Methods and devices for reading microarrays

Patent metadata

Field	Value
Publication number	US-10977478-B2
Application number	US-202016748731-A
Country	US
Kind code	B2
Filing date	Jan 21, 2020
Priority date	May 22, 2009
Publication date	Apr 13, 2021
Grant date	Apr 13, 2021

Abstract

In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.

First claim

What is claimed is:

1. A method for improving image flatness of a surface image of a probe array, the method comprising:
providing a probe array comprising a plurality of sub-arrays, wherein at least one corner sub-array of the plurality of sub-arrays comprises one or more fiducials;
imaging, at one or more positions, the one or more fiducials as focus of the at least one corner sub-array is adjusted;
determining a sharpness measurement for each of the images of the one or more fiducials;
generating a surface fit profile based on a plurality of the sharpness measurements; and
imaging the probe array and adjusting one or more surface non-flatness parameters based on the surface fit profile to improve the image flatness of the surface image of the probe array.

2. The method of claim 1 , wherein imaging the one or more fiducials comprises adjusting a position of a stage on which the probe array is mounted.

3. The method of claim 2 , wherein the focus of the at least one corner sub-array is adjusted by adjusting the position of the stage.

4. The method of claim 1 , wherein the focus of the at least one corner sub-array is adjusted in 1-micron to 10-micron steps.

5. The method of claim 1 , wherein imaging the one or more fiducials comprises illuminating the at least one corner sub-array.

6. The method of claim 5 , wherein the at least one corner sub-array is illuminated with 590-nm excitation.

7. The method of claim 1 , wherein at least one of the one or more fiducials is located near a corner of the at least one corner sub-array.

8. The method of claim 1 , wherein at least some of the one or more fiducials are in non-collinear locations that are not corners of the at least one corner sub-array.

9. The method of claim 1 , wherein one of the one or more fiducials is located at a middle or center mark of the at least one corner sub-array.

10. The method of claim 1 , wherein the one or more fiducials comprise at least 4, 5, 9, 12 or 15 fiducials.

11. The method of claim 1 , wherein a sharpness measurement at one or more other positions for the one or more fiducials is determined using quadratic interpolation.

12. The method of claim 1 , further comprising determining optimum focus for at least one other sub-array of the plurality of sub-arrays using interpolation.

13. The method of claim 12 , wherein the at least one other sub-array is a non-corner sub-array.

14. The method of claim 1 , wherein determining the sharpness measurement comprises determining a best focus measurement for each of the fiducials at which the imaging is sharpest.

15. The method of claim 1 , wherein the surface fit profile is generated using one or more of a least-square algorithm, sub-plane surface fit algorithm, and B spline surface fit algorithm.

16. The method of claim 1 , wherein adjusting the one or more surface non-flatness parameters comprises adjusting a position of a stage on which the probe array is mounted.

17. The method of claim 16 , wherein the stage is a two-axis tilt stage.

18. The method of claim 16 , wherein the stage is a three-axis translation stage.

19. The method of claim 1 , wherein the one or more surface non-flatness parameters comprise an array surface roughness parameter.

20. The method of claim 1 , wherein the one or more surface non-flatness parameters comprise an optical parameter.

21. The method of claim 1 , wherein the one or more surface non-flatness parameters comprise a focal plane position.

22. The method of claim 21 , wherein the focal plane position is adjustable by moving a lens.

23. The method of claim 1 , wherein the one or more positions are along an axis of translation.

24. The method of claim 23 , wherein the axis of translation is substantially perpendicular to a plane of the probe array.

25. The method of claim 1 , wherein the probe array is a DNA array.

26. The method of claim 1 , wherein the probe array is a peptide array.

27. The method of claim 1 , wherein the one or more fiducials comprise reflective features.

28. The method of claim 27 , wherein the reflective features comprise chrome square or L-shaped features.

Assignees

• Affymetrix Inc

Inventors

• Stern David
• Gao Chuan
• Yamamoto Melvin
• Nguyen Devin

Classifications

• G06V20/693 Primary

  Acquisition · CPC title

• G01N21/6452 Primary

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

• G02B21/16

  adapted for ultraviolet illumination {; Fluorescence microscopes (G02B21/0076 takes precedence)} · CPC title

• G02B21/361

  Optical details, e.g. image relay to the camera or image sensor (G02B21/364 takes precedence; illumination details G02B21/06 and subgroups) · CPC title

• G02B21/0076

  arrangements using fluorescence or luminescence · CPC title