Method and system for extracting data from surface array deposited features

• US 20020193962A1
• Filed: 02/28/2002
• Published: 12/19/2002
• Est. Priority Date: 06/06/2000
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Connell, Scott D., Delenstarr, Glenda C., Sampas, Nicholas M., Wolber, Paul K., Yakhini, Zohar, Enderwick, Cynthia Y., Cattell, Herbert F.
• Granted Patent: US 7,006,927 B2
• Time in Patent Office: Days
• US Class Current: 702/127
• CPC Class Codes: G06T 2207/30072 Microarray; Biochip, DNA array; Well plate
• CPC Class Codes: G06T 7/73 using feature-based methods

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.

Claims

1. A method for extracting data from a scanned image of an array composed of pixels having one or more associated intensity values, the method comprising:

computing row and column vectors by horizontal and vertical projection of pixel intensity values;

computing corner-feature-image positions from the horizontal and vertical pixel-value projections;

constructing a feature coordinate system using the computed corner-feature-image positions to index feature images in the scanned image of the array; and

using the coordinate system to index and extract data from feature images within the scanned image of the array.

2. A method for extracting data from a scanned image of an array composed of pixels having one or more associated intensity values, the method comprising:

indexing images of features within the scanned image of the array by constructing an initial feature coordinate system;

rotating the feature coordinate system over a range of rotational angles in order to precisely align the feature coordinate system with feature images within the scanned image of the array; and

using the coordinate system to index and extract data from feature images within the scanned image of the array.

3. A method for extracting data from a scanned image of an array composed of pixels having one or more associated intensity values, the method comprising:

indexing images of features within the scanned image of the array by constructing an initial feature coordinate system and rotating the feature coordinate system over a range of rotational angles in order to precisely align the feature coordinate system with feature images within the scanned image of the array;

extracting data from indexed feature images in order to identify strong features with relatively large signal-to-noise ratios;

precisely determining the coordinates of the images of the identified strong features;

using a linear regression technique to refine the feature coordinate system based on the precisely determined coordinates of the images of the identified strong features; and

using the refined feature coordinate system to index and extract data from feature images within the scanned image of the array.

4. A method for extracting data from a scanned image of an array composed of pixels having one or more associated intensity values, the method comprising:

indexing images of features within the scanned image of the array by constructing and refining a feature coordinate system;

for each indexed feature image, selecting a set of pixels within the feature image from which to compute one or more feature intensity signals; and

extracting data from the selected set of pixels for each feature image within the scanned image of the array.

5. A method for extracting data from a scanned image of an array composed of pixels having one or more associated intensity values, the method comprising:

indexing images of features within the scanned image of the array by constructing and refining a feature coordinate system;

for each indexed feature image, selecting a set of pixels within the feature image from which to compute one or more feature intensity signals; and

extracting two or more background-subtracted and normalized feature signal intensities from the selected set of pixels for each feature image within the scanned image of the array.