System, method, and computer software product for grid alignment of multiple scanned images

• US 6,965,704 B2
• Filed: 07/17/2001
• Issued: 11/15/2005
• Est. Priority Date: 08/22/2000
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Patil, Sangita B., Kaushikkar, Shantanu V.
• Primary Examiner(s): Johns, Andrew W.
• Assistant Examiner(s): EDWARDS, PATRICK L
• Application Number:
  US09/682,076
• Publication Number:
  US 20020025082A1
• Time in Patent Office: 1,582 Days
• Field of Search: 382/129, 382/294
• US Class Current: 382/294
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00533 essentially rectangular
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B82Y 15/00 Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/0494 Detecting or compensating piositioning errors
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 27/44717 : Arrangements for investigating the separated zones, e.g. localising zones
• CPC Class Codes: G01N 27/44721 : by optical means
• CPC Class Codes: G16B 25/00 : ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

Systems, methods, and computer program products are described for aligning multiple images of arrays of biological materials. One method includes aligning a grid with a first image, generating grid alignment data based on the alignment of the grid with the first image, storing the grid alignment data in memory, retrieving the grid alignment data responsive to an indication to align a second image, and analyzing the second image based on the retrieved grid alignment data. In some implementations, the first image and second images are generated by scanning the same array of biological materials. The array may be a spotted array, a synthesized array, or other type of parallel biological assay.

Claims

1. A method comprising the steps of:

(a) receiving one or more user-selected grid aligning parameters, wherein the user-selected grid aligning parameters includes a measure of probe feature size;

(b) aligning a grid with a first image based, at least in part, upon the one or more user-selected grid aligning parameters;

(c) generating grid alignment data based on the alignment of the grid with the first image;

(d) storing the grid alignment data in memory;

(e) retrieving the grid alignment data responsive to an indication to analyze a second image; and

(f) analyzing the second image based on the retrieved grid alignment data.

2. The method of claim 1, wherein:

the first image is generated by scanning a first probe array; and

the second image is generated by scanning the first probe array.

3. The method of claim 2, wherein:

the first image is generated by scanning the first probe array with a first excitation beam; and

the second image is generated by scanning the first probe array with a second excitation beam.

4. The method of claim 3, wherein:

the first excitation beam has a first wavelength; and

the second excitation beam has a second wavelength different from the first wavelength.

5. The method of claim 2, wherein:

the first probe array is a spotted array.

6. The method of claim 2, wherein:

the first probe array is a synthesized array.

7. The method of claim 1, wherein:

the user-selected grid aligning parameters include any one or more of the group consisting of a fixed algorithm shape with easy threshold, a fixed algorithm shape with tight threshold, a variable algorithm shape with easy threshold, a variable algorithm shape with tight threshold.

8. The method of claim 1, wherein:

the measure of probe feature size includes a dimension of a depositing element.

9. The method of claim 1, further comprising the step of:

(f) scanning a first probe array to generate the first and second images prior to performing step (a).

10. The method of claim 9, wherein:

the first and second images are scanned sequentially.

11. The method of claim 9, wherein:

the first and second images are scanned in parallel using two excitation beams.

12. The method of claim 1, further comprising the steps of:

(f) retrieving the grid alignment data responsive to an indication to analyze one or more images in addition to the first and second images; and

(g) analyzing each of the one or more additional images based on the retrieved grid alignment data.

13. The method of claim 12, further comprising the steps of:

(h) receiving a user selection of a number of images to scan; and

(i) scanning the user-selected number of images.

14. The method of claim 13, further comprising the step of:

(j) receiving a user selection of one or more parameters for scanning.

15. The method of claim 14, wherein:

the one or more parameters for scanning include a gain for one or more of the user-selected number of images.

16. The method of claim 14, wherein:

the one or more parameters for scanning include an indicator of an excitation source for one or more of the user-selected number of images.

17. A computer program product, stored on a computer readable medium, comprising:

(a) a GUI manager that receives one or more user-selected grid aligning parameters, wherein the user-selected grid aligning parameters include a measure of probe feature size;

(b) a grid aligner that aligns a grid with a first image based, at least in part, upon the one or more user-selected grid aligning parameters; and

(c) an image analysis manager comprising

(i) an image analyzer that generates grid alignment data based on the alignment of the grid with the first image,

(ii) an image analysis data storer that stores the grid alignment data in memory, and

(iii) a multiple scan alignment controller that retrieves the grid alignment data responsive to an indication to analyze a second image;

wherein the image analyzer analyzes the second image based on the retrieved grid alignment data.

18. The computer program product of claim 17, wherein:

the first image is generated by scanning a first probe array; and

the second image is generated by scanning the first probe array.

19. The computer program product of claim 18, wherein:

the first image is generated by scanning the first probe array with a first excitation beam; and

the second image is generated by scanning the first probe array with a second excitation beam.

20. The computer program product of claim 19, wherein:

the first excitation beam has a first wavelength; and

the second excitation beam has a second wavelength different from the first wavelength.

21. The computer program product of claim 18, wherein:

the first probe array is a spotted array.

22. The computer program product of claim 18, wherein:

the first probe array is a synthesized array.

23. The computer program product of claim 17, wherein:

the user-selected grid aligning parameters include any one or more of the group consisting of a fixed algorithm shape with easy threshold, a fixed algorithm shape with tight threshold, a variable algorithm shape with easy threshold, a variable algorithm shape with tight threshold.

24. The computer program product of claim 17, wherein:

the measure of probe feature size includes a dimension of a depositing element.

25. A scanning system, comprising:

a scanner that scans a first probe array to generate a first image and a second image; and

a computer program product, comprising

(a) a GUI manager that receives one or more user-selected grid aligning parameters, wherein the user-selected grid aligning parameters includes a measure of probe feature size;

(b) a grid aligner that aligns a grid with the first image based, at least in part, upon the one or more user-selected grid aligning parameters; and

(c) an image analysis manager including

(i) an image analyzer chat generates grid alignment data based on the alignment of the grid with the first image,

(ii) an image analysis data storer that stores the grid alignment data in memory, and

(iii) a multiple scan alignment controller that retrieves the grid alignment data responsive to an indication to analyze the second image;

wherein the image analyzer analyzes the second image based on the retrieved grid alignment data.

26. The system of claim 25, wherein:

the first and second images are scanned sequentially.

27. The system of claim 25, wherein:

the first and second images are scanned in parallel using two excitation beams.

28. The system of claim 25, wherein:

the computer program product further includes a GUI manager that receives a user-selected number of images to scan, wherein the number is greater than one; and

the scanner scans the first probe array to generate the user-selected number of images, including the first and second images.

29. The system of claim 28, wherein:

the user-selected number of images to scan is greater than two;

the multiple scan alignment controller retrieves the grid alignment data responsive to an indication to analyze one or more images in addition to the first and second images; and

the image analyzer analyzes at least one of the one or more additional images based on the retrieved grid alignment data.

30. A scanning system, comprising:

a scanner that scans a first probe array to generate a first image and a second image;

a computer; and

a computer program product rhar, when executed on the computer, performs a method comprising the steps of;

(a) a GUI manager that receives one or more user-selected grid aligning parameters, wherein the user-selected grid aligning parameters includes a measure of probe feature size;

(b) aligning a grid with the first image based, at least in part, upon the one or more user-selected grid aligning parameters;

(c) generating grid alignment data based on the alignment of the grid wit the first image,

(d) scoring the grid alignment data in memory;

(e) retrieving the grid alignment darn responsive to an indication to analyze the second image; and

(f) analyzing the second image based on the retrieved gild alignment data.

31. A method comprising the steps of:

(a) receiving one or more user-selected grid aligning parameters, wherein the user-selected grid aligning parameters includes a measure of probe feature size;

(b) aligning a grid with a first image based, at least in part, upon the one or more user-selected grid aligning parameters;

(c) generating grid alignment data based on the alignment of the grid with the first image;

(d) storing the grid alignment data in memory;

(e) retrieving the grid alignment data responsive to an indication to analyze a second image; and

(f) analyzing the second image based on the retrieved grid alignment data;

wherein the first image is generated by scanning a first probe array and the second image is generated by scanning a second probe array different from the first probe array.