Methods and devices for reading microarrays

• US 9,767,342 B2
• Filed: 05/14/2010
• Issued: 09/19/2017
• 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 SINGH
• Application Number:
  US12/780,825
• Publication Number:
  US 20100296727A1
• Time in Patent Office: 2,685 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 a plurality of fiducials at a plurality of z positions and determining a best z position measurement for each of the plurality of fiducials at which the imaging is sharpest;

generating a surface fit profile based on the best z position measurement for each of the plurality of fiducials; 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 surface fit profile is constructed using a surface-fitting algorithm.

3. The method of claim 2, wherein the surface-fitting algorithm comprises a least square algorithm.

4. The method of claim 2, wherein the surface-fitting algorithm comprises a sub-plane surface fit.

5. The method of claim 2, wherein the surface-fitting algorithm comprises a B spline surface fit.

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

8. The method of claim 1, wherein the one or more surface non-flatness parameters comprise positioning of a stage on which the probe array is mounted.

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

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

11. The method of claim 1, wherein the plurality of fiducials comprises 4 fiducials.

12. The method of claim 11, wherein the plurality of fiducials comprises 5 fiducials.

13. The method of claim 12, wherein the plurality of fiducials comprises 9 fiducials.

14. The method of claim 13, wherein the plurality of fiducials comprises 12 fiducials.

15. The method of claim 14, wherein the plurality of fiducials comprises 15 fiducials.

6. The method of 1, wherein the determining step comprises using quadratic interpolation.