Agilent Technologies, Inc.

Xiangyang Zhou

Jayati Ghosh

Charles David Troup

John Frederick Corson

Bo U Curry

Paul K Wolber

Eric M Leproust

Glenda Choate Delenstarr

Herbert F Cattell

Stanley P Woods

Debra A Sillman

Bill J Peck

Patrick James Collins

Russell Alan Parker

Chetan D Jadhaw

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.

System and methods for automated processing of multiple chemical arrays

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.

Method and system for quantifying and removing spatial-intensity trends in microarray data

Feature locations are determined in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array. A complete image of the array or a sub-array is presented on a display. Magnified images of corner regions of the displayed complete image are simultaneously presented on the display with the complete image. A user selection of corners for the array or sub-array are received and an array or sub-array actual outline is generated by linearly connecting the user selected corners. The generated actual outline is presented on the magnified image and may also be simultaneously presented on the complete image. Feature locations in the array or sub-array image may be determined based on the actual outline.

Feature locations in array reading

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.

Scanning parameterization for biopolymeric array scanner

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.

Method and system for automated focus-distance determination for molecular array scanners

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Mountain View, CA, United States of America

Xiangyang Zhou