Feature intensity reconstruction of biological probe array

• US 9,147,103 B2
• Filed: 11/21/2014
• Issued: 09/29/2015
• Est. Priority Date: 06/27/2006
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Hubbell, Earl A.
• Primary Examiner(s): Park, Chan
• Assistant Examiner(s): Thomas, Mia M
• Application Number:
  US14/549,694
• Publication Number:
  US 20150098637A1
• Time in Patent Office: 312 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: G06F 18/00 Pattern recognition
• CPC Class Codes: G06V 20/695 Preprocessing, e.g. image segmentation
• CPC Class Codes: G06V 2201/04 Recognition of patterns in DNA microarrays
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.

Claims

1. A computer-implemented method of modifying image data comprising:

accessing image data of a feature of a biological probe array hybridized with nucleic acids, wherein said image data of the feature comprises a set of observed pixel values;

determining a theoretical pixel intensity with a transfer function representing the proportion of the intensity in a set of pixels due to a feature, a feature intensity of said feature, and a background value of said feature;

determining an optimized multiplicative error function using a multiplicative error function and a standard deviation function, wherein said multiplicative error function comprises said theoretical pixel intensity and said set of observed pixel values; and

determining said feature intensity with an update rule for said feature intensity using a weight function representing the weight of said pixel and the optimized multiplicative error function where said update rule for said feature intensity iteratively generates a unique value to which said feature intensity converges

obtaining an observed pixel intensity chart comprised of cells including a plurality a pixels for each cell wherein each pixel has an observed pixel intensity and wherein each cell has a center pixel,

producing a feature intensity chart by averaging the pixel intensities of the plurality of pixels within each cell,

producing a transfer function intensity chart having pixel intensities calculated using a transfer function that relates the distance of each pixel from the center pixel with an intensity value that is proportional to the observed feature intensity,

multiplying the transfer function intensity chart by the feature intensity chart to form product image files, and

summing the product image files together to produce a summed image file.

2. The computer-implemented method of claim 1, further comprising adding background intensity to the summed image file to produce a theoretical pixel intensity chart.

3. The computer-implemented method of claim 1, further comprising adding background intensity to the summed image file to produce a theoretical pixel intensity chart and dividing the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value.

4. The computer-implemented method of claim 1, further comprising adding background intensity to the summed image file to produce a theoretical pixel intensity chart;

dividing the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value;

comparing the error value to a selected value; and

removing pixels having error values greater than the selected value.

5. The computer-implemented method of claim 1, further comprising adding background intensity to the summed image file to produce a theoretical pixel intensity chart, wherein the background intensity is initialized as the lowest observed value greater than zero for observed pixel intensity values within a cell.

6. An apparatus for modifying image data comprising;

a processor;

and a non-transitory medium storing computer-readable instructions that, when executed by the processor, cause the apparatus to;

access image data of a feature of a biological probe array hybridized with nucleic acids, wherein said image data of the feature comprises a set of observed pixel values;

based on the one or more sample image data, obtain an observed pixel intensity chart comprised of cells including a plurality of pixels for each cell wherein each pixel has an observed pixel intensity and wherein each cell has a center pixel,

produce a feature intensity chart by averaging the pixel intensities of the pixels within each cell,

produce a transfer function intensity chart having pixel intensities calculated using a transfer function that relates the distance of each pixel from the center pixel with an intensity value that is proportional to the observed feature intensity,

multiply the transfer function intensity chart by the feature intensity chart to form product image files, and

sum the product image files together to produce a summed image file.

7. The apparatus of claim 6, wherein the instructions, when executed by the processor, further cause the apparatus to:

add background intensity to the summed image file to produce a theoretical pixel intensity chart.

8. The apparatus of claim 6, wherein the instructions, when executed by the processor, further cause the apparatus to:

add background intensity to the summed image file to produce a theoretical pixel intensity chart; and

divide the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value.

9. The apparatus of claim 6, wherein the instructions, when executed by the processor, further cause the apparatus to:

add background intensity to the summed image file to produce a theoretical pixel intensity chart;

divide the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value;

compare the error value to a selected value; and

remove pixels having error values greater than the selected value.

10. The apparatus of claim 6, wherein the instructions, when executed by the processor, further cause the apparatus to:

add background intensity to the summed image file to produce a theoretical pixel intensity chart, wherein the background intensity is initialized as the lowest observed value greater than zero for observed pixel intensity values within a cell.

11. A system for modifying image data comprising;

a processor;

and a non-transitory computer readable medium coupled to the processor, with the non-transitory computer readable medium storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps comprise;

accessing image data of a feature of a biological probe array hybridized with nucleic acids, wherein said image data of the feature comprises a set of observed pixel values;

based on the one or more sample image data, obtaining an observed pixel intensity chart comprised of cells including a plurality of pixels for each cell wherein each pixel has an observed pixel intensity and wherein each cell has a center pixel,

producing a feature intensity chart by averaging the pixel intensities of the pixels within each cell,

producing a transfer function intensity chart having pixel intensities calculated using a transfer function that relates the distance of each pixel from the center pixel with an intensity value that is proportional to the observed feature intensity,

multiplying the transfer function intensity chart by the feature intensity chart to form product image files, and

summing the product image files together to produce a summed image file.

12. The system of claim 11, wherein the processor performs the logical step of adding background intensity to the summed image file to produce a theoretical pixel intensity chart.

13. The system of claim 11, wherein the processor performs the logical steps of adding background intensity to the summed image file to produce a theoretical pixel intensity chart and dividing the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value.

14. The system of claim 11, wherein the processor performs the logical steps of adding background intensity to the summed image file to produce a theoretical pixel intensity chart, dividing the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value, comparing the error value to a selected value, and removing pixels having error values greater than the selected value.

15. The system of claim 11, wherein the processor performs the logical step of adding background intensity to the summed image file to produce a theoretical pixel intensity chart, wherein the background intensity is initialized as the lowest observed value greater than zero for observed pixel intensity values within a cell.

16. A computer readable medium comprising computer-executable instructions for performing a method of modifying image data comprising:

accessing image data of a feature of a biological probe array hybridized with nucleic acids, wherein said image data of the feature comprises a set of observed pixel values;

based on the one or more sample image data, obtaining an observed pixel intensity chart comprised of cells including a plurality a pixels for each cell wherein each pixel has an observed pixel intensity and wherein each cell has a center pixel,

producing a feature intensity chart by averaging the pixel intensities of the pixels within each cell,

producing a transfer function intensity chart having pixel intensities calculated using a transfer function that relates the distance of each pixel from the center pixel with an intensity value that is proportional to the observed feature intensity,

multiplying the transfer function intensity chart by the feature intensity chart to form product image files, and

summing the product image files together to produce a summed image file,

wherein the medium is selected from the group consisting of CD-ROM, floppy disk, tape, flash memory, system memory and hard drive.

17. The computer readable medium of claim 16, wherein the method further includes adding background intensity to the summed image file to produce a theoretical pixel intensity chart.

18. The computer readable medium of claim 16, wherein the method further includes adding background intensity to the summed image file to produce a theoretical pixel intensity chart and dividing the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value.

19. The computer readable medium of claim 16, wherein the method further includes adding background intensity to the summed image file to produce a theoretical pixel intensity chart, dividing the observed pixel intensity chart by the theoretical pixel intensity chart to determine an error value, comparing the error value to a selected value, and removing pixels having error values greater than the selected value.

20. The computer readable medium of claim 16, wherein the method further includes adding background intensity to the summed image file to produce a theoretical pixel intensity chart, wherein the background intensity is initialized as the lowest observed value greater than zero for observed pixel intensity values within a cell.