METHODS AND DEVICES FOR READING MICROARRAYS

• US 20100296727A1
• Filed: 05/14/2010
• Published: 11/25/2010
• 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, Nguyen, Devin, Gao, Chuan, Yamamoto, Melvin
• Granted Patent: US 9,767,342 B2
• Time in Patent Office: Days
• US Class Current: 382/154
• 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 imaging a probe array, the method comprising:

(a) providing a surface on the probe array, wherein the probe array surface comprises a plurality of fiducials;

(b) a camera, wherein the camera can be moved in the z direction;

(c) an x and y stage, wherein the stage can be moved in the x and y directions;

(d) measuring an x, y, and z positions of the plurality of fiducials that are on the surface of the array, wherein the measuring step comprises;

providing an x-y and z home positions, wherein the x-y home position is a home stage position of an x, y stage and the z home position is a home camera position of the camera;

focusing on a fiducial on the surface of the probe array, wherein the focusing step comprises moving the camera and stage to the fiducial being measured;

determining the x and y distances traveled from the x-y home position to the x and y position of the fiducial to obtain a measured x-y data;

determining the z distance moved from the z home position to the z position of the fiducial to obtain a measured z data;

repeating the above providing, focusing and determining steps until each fiducial is measured;

(e) transmitting the measured x-y, and z measurement data to a computer, wherein the computer comprises a surface fitting algorithm;

(f) calculating a surface profile, wherein the calculating step is performed on the computer employing the surface fitting algorithm and the transmitted measurement data;

(g) adjusting one or more surface non-flatness parameters, wherein the surface non-flatness parameters are parameters that can be changed to improve the image flatness of the surface; and

repeating steps (d) to (g) until the relative distance of each fiducial on the probe array are positionally optimized for setting up the probe array to be imaged.

2. The method according to claim 1, wherein the method further comprises a tilt stage.

3. The method according to claim 2, wherein the focusing step further comprises tilting the tilt stage so that the array surface is made parallel to a focal plane of a microscope objective.

4. The method according to claim 1, wherein the surface non-flatness parameters comprise of an array tilt angle, stage movement effect and optical parameters.

5. The method according to claim 1, wherein the surface non-flatness parameters comprise of adjusting a focal plane, by moving a lens.

6. The method according to claim 1, wherein the plurality of fiducials is 4 fiducials.

7. The method according to claim 1, wherein the plurality of fiducials is 5 fiducials.

8. The method according to claim 1, wherein the plurality of fiducials is 9 fiducials.

9. The method according to claim 1, wherein the surface fitting algorithm comprises a least square, sub-plane surface fit, and B spline surface fit.

10. A method of manufacturing a filter slider for reading a biological array, the method comprising:

(a) providing a linear slide;

(b) providing a plurality of filter sets, wherein the filter sets are mounted in a filter block that is mounted on the linear slide;

(c) providing a linear actuator, wherein the linear actuator comprises a motor; and

(d) coupling the linear actuator to the linear slide such that the filer slider functions properly even if the linear actuator is misaligned relative to the linear slide.

11. The method according to claim 10, wherein the method further comprises a blade slider to couple the linear actuator with the filter slider.

12. The method according to claim 10, wherein the motor is a stepping motor.

13. A method for imaging a probe array, the method comprising:

a) providing a surface on the probe array, wherein the probe array surface comprises a plurality of fiducials;

b) a camera, wherein the camera can be moved in the z direction;

c) determining a best z position of at least one fiducial on the surface of the array;

d) taking a plurality of images at a plurality of z positions of the fiducial, wherein the z positions are different, wherein an image with the best z position and a plurality of images without the best z position are obtained;

e) determining how sharp the plurality of images are at each z position by using an image software package;

f) choosing the image with the best z position, wherein the best z position provides an image that is sharper compared to the plurality of images without the best z positions;

g) repeating steps (a) to (f) until the best z position of each fiducial on the probe array is determined;

h) transmitting the best z position data of the plurality of fiducials to a computer, wherein the computer comprises a surface fitting algorithm;

i) calculating a surface fit profile, wherein the calculating step is performed on the computer employing the surface fitting algorithm and the best z position data;

j) adjusting one or more surface non-flatness parameters based on the calculations of the surface fit profile, wherein the surface non-flatness parameters are parameters that can be changed to improve the image flatness of the surface image; and

k) repeating steps (g) to (j) to obtain an image of the probe array.

14. The method according to claim 13, wherein the method further comprises a tilt stage.

15. The method according to claim 14 wherein the method further comprises tilting the tilt stage so that the array surface is made parallel to a focal plane of a microscope objective.

16. The method according to claim 13, wherein the surface non-flatness parameters comprise of an array tilt angle, stage movement effect and optical parameters.

17. The method according to claim 13, wherein the surface non-flatness parameters comprise of adjusting a focal plane, by moving a lens.

18. The method according to claim 13, wherein the plurality of fiducials is 4 fiducials.

19. The method according to claim 13, wherein the plurality of fiducials is 5 fiducials.

20. The method according to claim 13, wherein the plurality of fiducials is 9 fiducials.

21. The method according to claim 13, wherein the surface fitting algorithm comprises a least square, sub-plane surface fit, and B spline surface fit.