Herbert F Cattell

US Patent:

6879915, Apr 12, 2005

Filed:

Jan 31, 2001

Appl. No.:

09/775387

Inventors:

Herbert F. Cattell - Mountain View CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

G06F019/00
G01N033/48
G01N033/50
C12Q001/68

US Classification:

702 20, 435 6, 422 681, 702 19

Abstract:

A method of using an addressable array of biopolymers on a substrate includes receiving the addressable array and an associated machine readable identifier carried on an array substrate or array housing. The array is exposed to a sample and read, and the identifier machine read as an identifier signal. Biological function data for one or more of the biopolymers is retrieved from a memory based on the identifier signal. Other methods in which first and updated sets of feature characteristic data may readily be provided to array users, and methods of generating arrays are also provided, as are apparatus and computer program products which can execute a method for generating or using arrays.

US Patent:

6913200, Jul 5, 2005

Filed:

Nov 20, 2002

Appl. No.:

10/301471

Inventors:

Debra Ann Sillman - Santa Clara CA, US
Xiangyang Zhou - Mountain View CA, US
Chetan D Jadhaw - Sunnyvale CA, US
Herbert F. Cattell - Mountain View CA, US
Jayati Ghosh - San Jose CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

G06F017/00
G06F019/00
G06F007/10

US Classification:

23546215, 235454, 23546201, 2504612, 435 6

Abstract:

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.

US Patent:

6993172, Jan 31, 2006

Filed:

Jun 29, 2001

Appl. No.:

09/895756

Inventors:

Scott D. Connell - Saratoga CA, US
Herbert F. Cattell - Mountain View CA, US
Glenda C. Delenstarr - Belmont CA, US
Nicholas M Sampas - San Jose CA, US
Andreas N. Dorsel - Menlo Park CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

G06K 9/00

US Classification:

382129

Abstract:

A method and system for employing pixel-based, signal-intensity data contained within areas of a scanned image of a molecular array corresponding to features and feature backgrounds in order to determine whether or not the features or feature backgrounds have non-uniform signal intensities and are thus outlier features and outlier feature backgrounds. A calculated, estimated variance for the signal intensities within a feature or feature background is compared to a maximum allowable variance calculated for the feature or feature background based on a signal intensity variance model. When the experimental variance is less than or equal to the maximum allowable variance, the feature or feature background is considered to have acceptable signal-intensity uniformity. Otherwise, the feature or feature background is flagged as an outlier feature or outlier feature background.

US Patent:

7006927, Feb 28, 2006

Filed:

Feb 28, 2002

Appl. No.:

10/086839

Inventors:

Zohar Yakhini - Zikhron Ya'acov, IL
Cynthia Y. Enderwick - San Jose CA, US
Glenda C. Delenstarr - Belmont CA, US
Paul K. Wolber - Los Altos CA, US
Nicholas M. Sampas - San Jose CA, US
Herbert F. Cattell - Mountain View CA, US
Scott D. Connell - Saratoga CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

G06F 11/32

US Classification:

702 28, 435 4, 356317

Abstract:

A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

US Patent:

7027629, Apr 11, 2006

Filed:

Sep 9, 2002

Appl. No.:

10/238922

Inventors:

Herbert F. Cattell - Mountain View CA, US
Andreas N. Dorsel - Menlo Park CA, US
John W. Sadler - Belmont CA, US
Nicholas M. Sampas - San Jose CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

G06K 9/00

US Classification:

382128, 382129, 382141

Abstract:

Methods for correcting systematic errors in the measured position of deposited features of a nucleic acid array on a substrate. Systematic errors are modeled by an algorithmic model based on measuring the positions (and possibly other properties) of a subset of the features, and a model is constructed for predicting deviations in feature position from an ideal grid. Deviations arising in the deposition process, the scanning process, or both may be corrected.

US Patent:

7027930, Apr 11, 2006

Filed:

Jan 31, 2001

Appl. No.:

09/775163

Inventors:

Herbert F. Cattell - Mountain View CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

G06T 7/60
G06K 9/34
G06K 9/20

US Classification:

702 19, 702 22, 382282, 382286, 382305

Abstract:

Methods of using an addressable array of biopolymers which has been exposed to a sample, and apparatus and computer program products for use of the arrays. In one embodiment the method includes detecting signals from the exposed array to obtain a signal image of the array. The array signal image is saved in a memory. Based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image is established. A definition of the shapes of the established regions of each set is saved in a memory. Each region of each set is processed according to a corresponding routine for that set.

US Patent:

7221785, May 22, 2007

Filed:

May 21, 2002

Appl. No.:

10/153394

Inventors:

Bo U. Curry - Redwood City CA, US
Herbert F. Cattell - Mountain View CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

G06K 9/00
G06K 9/40
G01N 33/48

US Classification:

382129, 382274, 702 19

Abstract:

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.

US Patent:

7412085, Aug 12, 2008

Filed:

Mar 13, 2006

Appl. No.:

11/375658

Inventors:

Herbert F. Cattell - Mountain View CA, US
Andreas N. Dorsel - Menlo Park CA, US
John W. Sadler - Belmont CA, US
Nicholas M. Sampas - San Jose CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

G06K 9/00

US Classification:

382128

Abstract:

Methods for correcting systematic errors in the measured position of deposited features of a nucleic acid array on a substrate. Systematic errors are modeled by an algorithmic model based on measuring the positions (and possibly other properties) of a subset of the features, and a model is constructed for predicting deviations in feature position from an ideal grid. Deviations arising in the deposition process, the scanning process, or both may be corrected.