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    Scanner with array anti-degradation features
    2.
    发明授权
    Scanner with array anti-degradation features 有权
    具有阵列抗降解功能的扫描仪

    公开(公告)号：US07247494B2

    公开(公告)日：2007-07-24

    申请号：US10788547

    申请日：2004-02-27

    申请人： John F. Corson ,  Russell A. Parker

    发明人： John F. Corson ,  Russell A. Parker

    IPC分类号： G01N21/00 ,  G01N27/416 ,  C12Q1/68 ,  B32B5/02 ,  G01N7/00

    CPC分类号： G01N21/15 ,  Y10T436/212

    摘要： A reader is provided that, itself, addresses the issue of damage or degradation to arrays within the reader by virtue of air exposure. In doing so, experimental variability is reduced, and read/scan signal strength degradation is minimized for arrays/slides scanned or otherwise read toward the end of a run. The subject scanners employ a filter that reduces the amount of chemicals in the air inside the device that are harmful to the array, or the dye on the array. The implementation of adding a chemical filter to the reader device may be such that air is either drawn into or, alternatively, pushed through the filter into the same. It is possible that the entirety of the device may be provided with filtered air, or just the region holding slides to be scanned. Array readers so-constructed as well as associated methodology involving filtering incoming air while reading arrays are covered.

    摘要翻译： 提供了一种阅读器，其本身通过空气曝光来解决读取器内的阵列的损坏或劣化的问题。 在这样做时，实验变异性降低，并且读/扫描信号强度退化被最小化以扫描或以其它方式读取到运行结束的阵列/幻灯片。 主题扫描仪采用一种过滤器，可以减少设备内对空气有害的化学物质量，或阵列上的染料。 向读取器装置添加化学过滤器的实现可以是这样的，即空气被吸入或者被抽入过滤器中。 可能的是，整个设备可以设置有过滤的空气，或者只是保持待扫描的幻灯片的区域。 涵盖了如此构造的阵列读取器以及在读取阵列时过滤进入的空气的相关方法。

    Method and system for automated focus-distance determination for molecular array scanners
    4.
    发明授权
    Method and system for automated focus-distance determination for molecular array scanners 失效
    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：US06770892B2

    公开(公告)日：2004-08-03

    申请号：US10086743

    申请日：2002-02-28

    申请人： John F. Corson ,  Stanley P. Woods ,  Russell A. Parker ,  Xiangyang Zhou ,  Bo U. Curry

    发明人： John F. Corson ,  Stanley P. Woods ,  Russell A. Parker ,  Xiangyang Zhou ,  Bo U. Curry

    IPC分类号： G01T2164

    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 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： 一种用于确定用于扫描分子阵列扫描仪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。

    Methods and systems for removing offset bias in chemical array data
    5.
    发明授权
    Methods and systems for removing offset bias in chemical array data 有权
    消除化学阵列数据中偏移偏移的方法和系统

    公开(公告)号：US07881876B2

    公开(公告)日：2011-02-01

    申请号：US11580744

    申请日：2006-10-12

    申请人： Christian A. Le Cocq ,  Glenda C. Delenstarr ,  John F. Corson

    发明人： Christian A. Le Cocq ,  Glenda C. Delenstarr ,  John F. Corson

    IPC分类号： G06F7/00

    CPC分类号： G06F19/24 ,  G06F19/20

    摘要： Methods, systems and computer readable media for quantifying and removing offset bias signals in a chemical array data set having one or more channels. In one embodiment, for each channel of data in the data set, a first set of features is selected from the data set. Surface intensities are calculated for features in the first selected set of features and surface intensifies of features not in the first selected set are calculated from the calculated surface intensities. A second set of features is selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Secondary surface intensifies are calculated for features in the second selected set of features and secondary surface intensities for all other locations on the array that were not locations corresponding to the features having secondary surface intensities calculated therefore, are calculated. Feature intensities of the channel features are then corrected as a function of the secondary surface intensities.

    摘要翻译： 用于在具有一个或多个通道的化学阵列数据集中量化和去除偏移偏移信号的方法，系统和计算机可读介质。 在一个实施例中，对于数据集中的每个数据通道，从数据集中选择第一组特征。 根据计算出的表面强度计算第一选定组特征中的特征的表面强度，而不是在第一选定组中的特征的表面强度。 选择第二组特征，其强度值在由上限和下限阈值强度定义的相应定位的表面强度值的范围内。 计算第二选定组特征中的特征的次表面强度，并且计算阵列上不是因此计算出的具有次表面强度的特征的位置的所有其它位置的次表面强度。 然后将通道特征的特征强度作为次表面强度的函数进行校正。

    Biopolymeric array scanners capable of automatic scale factor selection for a plurality of different dyes, and methods for making and using the same
    7.
    发明申请
    Biopolymeric array scanners capable of automatic scale factor selection for a plurality of different dyes, and methods for making and using the same 审中-公开

    公开(公告)号：US20080161206A1

    公开(公告)日：2008-07-03

    申请号：US12005542

    申请日：2007-12-26

    申请人： John F. Corson ,  Scott D. Connell ,  Srinka Ghosh

    发明人： John F. Corson ,  Scott D. Connell ,  Srinka Ghosh

    IPC分类号： C40B60/10 ,  G01N33/50

    CPC分类号： G01N21/6452 ,  G01N21/6428 ,  G01N2201/1241

    摘要： Biopolymeric array scanners that are capable of automatically selecting a dye specific scale factor to employ for a plurality of different dyes, as wells as methods for making and using the same, are provided. In many embodiments, the actual dye specific scale factor automatically selected by the scanner is one that is equal to a preset “master” scale factor, so that the scanner reads any supported dye using the same constant scale factor. The dye specific scale factor selection is typically made by reference to a collection of nominal scale factors for each member of the plurality of dyes. In using the subject scanners, a user simply inputs the one or more dyes being used in a given array assay, and the scanner automatically reads the array using an automatically chosen dye specific scale factor for the selected dyes. Also provided are methods of obtaining collections of nominal scale factors and computer readable mediums comprising the same. The subject invention finds use in a variety of different applications, including both genomics and proteomics applications.

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

    System and methods for characterization of chemical arrays for quality control
    9.
    发明授权
    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：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。

    Extended dynamic range reading of chemical arrays
    10.
    发明申请
    Extended dynamic range reading of chemical arrays 审中-公开
    扩大化学阵列的动态范围读数

    公开(公告)号：US20070178480A1

    公开(公告)日：2007-08-02

    申请号：US11344773

    申请日：2006-01-31

    申请人： John F. Corson ,  Bo Curry ,  Charles Troup ,  Xiangyang Zhou

    发明人： John F. Corson ,  Bo Curry ,  Charles Troup ,  Xiangyang Zhou

    IPC分类号： C12Q1/68 ,  G06F19/00

    CPC分类号： G16B25/00

    摘要： Methods of reading chemical arrays are provided. Aspects of the methods include reading an array at a first and second detector gain setting to produce linked data sets of an array, where each reading may be made using a different detector gain setting. Aspects of the methods further include extracting features from the linked data sets, where in certain embodiments a merged data set feature extraction protocol is employed. Aspects of the invention further include programming for operating devices, e.g., chemical array readers, as well as readers comprising such programming.

    摘要翻译： 提供读取化学阵列的方法。 方法的方面包括以第一和第二检测器增益设置读取阵列以产生阵列的相关联的数据集，其中可以使用不同的检测器增益设置来进行每次读取。 方法的方面还包括从链接的数据集中提取特征，其中在某些实施例中采用了合并的数据集特征提取协议。 本发明的方面还包括用于操作设备的编程，例如化学阵列读取器，以及包括这种编程的读取器。