Methods and devices for reading microarrays

• US 10,586,095 B2
• Filed: 04/03/2019
• Issued: 03/10/2020
• 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:
  US16/374,739
• Publication Number:
  US 20190311178A1
• Time in Patent Office: 342 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, the method comprising:

providing a probe array and one or more fiducials, said probe array comprising a plurality of sub-arrays;

imaging the one or more fiducials at one or more of positions;

determining a position measurement for each of the one or more fiducials;

generating a surface fit profile based on a plurality of the position measurements; and

imaging a sub-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 sub-array.

2. The method of claim 1, wherein the position measurement of each fiducial is determined based on image sharpness.

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

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

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

6. The method of claim 5, 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.

7. The method of claim 1, wherein the one or more surface non-flatness parameters comprise a sub-array tilt angle.

8. 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.

9. The method of claim 8, wherein the stage is a two-axis tilt stage.

10. The method of claim 8, wherein the stage is a three-axis translation stage.

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

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

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

14. The method of claim 1, wherein the one or more fiducials are imaged at one or more positions along an axis of translation.

15. The method of claim 14, wherein the axis of translation is substantially perpendicular to a plane of the probe array.

16. 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.

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

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

19. The method of claim 1, wherein the one or more fiducials are on the probe array.

20. The method of claim 1, wherein the one or more fiducials are of a corner sub-array of the probe array.