Optical lens system and method for microfluidic devices

• US 8,926,905 B2
• Filed: 07/09/2013
• Issued: 01/06/2015
• Est. Priority Date: 06/07/2004
• Status: Active Grant

• Current Assignee: Standard Biotools Incorporated
• Original Assignee: Fluidigm Corporation
• Inventors: Unger, Marc A., Facer, Geoffrey Richard, Clerkson, Barry, Cesar, Christopher G., Switz, Neil
• Primary Examiner(s): CHOI, WILLIAM C
• Application Number:
  US13/937,340
• Publication Number:
  US 20140011204A1
• Time in Patent Office: 546 Days
• Field of Search: 359/642, 204/602, 204/603, 422/68.1, 250/573
• US Class Current: 422/82.05
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00704 integrated with the reactor apparatus
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 21/64 Fluorescence; Phosphorescence
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6456 Spatial resolved fluorescence measurements; Imaging
• CPC Class Codes: G01N 21/6486 Measuring fluorescence of biological material, e.g. DNA, RNA, cells G01N21/6428 takes precedence
• CPC Class Codes: G01N 21/75 Systems in which material is subjected to a chemical reaction, the progress or the result of the reaction being investigated systems in which material is burnt in a flame or plasma G01N21/72, G01N21/73
• CPC Class Codes: G01N 21/8483 Investigating reagent band test-element handling not specific to a test method G01N33/4875; analytical elements specific to chemical analysis of biological material G01N33/52; autometer with reagent band G01N35/04
• CPC Class Codes: G01N 2201/061 Sources
• CPC Class Codes: G01N 27/44721 by optical means
• CPC Class Codes: G02B 21/16 adapted for ultraviolet illumination ; Fluorescence microscopes G02B21/0076 takes precedence
• CPC Class Codes: G02B 21/36 arranged for photographic purposes or projection purposes G02B21/18 takes precedenceor digital imaging or video purposes including associated control and data processing arrangements image data processing per se G06T

Abstract

An apparatus for imaging one or more selected fluorescence indications from a microfluidic device. The apparatus includes an imaging path coupled to least one chamber in at least one microfluidic device. The imaging path provides for transmission of one or more fluorescent emission signals derived from one or more samples in the at least one chamber of the at least one microfluidic device. The chamber has a chamber size, the chamber size being characterized by an actual spatial dimension normal to the imaging path. The apparatus also includes an optical lens system coupled to the imaging path. The optical lens system is adapted to transmit the one or more fluorescent signals associated with the chamber.

Claims

1. A method of imaging electromagnetic radiation emitted from a device having a plurality of reaction sites, the method comprising:

thermally cycling the plurality of reaction sites of the device with a thermal controller;

illuminating the device with electromagnetic radiation with an illumination system;

transmitting the electromagnetic radiation along an optical path and through an optical filter device and a multi-element optical system coupled to the optical path, wherein the multi-element optical system comprises at least five optical elements;

reducing chromatic aberration of light along the optical path;

capturing an image of a determined number of reaction sites simultaneously while maintaining a temperature of the determined number of reaction sites at a desired temperature; and

collecting multiple images of the device, wherein collecting multiple images comprises;

collecting at least a first image at a first wavelength; and

collecting at least a second image at a second wavelength different than the first wavelength.

2. The method of claim 1, wherein thermally cycling comprises maintaining the plurality of reaction sites at a first temperature for a first time period and at a second temperature for a second time period.

3. The method of claim 1, wherein thermally cycling comprises raising a temperature of the plurality of reaction sites for a first heating cycle and then lowering the temperature of the plurality of reaction sites for a second cooling cycle.

4. The method of claim 3, further comprising repeating the heating and cooling cycle for a number of cycles.

5. The method of claim 1, further comprising quantifying contents of the plurality of reaction sites of the device using the multiple images.

6. The method of claim 1, wherein the first image and the second image are sequential images.

7. The method of claim 1, further comprising calculating a fluorescence measurement of contents of the plurality of reaction sites using the first image and the second image.

8. The method of claim 1, further comprising detecting the electromagnetic radiation emitted by the plurality of reaction sites at a set of wavelengths substantially different from a wavelength of the electromagnetic radiation provided by the illumination system.

9. The method of claim 1, further comprising:

performing nucleic acid amplification in the plurality of reactions sites; and

regulating the nucleic acid amplification with the thermal controller.

10. The method of claim 1, further comprising performing genotyping or gene expression analysis.

11. The method of claim 1, further comprising:

providing a component associated with an enzymatic reaction; and

regulating the enzymatic reaction in the device with the thermal controller.

12. The method of claim 1, further comprising measuring a temperature associated with the device.

13. The method of claim 1, wherein the optical filter device comprises a wheel or filter holder, wherein the filter wheel or holder is positionable to at least two operating positions.

14. The method of claim 1, wherein limiting chromatic aberration is carried out by at least one zero-power doublet or corrective optical element disposed along the optical path.

15. The method of claim 1, wherein multi-element optical system comprises one or more lenses and one or more apertures.

16. The method of claim 1, wherein the multi-element optical system comprises a first multi-element optical train coupled to a first portion of the optical path and a second multi-element optical train coupled to a second portion of the optical path.

17. The method of claim 1, wherein the plurality of reaction sites of the device comprise greater than 383 reaction sites.

18. The method of claim 1, wherein the plurality of reaction sites is characterized by a density of about 100 reaction sites per cm² or greater.

19. The method of claim 1, wherein each of the reaction sites is sealed closed.

20. The method of claim 1, wherein each of the reaction sites is in fluidic isolation from any of the other reactions sites.

21. The method of claim 1, wherein the device comprises a microfluidic device.

22. The method of claim 1, wherein the plurality of reaction sites each contain reaction volumes less than or equal to about 100 nanoliters.

23. The method of claim 1, wherein the capturing is carried out in a time frame of less than one second.

24. The method of claim 1, wherein capturing is carried out by a multi-pixel detector comprising at least 262,144 pixels.

25. The method of claim 1, wherein capturing is carried out by a multi-pixel detector comprising at least 1,048,576 pixels.

26. A method of imaging electromagnetic radiation emitted from a device having a plurality of reaction sites, the method comprising:

thermally cycling greater than 383 reaction sites of the device with a thermal controller;

illuminating the greater than 383 reaction sites of the device with electromagnetic radiation with an illumination system;

transmitting the electromagnetic radiation along an optical path and through an optical filter device and a multi-element optical system coupled to the optical path;

reducing chromatic aberration of light along the optical path;

capturing a first fluorescence image of the greater than 383 reaction sites of the device while maintaining a temperature of the greater than 383 reaction sites at a desired temperature, wherein the first image is at a first wavelength;

repeating the thermally cycling of the greater than 383 reaction sites; and

capturing a second fluorescence image of the greater than 383 reaction sites of the device while maintaining the desired temperature, wherein the second image is at a second wavelength different than the first wavelength.

27. The method of claim 26, wherein the optical filter device comprises a wheel or filter holder, wherein the filter wheel or holder is positionable to at least two operating positions.

28. The method of claim 26, wherein limiting chromatic aberration is carried out by at least one zero-power doublet or corrective optical element disposed along the optical path.

29. The method of claim 26, wherein multi-element optical system comprises one or more lenses and one or more apertures.

30. The method of claim 26, wherein the multi-element optical system comprises a first multi-element optical train coupled to a first portion of the optical path and a second multi-element optical train coupled to a second portion of the optical path.

31. The method of claim 26, wherein the plurality of reaction sites is characterized by a density of about 100 reaction sites per cm² or greater.

32. The method of claim 26, wherein the plurality of reaction sites comprise closed reaction chambers.

33. The method of claim 26, wherein the device comprises a microfluidic device.

34. The method of claim 26, wherein each of the reaction sites contain reaction volumes less than or equal to about 100 nanoliters.

35. The method of claim 26, wherein the capturing is carried out in a time frame of less than one second.

36. The method of claim 26, wherein capturing is carried out by a multi-pixel detector comprising at least 262,144 pixels.

37. The method of claim 26, wherein capturing is carried out by a multi-pixel detector comprising at least 1,048,576 pixels.

38. An optical system for imaging a plurality of indications from a plurality of reaction sites of a device, the system comprising:

a thermal cycler thermally coupled to the plurality of reactions sites of the device, the thermal cycler configured to provide temperature control to the plurality of reaction sites;

an illumination system coupled to the device and configured to illuminate the device with electromagnetic radiation;

an optical lens system coupled to an optical path, the optical lens system being configured to transmit the electromagnetic radiation along the optical path, wherein the optical lens system comprises a first multi-element optical train coupled to a first portion of the optical path and a second multi-element optical train coupled to a second portion of the optical path, and wherein the optical lens system is configured to reduce chromatic aberration of light along the optical path; and

an optical detection system device having a detector for capturing at least first and second images of a determined number of reaction sites simultaneously while the thermal cycler maintains the determined number of reaction sites at a constant temperature, wherein the first image is at a first wavelength and the second image is at a second wavelength different than the first wavelength.

39. The system of claim 38, further comprising a temperature detecting sensor coupled to thermal cycler.

40. The system of claim 38, wherein the thermal cycler comprises a thermal platen or an integrated heat spreader.

41. The system of claim 38, further comprising an excitation filter disposed along the optical path between the illumination system and the device and an emission filter disposed along the optical path between the device and the optical detection system.

42. The system of claim 38, wherein the device has a dimension of about 30.7 mm by 30.7 mm or greater, the device dimension including greater than 383 reaction sites.

43. The system of claim 38, further comprising an optical filter device disposed along the optical path between the device and the optical detection system, wherein the optical filter comprises at least two operating positions.

44. The system of claim 38, further comprising means for imaging the device in multiple spectral bands.

45. The system of claim 38, wherein the optical lens system further comprises at least one zero-power doublet or corrective optical element disposed along the optical path.

46. The system of claim 38, wherein the detector comprises a multi-pixel detector comprising at least 262,144 pixels.

47. The system of claim 46, wherein the device has an area including greater than 383 reaction sites, wherein the multi-pixel detector is characterized by a detection area less than the device area.

48. The system of claim 38, wherein the detector comprises a multi-pixel detector comprising at least 1,048,576 pixels.

49. The system of claim 38, wherein the plurality of reaction sites each contain reaction volumes less than or equal to about 100 nanoliters.

50. The system of claim 38, wherein the plurality of reaction sites is characterized by a density of about 100 reaction sites per cm² or greater.

51. The system of claim 38, wherein each of the reaction sites is in fluidic isolation from any of the other reactions sites.

52. The system of claim 38, wherein the plurality of reaction sites comprise closed reaction chambers.

53. The system of claim 38, wherein the device comprises a microfluidic device.