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

Patent metadata

Field	Value
Publication number	US-9445025-B2
Application number	US-201313974959-A
Country	US
Kind code	B2
Filing date	Aug 23, 2013
Priority date	Jan 27, 2006
Publication date	Sep 13, 2016
Grant date	Sep 13, 2016

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.

First claim

What is claimed is:

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.

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 recon

Assignees

• Kaiser Michael D
• Smith David R
• Affymetrix Inc

Inventors

• Kaiser Michael D
• Smith David R

Classifications

• H04N25/71 Primary

  Charge-coupled device [CCD] sensors; Charge-transfer registers specially adapted for CCD sensors · CPC title

• G06T3/4069

  by subpixel displacements · CPC title

• G06T2207/30072

  Microarray; Biochip, DNA array; Well plate · CPC title

• G01N21/6452

  Individual samples arranged in a regular 2D-array, e.g. multiwell plates · CPC title

• G06T5/50

  using two or more images, e.g. averaging or subtraction · CPC title