectors and initial stages of signal processing within a molecular array scanner in order to promote the signal above the level where signal information is lost during analog-to-digital signal conversion and/or digital signal integration. A portion of the offset is then subtracted from the digital signal or integrated digital signals, leaving a smaller, constant offset that is reported to the user, stored in a data file, or otherwise made available for further correction during later molecular array data processing.

摘要翻译： 一种用于在分子阵列扫描器中防止信号限幅的方法和系统，该方法和系统通过将偏移信号加到由光电检测器产生的信号和分子阵列扫描器内的信号处理的初始阶段，以便将信号提升到信号信息丢失的水平之上 在模数转换和/或数字信号集成期间。 然后从数字信号或集成的数字信号中减去偏移的一部分，留下一个较小的恒定偏移，报告给用户，存储在数据文件中，或者在以后的分子阵列数据处理中可用于进一步校正。

公开(公告)号：US07302348B2

公开(公告)日：2007-11-27

申请号：US10859868

申请日：2004-06-02

申请人： Jayati Ghosh ,  Bill J. Peck ,  Eric M. Leproust ,  Charles David Troup ,  Glenda Choate Delenstarr ,  Patrick J. Collins ,  John F. Corson ,  Paul K. Wolber ,  Xiangyang Zhou

发明人： Jayati Ghosh ,  Bill J. Peck ,  Eric M. Leproust ,  Charles David Troup ,  Glenda Choate Delenstarr ,  Patrick J. Collins ,  John F. Corson ,  Paul K. Wolber ,  Xiangyang Zhou

IPC分类号： G06F19/00 ,  G06F15/00 ,  G11C17/00

CPC分类号： G06F19/24 ,  G06F19/20

摘要： A method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the selected set of features, a surface is used to determine the intensities for all features in each channel of the microarray data set. Spatial-intensity trends within the microarray data set are quantified, based on the surface to the intensities for each channel of the microarray data set. After the surface has been determined, the spatial-intensity trend can be removed from the microarray data set.

摘要翻译： 一种用于量化和校正具有一个或多个通道的微阵列数据集的每个通道的空间强度趋势的方法和系统。 本发明的一个实施例的方法和系统从微阵列数据集的每个通道中选择一组特征。 基于所选择的特征集合，使用表面来确定微阵列数据集的每个通道中的所有特征的强度。 基于微阵列数据集的每个通道的表面到强度，量化微阵列数据集内的空间强度趋势。 在确定表面后，可以从微阵列数据集中去除空间强度趋势。

公开(公告)号：US07333907B2

公开(公告)日：2008-02-19

申请号：US11192680

申请日：2005-07-29

申请人： Glenda C. Delenstarr ,  Jayati Ghosh ,  John F. Corson

发明人： Glenda C. Delenstarr ,  Jayati Ghosh ,  John F. Corson

IPC分类号： 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。

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。

公开(公告)号：US07437249B2

公开(公告)日：2008-10-14

申请号：US11479269

申请日：2006-06-30

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

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

IPC分类号： G06F19/00 ,  G01N33/50

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.

公开(公告)号：US20080120038A1

公开(公告)日：2008-05-22

申请号：US11492472

申请日：2006-07-24

申请人： Jayati Ghosh ,  Amir Ben-dor ,  Anya Tsalenko ,  Bo Curry

发明人： Jayati Ghosh ,  Amir Ben-dor ,  Anya Tsalenko ,  Bo Curry

IPC分类号： G06F19/00

CPC分类号： G06F19/20 ,  G06F19/24 ,  G06F19/26

摘要： Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

摘要翻译： 本发明的实施方案包括用于分析比较基因组杂交（“CGH”）数据的方法和系统，包括从微阵列实验获得的CGH数据。

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。

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。