Optical lens system and method for microfluidic devices

• US 20060006067A1
• Filed: 06/07/2005
• Published: 01/12/2006
• Est. Priority Date: 06/07/2004
• Status: Active Grant

• Current Assignee: Standard Biotools Incorporated
• Original Assignee: Fluidigm Corporation
• Inventors: Unger, Marc A.
• Granted Patent: US 7,307,802 B2
• Time in Patent Office: Days
• US Class Current: 204/452
• 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. An apparatus for imaging one or more selected fluorescence indications from a microfluidic device, the apparatus comprising:

an imaging path coupled to least one chamber in at least one microfluidic device, the imaging path providing 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 having a chamber size, the chamber size being characterized by an actual spatial dimension normal to the imaging path; and

an optical lens system coupled to the imaging path, the optical lens system being adapted to transmit the one or more fluorescent signals associated with the chamber.

2. The apparatus of claim 1 wherein the optical lens system is adapted to reduce a size of the actual spatial dimension to a determined level and being adapted to transmit the one or more fluorescent emission signals associated with the chamber at the reduced size at the determined level.

3. The apparatus of claim 1 wherein the at least one microfluidic device is characterized by a microfluidic dimension and the optical lens system is adapted to provide an image of the at least one microfluidic device that is about a similar size as the microfluidic dimension and adapted to transmit the one or more fluorescent emission signals associated with the chamber at the about the similar size.

4. The apparatus of claim 2 wherein the reduced size of the actual spatial dimension and the actual spatial dimension are characterized by a ratio of less than one.

5. The apparatus of claim 4 wherein the ratio is less than 0.9.

6. The apparatus of claim 5 wherein the ratio is less than 0.5.

7. The apparatus of claim 1 wherein the microfluidic device is an elastomeric microfluidic device and wherein the at least one chamber is a closed reaction chamber.

8. A method of imaging one or more selected fluorescence indications from at least one chamber of a microfluidic device, the method comprising:

transmitting one or more fluorescent emission signals derived from one or more samples in the at least one chamber of at least one microfluidic device along an imaging path coupled to the at least one chamber, wherein the at least one chamber has a chamber size, the chamber size being characterized by an actual spatial dimension normal to the imaging path; and

transmitting the one or more fluorescent emission signals associated with the chamber through an optical lens system coupled to the imaging path, wherein the optical lens system is adapted to reduce a size of the actual spatial dimension to a determined level.

9. The method of claim 8 wherein the reduced size of the actual spatial dimension and the actual spatial dimension are characterized by a ratio of less than one.

10. The method of claim 9 wherein the ratio is less than 0.9.

11. The method of claim 10 wherein the ratio is less than 0.5.

12. The method of claim 8 wherein the microfluidic device is an elastomeric microfluidic device and wherein the at least one chamber is a closed reaction chamber.

13. A system for imaging one or more indications from one or more chambers of a microfluidic device, the system comprising:

an optical path, the optical path being capable of transmitting one or more images of a portion of a spatial region of a microfluidic device from the portion of the spatial region of the microfluidic device, the portion of the spatial region of the microfluidic device being characterized by a first dimension;

a first lens system coupled to a first portion of the optical path, the first lens system being characterized by a first optical characteristic;

a second lens system coupled to a second portion of the optical path, the second lens system being characterized by a second optical characteristic; and

a detector device coupled to a third portion of the optical path, the detector device capturing the one or more images of the portion of the spatial region, the detector being adapted to capture the one or more images, the one or more images having a determined size at the detector device of about the first dimension or less.

14. The system of claim 13 wherein the determined size is about 0.99 of the first dimension and less.

15. The system of claim 13 wherein the first lens system and the second lens system are characterized as a tandem lens system.

16. The system of claim 13 wherein the microfluidic device is characterized by a microfluidic dimension and the detector device is characterized by a spatial dimension for an active region.

17. The system of claim 16 wherein the microfluidic dimension is about a similar size as the spatial dimension.

18. The system of claim 16 wherein the microfluidic dimension is less than the spatial dimension.

19. The system of claim 13 wherein the microfluidic device is an elastomeric microfluidic device comprising at least 48 closed reaction chambers.

20. The system of claim 19 wherein the at least 48 closed reaction chambers are in fluidic isolation from any of the other reaction chambers.

21. A method for imaging one or more indications from one or more chambers of a microfluidic device, the method comprising:

transmitting one or more images of a portion of a spatial region of a microfluidic device from the portion of the spatial region of the microfluidic device along an optical path, the portion of the spatial region of the microfluidic device being characterized by a first dimension;

coupling a first lens system to a first portion of the optical path, the first lens system being characterized by a first optical characteristic;

coupling a second lens system to a second portion of the optical path, the second lens system being characterized by a second optical characteristic; and

capturing the one or more images of the portion of the spatial region using a detector device, the detector device being coupled to a third portion of the optical path, the one or more images having a determined size at the detector device of about the first dimension or less.

22. The method of claim 21 wherein the determined size is about 0.99 of the first dimension and less.

23. The method of claim 21 wherein the first lens system and the second lens system are characterized as a tandem lens system.

24. The method of claim 21 wherein the microfluidic device is characterized by a microfluidic dimension and the detector device is characterized by a spatial dimension for an active region, the microfluidic dimension being about a similar size as the spatial dimension.

25. A method of imaging microfluidic devices, the method comprising:

transmitting an image of a spatial region of a microfluidic device, the spatial region being associated with more than 96 chambers; and

capturing the image of the spatial region using an image detection spatial region associated with an image detecting device, the image detection spatial region being of about an equal size of the spatial region of the microfluidic device.

26. The method of claim 25 wherein the spatial region divided by the image detection spatial region is about one (1).

27. The method of claim 25 wherein the spatial region divided by the image detection spatial region is about 0.99 or less.

28. The method of claim 27 wherein the spatial region divided by the image detection spatial region is about 0.88 or less.

29. The method of claim 25 wherein the image detection spatial region is about 30.7 mm by about 30.7 mm and greater.

30. The method of claim 25 wherein the image detection spatial region is about 27.6 mm by about 27.6 mm and greater.

31. The method of claim 25 wherein the image detection spatial region comprises about 2048 by 2048 pixel regions.

32. The method of claim 25 wherein the image detection spatial region comprises about 2048 by 2048 pixel regions, each of the pixel regions having a spatial dimension of about 15 μ

m by about 15 μ

m and greater.

33. The method of claim 32 at least two pixel regions are associated with at least one of the chambers.

34. The method of claim 33 wherein at least nine pixel regions are associated with at least one of the chambers.

35. The method of claim 34 wherein more than 20 pixel regions are associated with at least one of the chambers.

36. A method of imaging microfluidic devices, the method comprising:

capturing an image of a spatial region associated with at least a determined number of chambers of a microfluidic device using an image detection spatial region during a time frame of less than one minute, whereupon the capturing of the image of the spatial region is substantially free from a stitching and/or scanning process.

37. The method of claim 36 further comprising capturing the image of the spatial region associated with at least the determined number of chambers of the microfluidic device using the image detection spatial region during a time frame of greater than 10 milliseconds.

38. The method of claim 36 wherein capturing the image of the spatial region occurs is a time frame of less than 30 seconds.

39. The method of claim 36 wherein capturing the image of the spatial region occurs is a time frame of less than 15 seconds.

40. The method of claim 36 wherein the capturing occurs synchronously for the time frame of less than one minute for the determined number of chambers.

41. The method of claim 36 wherein the capturing occurs while the determined number of chambers are maintained in a determined temperature range.

42. The method of claim 41 wherein the determined temperature range is ±

2°

C.

43. The method of claim 41 wherein the determined temperature is a portion of a cyclical temperature environment associated with a PCR process.

44. The method of claim 36 wherein the determined number of chambers is at least 96 and greater.

45. The method of claim 36 further comprising capturing at least a second image of the spatial region associated with at least the determined number of chambers of the microfluidic device using the image detection spatial region during the time frame of less than one minute, whereupon the capturing of the second image of the spatial region represents a fluorescent emission.

46. An apparatus for imaging one or more selected fluorescence indications from a microfluidic device, the apparatus comprising:

an imaging path coupled to least one chamber in at least one microfluidic device, the imaging path providing 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; and

an optical filter device coupled to a first spatial portion of the imaging path provided for transmission of the one or more emission signals, the optical filter device being adapted to transmit a selected spectral bandwidth from the one or more fluorescent emission signals and being adapted to process one or more chromatic aberrations associated with the one or more fluorescent emission signals to a determined level.

47. The apparatus of claim 46 further comprising:

a detector coupled to a second spatial portion of the imaging path to read a portion of the one or more fluorescent emission signals;

a first lens system coupled to a third spatial portion of the imaging path, the first lens system being adapted to capture one or more fluorescent emission signals derived from the at least one chamber in the at least one microfluidic device;

an optical source providing electromagnetic radiation characterized by one or more spectral bandwidths; and

an optical element coupled to the optical source, the optical element being adapted to irradiate at least 96 chambers in the at least one microfluidic device, wherein a group of more than 48 chambers is in fluidic isolation from any of the other chambers in the group of more than 48 chambers.

48. The apparatus of claim 47 further comprising:

a second lens system coupled to a fourth spatial portion of the imaging path; and

a thermal control module adapted to provide thermal control for the at least one microfluidic device, wherein the optical filter device comprises a plurality of spectral filters and a plurality of zero-power doublets.

49. The apparatus of claim 46 wherein the plurality of zero-power doublets comprises a first zero-power doublet adapted to reduce chromatic aberrations at a first predetermined wavelength and a second zero-power doublet adapted to reduce chromatic aberrations at a second predetermined wavelength.

50. The apparatus of claim 46 wherein the optical filter device reduces a background signal associated with a portion of the imaging path to a predetermined level.

51. The apparatus of claim 46 wherein processing the one or more chromatic aberrations comprises correcting the one or more chromatic aberrations.

52. The apparatus of claim 51 wherein correcting the one or more chromatic aberrations comprises reducing the one or more chromatic aberrations to a predetermined level, the predetermined level being characterized by a predetermined shift in a focal point associated with a first ray characterized by a first color and a second ray characterized by a second color.

53. A method of analyzing processes in elastomeric microfluidic devices, the method comprising:

capturing an image of at least 96 chambers in a time period of less than one minute, wherein each of the chambers in the at least 96 chambers is in fluidic isolation from any of the other chambers in the at least 96 chambers; and

processing the image.

54. The method of claim 53 further comprising:

capturing a second image of the at least 96 chambers in a time period of less than one minute; and

processing the second image.

55. The method of claim 53 wherein capturing an image is performed using an optical system having a numerical aperture greater than or equal to 0.23 and a magnification less than or equal to two.

56. The method of claim 55 wherein the optical system has a numerical aperture greater than or equal to 0.23.

57. The method of claim 53 wherein each of the at least 96 chambers comprises a volume of about 100 nanoliters and less.

58. The method of claim 57 wherein each of the at least 96 chambers comprises a volume of about 10 nanoliters and less.

59. The method of claim 58 wherein each of the at least 96 chambers comprises a volume of about 100 picoliters and less.

60. The method of claim 53 wherein the density of each of the at least 96 chambers is about 100 chambers per cm² and greater.

61. The method of claim 60 wherein the density of each of the at least 96 chambers is about 250 chambers per cm² and greater.

62. The method of claim 61 wherein the density of each of the at least 96 chambers is about 1,000 chambers per cm² and greater.

63. An apparatus for imaging an microfluidic device comprising a plurality of processing sites, the plurality of processing sites containing at least one sample selected from M samples and at least one reagent selected from N reagents, the apparatus comprising:

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

an imaging system coupled to the microfluidic device and adapted to receive electromagnetic radiation emitted from the plurality of processing sites; and

a detector coupled to the imaging system.

64. The apparatus of claim 63 wherein the microfluidic device is an elastomeric microfluidic device.

65. The apparatus of claim 63 wherein the processing sites are closed reaction chambers.

66. The apparatus of claim 65 wherein the plurality of closed reaction chambers comprise a reaction density of about 250 reactions in fluidic isolation per square cm of area and greater.

67. The apparatus of claim 63 wherein the electromagnetic radiation emitted from the plurality of processing sites is a fluorescent signal.

68. The apparatus of claim 67 further comprising a thermal controller coupled the microfluidic device.

69. The apparatus of claim 68 wherein the plurality of processing sites are characterized by a volume of about 100 nanoliters and less.

70. The apparatus of claim 69 wherein the plurality of processing sites are characterized by a volume of about 10 nanoliters and less.

71. The apparatus of claim 69 wherein the plurality of processing sites are characterized by an array density of 250 sites per cm² and greater.

72. The apparatus of claim 69 wherein the plurality of processing sites are characterized by an array density of 1,000 sites per cm² and greater.

73. The apparatus of claim 63 wherein the plurality of processing sites are adapted to support protein crystallization processes.

74. The apparatus of claim 63 wherein the electromagnetic radiation is optical radiation.

75. An optical imaging system, the system comprising:

a computer;

an optical illumination system adapted to illuminate an elastomeric microfluidic array device including at least 1,536 reaction chambers in fluidic isolation, the elastomeric microfluidic array device comprising an elastomeric block formed from a plurality of layers, wherein at least one layer has at least one recess formed therein, the recess having at least one deflectable membrane integral to the layer with the recess; and

an optical detection system.

76. The optical imaging system of claim 75 wherein the at least 1,536 reaction chambers are characterized by a volume of less than 100 nanoliters.

77. The optical imaging system of claim 75 wherein the at least 1,536 reaction chambers are spatially arranged with an array density greater than or equal 250 chambers per square centimeter.

78. The optical imaging system of claim 75 wherein M samples and N reagents are distributed among the at least 1,536 reaction chambers.

79. The optical imaging system of claim 75 wherein the optical illumination system induces the emission of one or more fluorescent signals from a subset of the at least 1,536 reaction chambers.

80. The optical imaging system of claim 75 wherein the optical detection system is adapted to provide one or more images of a protein crystallization process associated with a subset of the at least 1,536 reaction chambers.