Methods and devices for reading microarrays

• US 10,303,922 B2
• Filed: 05/30/2018
• Issued: 05/28/2019
• Est. Priority Date: 05/22/2009
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Stern, David, Gao, Chuan, Yamamoto, Melvin, Nguyen, Devin
• Primary Examiner(s): Saini, Amandeep
• Application Number:
  US15/993,512
• Publication Number:
  US 20180341802A1
• Time in Patent Office: 363 Days
• Field of Search: 382100
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G02B 21/0076 arrangements using fluorescence or luminescence
• CPC Class Codes: G02B 21/008 Details of detection or image processing, including general computer control
• CPC Class Codes: G02B 21/16 adapted for ultraviolet illumination ; Fluorescence microscopes G02B21/0076 takes precedence
• CPC Class Codes: G02B 21/361 Optical details, e.g. image relay to the camera or image sensor G02B21/364 takes precedence; illumination details G02B21/06 and subgroups
• CPC Class Codes: G06V 20/693 Acquisition
• CPC Class Codes: Y10T 29/49826 Assembling or joining

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.

Claims

1. A method for improving image flatness of a surface image of a probe array having an array surface roughness, the method comprising:

imaging one or more fiducials of the probe array and determining a position measurement for each of the one or more fiducials based on at least image sharpness;

generating a surface fit profile based on one or more of the position 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 the one or more fiducials are imaged at one or more positions along an axis of translation.

3. The method of claim 1, wherein the surface fit profile is generated using a surface-fitting algorithm.

4. The method of claim 3, wherein the surface-fitting algorithm comprises at least one of a least square algorithm, a sub-plane surface fit algorithm, and a B spline surface fit.

6. The method of claim 1, wherein the one or more surface non-flatness parameters comprises a probe array tilt angle.

7. The method of claim 6, wherein adjusting the one or more surface non-flatness parameters comprises adjusting a position of a stage on which the probe array is mounted.

8. The method of claim 7, wherein the stage comprises a two-axis tilt stage.

9. The method of claim 7, wherein the stage comprises a three-axis translation stage.

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

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

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

13. The method of claim 12, wherein the one or more fiducials comprise at least 5 fiducials.

14. The method of claim 13, wherein the one or more fiducials comprise at least 9 fiducials.

15. The method of claim 14, wherein the one or more fiducials comprise 12 fiducials.

16. The method of claim 15, wherein the one or more fiducials comprise 15 fiducials.

17. The method of claim 1, wherein the axis of translation is substantially perpendicular to a plane of the probe array.

18. 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.

19. The method of claim 1, wherein the probe array comprises a DNA array.

20. The method of claim 1, wherein the probe array comprises a peptide array.

21. The method of claim 1, wherein the probe array comprises a plurality of sub-arrays.

22. The method of claim 21, wherein the one or more fiducials are of a corner sub-array of the probe array.

23. The method of claim 21, wherein the probe array is positioned such that a selected sub-array is centered in a field of view of an image detector device.

24. The method of claim 1, wherein the one or more fiducials comprise a plurality of fiducials located in non-collinear locations on the probe array.

25. The method of claim 1, wherein the one or more fiducials comprise one of an L-shaped or square shaped feature.

26. The method of claim 1, wherein at least one of the one or more fiducials is located near a middle of the probe array.

5. The method of 1, wherein determining the position measurement comprises using quadratic interpolation for at least one of the one or more fiducials.

27. A system for improving image flatness of a surface image of a probe array having an array surface roughness, the system comprising:

an image detector device comprising at least one imaging sensor configured to;

image one or more fiducials of the probe array and determine a position measurement for each of the one or more fiducials based on at least image sharpness; and

at least one server coupled with the image detector device, the at least one server comprising a non-transitory computer readable memory and at least one processor and that is, upon execution of software instructions stored in the non-transitory computer readable memory, configured to;

generate a surface fit profile based on one or more of the position measurements; and

facilitate imaging the probe array by 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.

28. A computer program product embedded in a non-transitory computer readable medium comprising instructions executable by a computer processor for improving image flatness of a surface image of a probe array having an array surface roughness, the instructions being executable by a computer processor to execute processing comprising:

imaging one or more fiducials of the probe array and determining a position measurement for each of the one or more fiducials based on at least image sharpness;

generating a surface fit profile based on one or more of the position 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.