Biological microarray line scanning method and system

• US 7,791,013 B2
• Filed: 11/21/2006
• Issued: 09/07/2010
• Est. Priority Date: 11/21/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Wang, Mark, Feng, Wenyi, Kain, Robert
• Primary Examiner(s): Sohn; Seung C
• Application Number:
  US11/602,887
• Publication Number:
  US 20080117518A1
• Time in Patent Office: 1,386 Days
• Field of Search: 250/222.1, 250/227.11
• US Class Current: 250/222.1
• CPC Class Codes: G01N 2021/6484 Optical fibres
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G02B 21/0032 Optical details of illumination, e.g. light-sources, pinholes, beam splitters, slits, fibers G02B21/0036 - G02B21/008; means for illumination of specimens in general G02B21/06
• CPC Class Codes: G02B 21/0036 Scanning details, e.g. scanning stages

Abstract

A line scanning arrangement for imaging microarrays includes a line illuminator that converts output from one or more lasers to a radiation line. The laser output passes through a single mode fiber and a module that converts the laser light to the radiation line. The line is confocally directed to sites on the microarray, and retrobeams returned from the sites are collected on an imaging detector. The microarray is moved in the imaging apparatus so as to progressively illuminate an array or matrix of sites for imaging.

Claims

1. A system for imaging a microarray comprising:

a laser light source;

a single mode fiber optic cable coupled to the laser light source for transmitting laser light in single mode transmission;

a line illuminator for converting laser light from the source to a line of radiation, the line illuminator including a collimator arranged to receive the laser light from the source and an aspherical lens for converting collimated light from the collimator to the line of radiation; and

a focusing device for simultaneously directing the line of radiation onto sites of a microarray in one dimension of a two-dimensional plane at the surface of the microarray.

2. The system of claim 1, wherein the line illuminator is configured to convert laser light from the source to a line of radiation of substantially uniform intensity over a desired line length.

3. The system of claim 1, wherein the collimator and aspherical lens are prealigned within a module to permit installation of the module in the system without further alignment within the module during installation.

4. The system of claim 1, wherein the focusing device is configured to create a uniform line of radiation that is diffraction limited in the narrow dimension of the line.

5. The system of claim 3, further comprising a laser line filter disposed in the module intermediate the collimator and the aspherical lens.

6. The system of claim 1, wherein the aspherical lens is a Powell lens.

7. The system of claim 1, wherein the aspherical lens is a cylindrical lens.

8. The system of claim 1, wherein individual sites on the microarray are separated by a distance in the range of about 0.1 to 50 micrometers.

9. The system of claim 8, wherein the system is configured to distinguish the individual sites.

10. The system of claim 1, wherein the system is configured to obtain an image of the microarray at a Rayleigh resolution between about 0.2 and 10 micrometers.

11. The system of claim 1, wherein the line illuminator includes an integral connector, and the single mode fiber optic cable is terminated with a mating connector for coupling to the line illuminator.

12. The system of claim 1, wherein one end of the single mode fiber optic cable is integrally coupled to the line illuminator.

13. The system of claim 1, wherein one end of the single mode fiber optic cable is removably coupled to the line illuminator.

14. The system of claim 1, comprising a second fiber optic cable coupled to the laser light source at one end thereof and coupled to the single mode fiber optic cable at an opposite end thereof.

15. The system of claim 14, wherein the second fiber optic cable is a single mode fiber optic cable.

16. The system of claim 15, wherein the fiber optic cables are coupled to one another via an optical connector.

17. The system of claim 15, wherein the fiber optic cables are spliced to one another.

18. The system of claim 1, wherein the single mode fiber optic cable is configured for single mode transmission of laser light with a wavelength of approximately 405 nm, 488 nm, 532 nm or 633 nm.

19. A system for imaging a microarray comprising:

a laser light source;

a fiber optic cable coupled to the laser light source;

a line illuminator for converting laser light from the source to a line of radiation, the line illuminator including a collimator arranged to receive the laser light from the source and an aspherical lens for converting collimated light from the collimator to the line of radiation;

a second fiber optic cable coupled to the first single mode fiber optic cable at one end thereof and to the line illuminator at another end thereof, at least one of the fiber optic cables being a single mode fiber optic cable; and

a focusing device for simultaneously directing the line of radiation onto sites of a microarray in one dimension of a two-dimensional plane at the surface of the microarray.

25. The system of claim 19, wherein the line illuminator is configured to convert laser light from the source to a line of radiation of substantially uniform intensity over a desired line length.

26. The system of claim 19, wherein the collimator and aspherical lens are prealigned within a module to permit installation of the module in the system without further alignment within the module during installation.

27. The system of claim 19, wherein the focusing device is configured to create a uniform line of radiation that is diffraction limited in the narrow dimension of the line.

28. The system of claim 26, further comprising a laser line filter disposed in the module intermediate the collimator and the aspherical lens.

29. The system of claim 19, wherein individual sites on the microarray are separated by a distance in the range of about 0.1 to 50 micrometers, and wherein the system is configured to distinguish the individual sites.

30. The system of claim 19, wherein the system is configured to obtain an image of the microarray at a Rayleigh resolution between about 0.2 and 10 micrometers.

20. A system for imaging a microarray comprising:

first and second laser light sources, each source configured to output laser light in a different predetermined frequency band;

first and second single mode fiber optic cables coupled to the first and second laser light sources, respectively, for transmitting laser light in single mode transmission; and

first and second line illuminators coupled to the first and second single mode fiber optic cables, respectively, for converting laser light from the respective source to a line of radiation, the line illuminators each including a collimator arranged to receive the laser light from the source and an aspherical lens for converting collimated light from the collimator to the line of radiation; and

a focusing device for simultaneously directing the line of radiation onto sites of a microarray in one dimension of a two-dimensional plane at the surface of the microarray.

21. The system of claim 20, further comprising:

a combiner for combining the lines of radiation from the first and second illuminators;

means for confocally irradiating the microarray with the combined lines of radiation and for returning radiation from the microarray; and

a detector for receiving the returned radiation and for generating signals for use in analysis of the microarray.

31. The system of claim 20, wherein the line illuminators are configured to convert laser light from the source to lines of radiation of substantially uniform intensity over a desired line length.

32. The system of claim 20, wherein the collimator and aspherical lens are prealigned within a module to permit installation of the module in the system without further alignment within the module during installation.

33. The system of claim 20, wherein the focusing device is configured to create uniform lines of radiation that are diffraction limited in the narrow dimension of the line.

34. The system of claim 32, further comprising a laser line filter disposed in the module intermediate the collimator and the aspherical lens.

35. The system of claim 20, wherein individual sites on the microarray are separated by a distance in the range of about 0.1 to 50 micrometers, and wherein the system is configured to distinguish the individual sites.

36. The system of claim 20, wherein the system is configured to obtain an image of the microarray at a Rayleigh resolution between about 0.2 and 10 micrometers.

22. A method for making a system for imaging a microarray comprising:

placing a laser light source, a line illuminator, a focusing device and a stage in a configuration wherein;

the laser light source is coupled to the line illuminator via a single mode fiber optic cable, the fiber optic cable configured for transmitting laser light from the source in single mode transmission, and the line illuminator configured for converting laser light from the source to a line of radiation,

the line illuminator includes a collimator arranged to receive the laser light from the source and an aspherical lens for converting collimated light from the collimator to the line of radiation;

the focusing device simultaneously directs the line of radiation onto sites of a microarray in one dimension of a two-dimensional plane; and

the stage is configured to place the microarray surface at the plane.

23. A method for imaging a microarray comprising:

generating laser light;

transmitting the laser light to a line illuminator via a single mode fiber optic cable, the fiber optic cable configured for transmitting laser light from the source in single mode transmission, and the line illuminator configured for converting laser light from the source to a line of radiation, the line illuminator including a collimator arranged to receive the laser light from the source and an aspherical lens for converting collimated light from the collimator to the line of radiation; and

directing the line of radiation with a focusing device, wherein the line of radiation is simultaneously directed onto sites of a microarray in one dimension of a two-dimensional plane at the surface of the microarray.

37. The method of claim 23, wherein the line illuminator converts laser light from the source to a line of radiation of substantially uniform intensity over a desired line length.

38. The method of claim 23, wherein the focusing device creates a uniform line of radiation that is diffraction limited in the narrow dimension of the line.

39. The method of claim 23, wherein individual sites on the microarray are separated by a distance in the range of about 0.1 to 50 micrometers, and wherein the individual sites are distinguished by the method.

40. The method of claim 23, wherein an image of the microarray is obtained at a Rayleigh resolution between about 0.2 and 10 micrometers.

24. A method for imaging a microarray comprising:

generating laser light at first and second wavelengths;

transmitting the first and second wavelength laser light to respective line illuminators via respective first and second single mode fiber optic cables, each fiber optic cable configured for transmitting laser light from the respective source in single mode transmission, and each line illuminator configured for converting laser light from the respective source to a line of radiation, each line illuminator including a collimator arranged to receive the laser light from the source and an aspherical lens for converting collimated light from the collimator to the line of radiation;

combining the lines of radiation from the line illuminators;

directing the combined lines of radiation with a focusing device, wherein the line of radiation is simultaneously directed onto sites of a microarray in one dimension of a two-dimensional plane at the surface of the microarray, thereby confocally irradiating the microarray with the combined lines of radiation; and

directing radiation returned from the microarray to a detector configured to generate signals for analysis of the microarray.

41. The method of claim 24, wherein the line illuminators convert laser light from the source to lines of radiation of substantially uniform intensity over a desired line length.

42. The method of claim 24, wherein the focusing device creates uniform lines of radiation that is diffraction limited in the narrow dimension of the line.

43. The method of claim 24, wherein individual sites on the microarray are separated by a distance in the range of about 0.1 to 50 micrometers, and wherein the individual sites are distinguished by the method.

44. The method of claim 24, wherein an image of the microarray is obtained at a Rayleigh resolution between about 0.2 and 10 micrometers.