公开(公告)号：US20050208504A1

公开(公告)日：2005-09-22

申请号：US10803510

申请日：2004-03-17

申请人： Srinka Ghosh ,  Eric Leproust

发明人： Srinka Ghosh ,  Eric Leproust

IPC分类号： C12M1/34 ,  C12Q1/68

CPC分类号： C12Q1/6837 ,  C12Q2545/101 ,  C12Q2565/513

摘要： A method and system for monitoring the feature-extractability of microarrays by integrating control-feature blocks, or reference pattern blocks within a microarrray. The embedded control features comprise an array of pattern blocks, or reference pattern, in which each pattern block is composed of a set of microarray features arranged in a specific pattern of low-intensity and high-intensity features. Positive control features are designed to generate high-intensity signals following exposure of the microarray to a sample solution, and negative control features are designed to generate no signal or a low-intensity signal. The pattern blocks may be visually inspected to determine the feature extractability of a microarray prior to undertaking full, automated feature extraction, or may select a feature-extraction method based on an analysis of the reference pattern.

摘要翻译： 通过集成微阵列内的控制特征块或参考图案块来监测微阵列的特征提取性的方法和系统。 嵌入式控制特征包括一组图案块或参考图案，其中每个图案块由以低强度和高强度特征的特定图案排列的一组微阵列特征组成。 正面控制特征被设计为在将微阵列暴露于样品溶液之后产生高强度信号，而阴性控制特征被设计成不产生信号或低强度信号。 可以目视检查图案块以在进行全自动特征提取之前确定微阵列的特征提取能力，或者可以基于参考图案的分析来选择特征提取方法。

公开(公告)号：US20060036373A1

公开(公告)日：2006-02-16

申请号：US10915849

申请日：2004-08-11

申请人： Srinka Ghosh ,  Peter Webb

发明人： Srinka Ghosh ,  Peter Webb

IPC分类号： G06F19/00 ,  G06K9/00 ,  G01N33/48 ,  G01N33/50

CPC分类号： G06K9/00 ,  G06T7/12 ,  G06T7/70 ,  G06T2207/20056 ,  G06T2207/20068 ,  G06T2207/30072

摘要： A method and system for cropping a digital image of multiple individual microarrays. Various embodiments of the present invention include, a digital image of multiple individual microarrays projected along a first coordinate axis by summing columns of pixel intensity values. A transformation maps the projected pixel intensity values to a transform in a frequency domain. A filter function is constructed from a power spectrum of the transform and multiplied by the transform to obtain a filtered transform. The filtered transform is mapped back to the spatial domain to give the filtered, spatial-domain image. The filtered, spatial-domain image is used to determine the coordinates of boundaries separating the individual microarrays along the first coordinate axis. The multi-pack of microarrays is rotated, and the method may be repeated for a second coordinate axis that is perpendicular to the first coordinate axis. The boundaries are used to identify the boundaries separating individual microarrays.

摘要翻译： 用于裁剪多个单个微阵列的数字图像的方法和系统。 本发明的各种实施例包括通过对像素强度值的列求和来沿着第一坐标轴投影的多个单独的微阵列的数字图像。 A变换将投影像素强度值映射到频域中的变换。 滤波函数由变换的功率谱构成，并与变换相乘以获得滤波变换。 滤波后的变换映射回空间域，以给出过滤的空间域图像。 滤波后的空间域图像用于确定沿着第一坐标轴分开各个微阵列的边界的坐标。 旋转多组微阵列，并且对于垂直于第一坐标轴的第二坐标轴可以重复该方法。 边界用于识别分离各个微阵列的边界。

公开(公告)号：US20050177315A1

公开(公告)日：2005-08-11

申请号：US10773890

申请日：2004-02-06

申请人： Srinka Ghosh

发明人： Srinka Ghosh

IPC分类号： G01N33/48 ,  G01N33/50 ,  G06F19/00

CPC分类号： G16B25/00

摘要： A microarray processing system provides to a user an ability to draw one or more contour lines around portions of the microarray considered by the user to be undamaged, non-defective, and otherwise not compromised and therefore suitable for feature extraction. The microarray processing system then constructs one or more rectangular regions of feature extractability based on the user-indicated subregions of feature extractability, and proceeds to extract data from the one or more rectangular regions of feature extractability.

摘要翻译： 微阵列处理系统向用户提供将用户认为要损坏的，无缺陷的，并且不受损害的微阵列的一部分周围绘制一个或多个轮廓线的能力，因此适合于特征提取。 然后，微阵列处理系统基于特征提取能力的用户指定子区域构建一个或多个特征抽取能力的矩形区域，并进行从特征提取能力的一个或多个矩形区域提取数据。

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。

公开(公告)号：US20060046252A1

公开(公告)日：2006-03-02

申请号：US10929848

申请日：2004-08-30

申请人： Srinka Ghosh ,  Patrick Collins

发明人： Srinka Ghosh ,  Patrick Collins

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6876 ,  C12Q2600/158 ,  C12Q2600/166 ,  G16B25/00

摘要： A method and system for determining a set of dye-normalization microarray probes that consistently hybridize to approximately the same number of target molecules in a wide range of sample solutions. The method of one embodiment of the method of the present invention generates a set of candidate probe molecules. The set of candidate probe molecules are arrayed on one or more replicate microarrays. Sample solutions are made from one or more tissues of one or more species. Microarray-base hybridization assays are conducted by using the replicate microarrays and different sample solutions. A subset of the candidate probe molecules that are functional for the microarray-base hybridization assays are determined.

摘要翻译： 用于确定在宽范围的样品溶液中与大致相同数量的靶分子一致杂交的染料标准化微阵列探针的集合的方法和系统。 本发明方法的一个实施方案的方法产生一组候选探针分子。 候选探针分子的集合被排列在一个或多个重复的微阵列上。 样品溶液由一种或多种物质的一种或多种组织制成。 通过使用重复的微阵列和不同的样品溶液进行微阵列基杂交测定。 测定用于微阵列杂交测定功能的候选探针分子的子集。

公开(公告)号：US10229244B2

公开(公告)日：2019-03-12

申请号：US12143754

申请日：2008-06-20

申请人： Srinka Ghosh

发明人： Srinka Ghosh

IPC分类号： G06F19/18 ,  G06F19/20 ,  G06F19/24 ,  C12Q1/6827

摘要： Methods for estimating genomic copy number and loss of heterozygosity using Hidden Markov Model based estimation are disclosed.

公开(公告)号：US07221785B2

公开(公告)日：2007-05-22

申请号：US10153394

申请日：2002-05-21

申请人： Bo U. Curry ,  Herbert F. Cattell ,  Srinka Ghosh

发明人： Bo U. Curry ,  Herbert F. Cattell ,  Srinka Ghosh

IPC分类号： G06K9/00 ,  G06K9/40 ,  G01N33/48

CPC分类号： G06K9/00 ,  G06T7/11 ,  G06T7/194 ,  G06T2207/10056 ,  G06T2207/10064 ,  G06T2207/30072

摘要： A method and system for estimating the background signal over an arbitrarily-sized region of a scanned image of a molecular array, including a background region surrounding the ROI corresponding to the feature. A bit mask is generated, based on a molecular-array, feature-based data set that includes pixel-based intensities and a list of features, including feature coordinates and feature ROI radii, to indicate those pixels in the scanned image of the molecular array corresponding to background, and those pixels in the scanned image of the molecular array corresponding to features and ROIs. An integrated intensity for a background region of arbitrary size and shape can be efficiently determined by selecting pixels within the background region that are indicated to be background pixels in the bit mask. By selecting background anuli of sufficient size to overlap with the background anuli of neighboring features, a relatively continuous function of background-signal-verusus-position can be obtained across the surface of a molecular array in order to examine non-local, background-signal-related phenomena.

摘要翻译： 一种用于在分子阵列的扫描图像的任意大小的区域上估计背景信号的方法和系统，包括与特征对应的ROI的背景区域。 基于分子阵列生成位掩模，基于特征的数据集，其包括基于像素的强度和包括特征坐标和特征ROI半径的特征列表，以指示分子阵列的扫描图像中的那些像素 对应于背景，并且分子阵列的扫描图像中的像素对应于特征和ROI。 可以通过选择背景区域中被指示为位掩码中的背景像素的像素来有效地确定用于任意尺寸和形状的背景区域的积分强度。 通过选择具有足够大小的背景与相邻特征的背景重叠的背景，可以跨分子阵列的表面获得背景信号 - 维基位置的相对连续的函数，以便检查非局部背景信号 相关现象。

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.

公开(公告)号：US20050226535A1

公开(公告)日：2005-10-13

申请号：US10823055

申请日：2004-04-13

申请人： Srinka Ghosh

发明人： Srinka Ghosh

IPC分类号： G06F19/00 ,  G06K9/00 ,  G06K9/32 ,  G06K9/36 ,  G06T7/00

CPC分类号： G06K9/3275 ,  G06K2209/07 ,  G06T3/00 ,  G06T7/73 ,  G06T2207/30072 ,  G16B25/00

摘要： A method and system for rectilinearizing an image of a double-density, microarray having a non-rectilinear, outermost feature-position arrangement. In a disclosed embodiment, an image of a microarray having a non-rectilinear, outermost, feature-position arrangement is obtained from the signal intensity data of a microarray of features. A coordinate scheme of horizontal and vertical grid lines is superimposed on the image in order to assign a coordinate location to each feature of the microarray. Three corner features of the microarray are selected and used to determine one or more feature positions to add to the non-rectilinear, outermost, feature-position arrangement to form a rectilinear, outermost, feature-position arrangement of the microarray features.

摘要翻译： 用于使具有非直线，最外面的特征位置布置的双重密度微阵列的图像直线化的方法和系统。 在所公开的实施例中，从特征的微阵列的信号强度数据获得具有非直线，最外面的特征位置布置的微阵列的图像。 水平和垂直网格线的坐标方案叠加在图像上，以便为微阵列的每个特征分配坐标位置。 选择微阵列的三个角特征并用于确定一个或多个特征位置以添加到非直线的，最外面的特征位置布置以形成微阵列特征的直线，最外面的特征位置布置。

公开(公告)号：US20050038839A1

公开(公告)日：2005-02-17

申请号：US10639184

申请日：2003-08-11

申请人： Srinka Ghosh ,  Mark Hartnett

发明人： Srinka Ghosh ,  Mark Hartnett

IPC分类号： G06F7/00

CPC分类号： G16B25/00 ,  B01J2219/00693 ,  B01J2219/00722

摘要： A method and system for evaluating the quality of normalizing feature sets used in normalizing two or more data sets obtained from microarrays, and for iteratively normalizing two or more data sets. In a described implementation, a rank-consistency threshold employed in selection and/or refinement of invariant features from the one or more data sets varied, as needed, during each iteration of an iterative normalization method, so that the iterative normalization converges on a set of invariant features for which a metric Φ falls below a threshold value. The metric Φ may be calculated as the percentage of selected invariant features, or normalizing features, that are differentially expressed in one or more data sets, to a specified level of significance. For a perfect set of invariant, or normalizing, features, the metric Φ has the value of 0. Φ-metric values of increasing magnitude correspond to normalizing feature sets of decreasing utility for normalization.

摘要翻译： 一种用于评估用于归一化从微阵列获得的两个或多个数据集的归一化特征集的质量的方法和系统，以及用于迭代地归一化两个或更多个数据集。 在所描述的实现中，用于在来自一个或多个数据集的不变特征的选择和/或细化中使用的秩一致性阈值根据需要在迭代归一化方法的每次迭代期间变化，使得迭代归一化收敛于集合 不变特征，其度量Phi低于阈值。 度量Phi可以被计算为在一个或多个数据集中差分表示的所选不变特征或标准化特征的百分比达到指定的重要程度。 对于一组不变量或归一化特征，度量Phi的值为0. Phi度量值的增加幅度对应于归一化特征集降低效用的正常化。