System, method, and product for imaging probe arrays with small feature sizes

• US 9,445,025 B2
• Filed: 08/23/2013
• Issued: 09/13/2016
• Est. Priority Date: 01/27/2006
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Kaiser, Michael D., Smith, David R.
• Primary Examiner(s): Chu, Randolph I
• Application Number:
  US13/974,959
• Publication Number:
  US 20150057167A1
• Time in Patent Office: 1,117 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G06T 2207/10056 Microscopic image
• CPC Class Codes: G06T 2207/10148 Varying focus
• CPC Class Codes: G06T 2207/30072 Microarray; Biochip, DNA array; Well plate
• CPC Class Codes: G06T 3/4069 by subpixel displacements
• CPC Class Codes: G06T 5/50 using two or more images, e.g. averaging or subtraction
• CPC Class Codes: G06T 5/73 Deblurring; Sharpening
• CPC Class Codes: H04N 25/71 Charge-coupled device [CCD] sensors; Charge-transfer registers specially adapted for CCD sensors

Abstract

An embodiment of a method for resolving features on a probe array is described that, comprises acquiring a plurality of micro-shifted images of a region of a probe array; reconstructing an image of the probe array using the micro-shifted images; and deriving intensity values for one or more probe features disposed on the probe array from the reconstructed image.

Claims

1. A method for resolving features on a probe array, comprising:

acquiring a set of micro-shifted images of a region of a probe array comprising features, wherein the images are acquired using an image acquisition device comprising an objective lens and a sensing element having pixels, and wherein each image in the set is shifted from other images in the set by less than one half a size of a pixel of the sensing element;

reconstructing an image of the probe array using the set of micro-shifted images, wherein reconstructing the image comprises;

creating a single image from the set of micro-shifted images by taking a pixel from a common location within each of the micro-shifted images and tiling the pixels in the single image according to the spatial orientation corresponding to the shift direction and magnitude used during image acquisition, and repeating for each pixel associated with the set of micro-shifted images; and

creating an unboxed image from the single image, wherein the unboxed image is made up of subpixels defined by the shifts used to produce the micro-shifted images, and wherein creating the unboxed image comprises solving a system of linear algebraic equations to determine the value of each subpixel from the values of the pixels in the single image; and

deriving intensity values for one or more probe features on the region of the probe array from a reconstructed image, wherein the reconstructed image is created from at least one of the unboxed image or a deconvolved image.

2. The method according to claim 1, wherein each image in the set of micro-shifted images is shifted in increments of (1/N)*PixelSize, where N is any integer greater than 2.

3. The method according to claim 1, wherein a fixed spatial relationship is maintained between the probe array and the objective lens during image acquisition.

4. The method according to claim 3, wherein acquiring the set of micro-shifted images comprises shifting an element of the objective lens relative to the positions of the objective lens and the sensing element.

5. The method according to claim 3, wherein acquiring the set of micro-shifted images comprises shifting an element of the sensing element.

6. The method according to claim 1, wherein reconstructing the image further comprises creating the deconvolved image by using the single image as the starting image, the unboxed image as the initial guess, and a point spread function of the image acquisition device.

7. The method according to claim 6, wherein the deconvolved image is created using the Richardson-Lucy algorithm.

8. The method according to claim 7, further comprising using the Richardson-Lucy with Total Variation Regularization algorithm which has been modified to use, on a per iteration basis, parameters alpha, which includes over-relaxation or acceleration, and beta, which includes momentum.

9. The method according to claim 1, wherein the probe array comprises molecules labeled with semiconductor nanocrystals.

21. The method according to claim 1, wherein creating the unboxed image further comprises solving the system of linear algebraic equations using least squares or matrix notation.

10. A method for obtaining an image, comprising:

providing a probe array in an image acquisition device comprising an objective lens, a shift element, and a sensing element having pixels;

acquiring an image of the probe array;

moving the shift element such that the image as observed at the sensing element shifts by less than one half the size of a pixel of the sensing element, while maintaining a fixed spatial relationship between the probe array and the objective lens of the image acquisition device;

acquiring a second image of the probe array;

repeating as necessary, in both X and Y dimensions, to produce a set of micro-shifted images;

reconstructing an image of the probe array using the set of micro-shifted images, wherein reconstructing the image comprises;

creating a single image from the set of micro-shifted images by taking a pixel from a common location within each of the micro-shifted images and tiling the pixels in the single image according to the spatial orientation corresponding to the shift direction and magnitude used during image acquisition, and repeating for each pixel associated with the set of micro-shifted images; and

creating an unboxed image from the single image, wherein the unboxed image is made up of subpixels defined by the shifts used to produce the micro-shifted images, and wherein creating the unboxed image comprises solving a system of linear algebraic equations to determine the value of each subpixel from the values of the pixels in the single image; and

deriving intensity values for one or more probe features on the region of the probe array from the reconstructed image, wherein the reconstructed image is created from at least one of the unboxed image or a deconvolved image.

11. The method according to claim 10, wherein each image in the set of micro-shifted images is shifted in increments of (1/N)*PixelSize, where N is any integer greater than 2.

12. The method according to claim 10, wherein reconstructing the image further comprises creating the deconvolved image by using the single image as the starting image, the unboxed image as the initial guess, and a point spread function of the image acquisition device.

13. The method according to claim 12, wherein the deconvolved image is created using the Richardson-Lucy algorithm.

14. The method according to claim 13, further comprising using the Richardson-Lucy with Total Variation Regularization algorithm which has been modified to use, on a per iteration basis, parameters alpha, which includes over-relaxation or acceleration, and beta, which includes momentum.

15. The method according to claim 10, wherein the probe array comprises molecules labeled with semiconductor nanocrystals.

16. A method for obtaining an image, comprising;

acquiring an image of a nucleic acid probe array using an image acquisition device comprising a CCD camera, an objective lens, and a tube lens;

translating the tube lens relative to the CCD camera such that the image of the nucleic acid probe array at the CCD camera is shifted by less than one half a pixel size of the CCD camera;

acquiring a second image of the nucleic acid probe array;

repeating as necessary to produce a set of micro-shifted images;

reconstructing an image of the nucleic acid probe array using the set of micro-shifted images, wherein reconstructing the image comprises;

creating a single image from the set of micro-shifted images by taking a pixel from a common location within each of the micro-shifted images and tiling the pixels in the single image according to the spatial orientation corresponding to the shift direction and magnitude used during image acquisition, and repeating for each pixel associated with the set of micro-shifted images; and

creating an unboxed image from the single image, wherein the unboxed image is made up of subpixels defined by the shifts used to produce the micro-shifted images, and wherein creating the unboxed image comprises solving a system of linear algebraic equations to determine the value of each subpixel from the values of the pixels in the single image; and

deriving intensity values for one or more probe features on the region of the nucleic acid probe array from the reconstructed image, wherein the reconstructed image is created from at least one of the unboxed image or a deconvolved image.

17. The method according to claim 16, wherein each image in the set of micro-shifted images is shifted in increments of (1/N)*PixelSize, where N is any integer greater than 2.

18. The method according to claim 16, wherein reconstructing the image further comprises creating the deconvolved image by using the single image as the starting image, the unboxed image as the initial guess, and a point spread function of the image acquisition device.

19. The method according to claim 18, wherein the deconvolved image is created using the Richardson-Lucy algorithm.

20. The method according to claim 19, further comprising using the Richardson-Lucy with Total Variation Regularization algorithm which has been modified to use, on a per iteration basis, parameters alpha, which includes over-relaxation or acceleration, and beta, which includes momentum.