Methods and devices for reading microarrays

Patent metadata

Field	Value
Publication number	US-9767342-B2
Application number	US-78082510-A
Country	US
Kind code	B2
Filing date	May 14, 2010
Priority date	May 22, 2009
Publication date	Sep 19, 2017
Grant date	Sep 19, 2017

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 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.

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

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.

Assignees

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

Inventors

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

Classifications

• G02B21/0076

  arrangements using fluorescence or luminescence · CPC title

• G02B21/16

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

• Y10T29/49826

  Assembling or joining · 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

• G02B21/008

  Details of detection or image processing, including general computer control · CPC title