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。

公开(公告)号：US06929951B2

公开(公告)日：2005-08-16

申请号：US10086932

申请日：2002-02-28

申请人： John F. Corson ,  Andreas N. Dorsel ,  Russell A. Parker ,  Andre B. Chow

发明人： John F. Corson ,  Andreas N. Dorsel ,  Russell A. Parker ,  Andre B. Chow

IPC分类号： G01N21/27 ,  G01N21/64 ,  G01N31/00 ,  G01N33/53

CPC分类号： G01N21/6452 ,  G01N21/274 ,  G01N21/278 ,  G01N21/6428 ,  G01N21/6456 ,  Y10T436/10

摘要： A method and system for calibrating molecular arrays to a reference molecular array, and for subsequently calibrating the molecular arrays to maintain a constant signal-intensity-to-label-concentration ratio. In the first step of the two-step calibration method, a reference array coated with the fluorophore or chromophore used to label probe molecules is employed, while in the second step of the two-step method, a reference array coated with a stable dye is employed.

摘要翻译： 用于将分子阵列校准为参考分子阵列的方法和系统，并且用于随后校准分子阵列以维持恒定的信号强度与标记 - 浓度比。 在两步校准方法的第一步中，使用涂布有用于标记探针分子的荧光团或发色团的参考阵列，而在两步法的第二步中，涂有稳定染料的参考阵列是 雇用。

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。

公开(公告)号：US20080125979A1

公开(公告)日：2008-05-29

申请号：US11580973

申请日：2006-10-13

申请人： Zohar Yakhini ,  John F. Corson ,  Amir Ben-Dor

发明人： Zohar Yakhini ,  John F. Corson ,  Amir Ben-Dor

IPC分类号： G06F19/00

CPC分类号： G16B25/00 ,  G16B40/00 ,  G16B45/00

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：US07877212B2

公开(公告)日：2011-01-25

申请号：US10912661

申请日：2004-08-04

申请人： Kenneth L. Staton ,  John F. Corson

发明人： Kenneth L. Staton ,  John F. Corson

IPC分类号： G06K9/46 ,  G06K9/60 ,  G06K9/52 ,  G01N33/48

CPC分类号： G06T1/0007 ,  G06F19/20

摘要： Methods for producing data for a partially saturated pixel produced during scanning of a chemical array are provided. In general, an analog signal for a partially saturated pixel is sampled to obtain a set of non-saturated digital signals and a set of saturated digital signals. The saturated digital signals are then processed to produce data for the pixel. Also provided are computer program products comprising programming for performing the subject methods, and a chemical array scanner containing this programming. The invention finds use in a variety of different applications, including both genomics and proteomics applications.

摘要翻译： 提供了在扫描化学阵列期间产生的部分饱和像素的数据生成方法。 通常，对部分饱和像素的模拟信号进行采样，以获得一组非饱和数字信号和一组饱和数字信号。 然后处理饱和数字信号以产生像素的数据。 还提供了包括用于执行主题方法的编程的计算机程序产品和包含该编程的化学阵列扫描器。 本发明可用于各种不同的应用，包括基因组学和蛋白质组学应用。

公开(公告)号：US07206438B2

公开(公告)日：2007-04-17

申请号：US10427652

申请日：2003-04-30

申请人： John F. Corson ,  Glenda C. Delenstarr ,  Nicholas M. Sampas

发明人： John F. Corson ,  Glenda C. Delenstarr ,  Nicholas M. Sampas

IPC分类号： G06K9/00

CPC分类号： G06K9/00 ,  G06K2209/07 ,  G06T7/73 ,  G06T2207/30072

摘要： A method of processing one or more detected signal images each acquired from a field of view of a chemical array reader. A location correction is determined based on different detected signals at different image regions which represent regions in the field of view having the same actual signal. Alternatively or additionally, a location correction is applied to a detected signal at an image region. The location correction reduces detected signal discrepancy between different regions in an acquired image which represent different regions in the field of view having the same actual signal. An array reading system and computer program products are also provided.

摘要翻译： 一种处理一个或多个检测信号图像的方法，每个都从化学阵列读取器的视场中获取。 基于表示具有相同实际信号的视野中的区域的不同图像区域处的不同检测信号来确定位置校正。 或者或另外，位置校正被应用于图像区域处的检测信号。 位置校正减少了在具有相同实际信号的视场中表示不同区域的获取图像中的不同区域之间的检测信号差异。 还提供阵列阅读系统和计算机程序产品。

公开(公告)号：US07205154B2

公开(公告)日：2007-04-17

申请号：US10066157

申请日：2002-01-31

申请人： John F. Corson

发明人： John F. Corson

IPC分类号： G01N30/00

CPC分类号： G01N21/253 ,  G01N21/274 ,  Y10T436/10

摘要： A method of using a chemical array reader, chemical array readers, and computer program products for use with a chemical array reader. The chemical array reader may include a holder to mount an array and hold the array at a reading position. A light system illuminates a mounted array when at a reading position. A detection system having a focal plane, to detect light from different regions across the array emitted in response to the illumination, when at the reading position, and which generates a resulting signal for each of the regions across the array. An autofocus system which detects and reduces offset between the different regions of an array at the reading position and a determined position of the focal plane.

摘要翻译： 一种使用化学阵列读取器，化学阵列读取器和计算机程序产品与化学阵列读取器一起使用的方法。 化学阵列读取器可以包括用于安装阵列并将阵列保持在读取位置的保持器。 当在读取位置时，光系统照亮安装的阵列。 一种具有焦平面的检测系统，用于当在读取位置时检测响应于照明而发射的阵列的不同区域的光，并且对阵列中的每个区域产生结果信号。 自动对焦系统，其检测并减少读取位置处的阵列的不同区域与焦平面的确定位置之间的偏移。

公开(公告)号：US07018842B2

公开(公告)日：2006-03-28

申请号：US10087447

申请日：2002-02-28

申请人： Andreas N. Dorsel ,  John F. Corson

发明人： Andreas N. Dorsel ,  John F. Corson

IPC分类号： G01N21/64

CPC分类号： G01N21/6452 ,  G01N2021/6463 ,  Y10T436/143333

摘要： A method of interrogating an addressable array unit having a transparent substrate with a back surface, and an array with a plurality of different chemical features on a front surface. The method may include illuminating the features while the array is dry, with an interrogating light which is directed through the substrate from the back surface and onto the chemical features on the front surface. The light emitted from respective features in response to the interrogating light may be detected, which detected light has passed from the front surface, through the substrate and out the back surface. In one arrangement the light is emitted from locations of the features which are spaced from the front surface a distance of less than one-eighth of the wavelength of the illuminating light in a gas or a vacuum which is in contact with the dry array. Other methods and a package containing an addressable array are also provided.

公开(公告)号：US07761241B2

公开(公告)日：2010-07-20

申请号：US11503756

申请日：2006-08-14

申请人： John F. Corson

发明人： John F. Corson

IPC分类号： G06F19/00 ,  G06F15/00

CPC分类号： G01N21/6452 ,  G01N21/6428 ,  G01N21/6445 ,  G01N2021/6419 ,  G01N2021/6421

摘要： Disclosed herein is a computer programmed to carry out a method for reducing directional error in scanned intensity values. The method includes scanning some rows of a substrate in a first direction, and some rows of the substrate in a second, different, direction, in order to obtain intensity values exhibited by various regions of the various rows. The intensity values from rows scanned in the first direction are analyzed, and the intensity values from rows scanned in the second direction are analyzed, in order to determine the directional error. The intensity values from rows scanned in the first direction and the intensity values from rows scanned in the second direction are then adjusted to reduce the directional error.

摘要翻译： 本文公开了一种被编程为执行减少扫描强度值中的方向误差的方法的计算机。 该方法包括在第一方向上扫描衬底的一些行，以及在第二，不同的方向上扫描衬底的一些行，以便获得各行的各个区域表现出的强度值。 分析从第一方向扫描的行的强度值，并分析从第二方向扫描的行的强度值，以便确定方向误差。 然后调整来自沿第一方向扫描的行的强度值和在第二方向扫描的行的强度值，以减少方向误差。

公开(公告)号：US07331511B2

公开(公告)日：2008-02-19

申请号：US10328109

申请日：2002-12-23

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： G06F17/00

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.

摘要翻译： 提供了能够自动选择染料比例因子以用于多种不同染料的生物聚合物阵列扫描仪，作为制备和使用它们的方法的孔。 在许多实施例中，由扫描仪自动选择的实际染料特异性比例因子等于预设的“主”比例因子，使得扫描器使用相同的恒定比例因子读取任何支持的染料。 染料比例因子选择通常参考多个染料中每个成员的标称比例因子的集合来进行。 在使用主题扫描仪时，用户只需输入在给定阵列测定中使用的一种或多种染料，并且扫描仪使用所选染料的自动选择的染料比例因子自动读取阵列。 还提供了获得标称比例因子的集合的方法以及包括其的计算机可读介质。 本发明可用于各种不同的应用，包括基因组学和蛋白质组学应用。