System and method for structured illumination and collection for improved optical confocality of raman fiber array spectral translator imaging and interactive raman probing

1. A system for detecting photons from a sample, comprising: a photon source for illuminating a first portion of a sample with first photons to thereby produce second photons; a telescope optic through which said second photons pass; a fiber array spectral translator comprising plural fibers for receiving said second photons and directing said second photons to said photon detector, wherein only a first predetermined group of said plural fibers receive and direct said second photons to said photon detector, and wherein each fiber in said first predetermined group is associated with a predetermined different second portion of said sample wherein each of said predetermined different second portions is smaller than said first portion; and said photon detector for detecting said second photons.

2. The system of claim 1 wherein a number of fibers in said predetermined group is less than or equal to twenty-five percent of a total number of fibers in said fiber array spectral translator.

3. The system of claim 1 wherein a number of fibers in said predetermined group is less than or equal to ten percent of a total number of fibers in said fiber array spectral translator.

4. The system of claim 1 wherein a number of fibers in said predetermined group is less than or equal to one percent of a total number of fibers in said fiber array spectral translator.

5. The system of claim 1 wherein ones of said predetermined different second portions overlap.

6. The system of claim 1 wherein said photon detector is selected from the group consisting of: charge-coupled device (“CCD”), complementary metal oxide semiconductor (“CMOS”) detector, and focal plane array sensor.

7. The system of claim 1 wherein said photon source is a laser.

8. The system of claim 1 wherein said, second photons are selected from the group consisting of: fluorescence photons from said sample, photons emitted by said sample, photons reflected from said sample, and photons refracted by said sample.

9. The system of claim 1 wherein said second photons are scattered photons.

10. The system of claim 1 wherein said second photons are Raman scattered photons.

11. The system of claim 1 wherein a number of fibers in said predetermined group is one.

12. The system of claim 1 wherein said photon source illuminates said first portion of the sample with first photons via a second predetermined group of said plural fibers.

13. The system of claim 12 wherein said first and second predetermined groups are the same and said first and second portions of the sample are substantially the same.

14. The system of claim 12 wherein said first predetermined group is a first predetermined one of said plural fibers.

15. The system of claim 14 wherein said first portion is smaller than said second portion.

16. The system of claim 12 wherein said second predetermined group is a second predetermined one of said plural fibers.

17. The system of claim 16 wherein said second portion is smaller than said first portion.

18. The system of claim 12 wherein said first predetermined group is a first predetermined one of said plural fibers and wherein said second predetermined group is a second predetermined one of said plural fibers.

19. The system of claim 1 further comprising: a display device, and a microprocessor unit operatively connected to said photon detector and to said display device, wherein said photon detector sends to said microprocessor a first signal representative of said second photons, and wherein said microprocessor unit forms a second signal from said first signal and sends said second signal to said display device to display a first visual representation of said second signal.

20. The system of claim 19 wherein said first visual representation is a spectrum.

21. The system of claim 20 wherein said spectrum is a Raman spectrum.

22. The system of claim 19 wherein said first visual representation is an image.

23. The system of claim 22 wherein said image is a Raman image.

24. The system of claim 22 wherein said microprocessor unit runs a software program for forming said second signal from said first signal.

25. The system of claim 19 wherein said display device comprises a user-input screen for a user to select a portion of said first visual representation.

26. The system of claim 19 wherein said user-input screen is a touch-screen.

27. The system of claim 19 further comprising a user input device operatively connected to said microprocessor unit, wherein said input device enables a user to select a portion of said first visual representation.

28. The system of claim 27 wherein said user input device is a computer mouse.

29. The system of claim 19 wherein a memory stores a second visual representation, and wherein said microprocessor unit further comprises circuitry for overlaying said first visual representation on said second visual representation.

30. The system of claim 29 wherein said second visual representation is an optical image of said sample.

31. The system of claim 30 wherein said second visual representation is an optical image of a third portion of said sample.

32. The system of claim 31 wherein said third portion of said sample is substantially the same as said first portion of said sample.

33. The system of claim 1 wherein said first photons have a wavelength selected from the group of wavelengths consisting of: ultraviolet light, visible light, near infrared light, infrared light, and combinations thereof.

34. The system of claim 1 wherein said second photons are fluorescence emission photons from said sample.

35. A method for detecting photons from a sample, comprising: illuminating a first portion of a sample with first photons to thereby produce second photons; passing said second photons through a lens wherein said lens comprises a telescope optic; receiving said second photons using a fiber array spectral translator comprising plural fibers and directing said second photons to said photon detector using said fiber array spectral translator, wherein only a first predetermined group of said plural fibers receive and direct said second photons to said photon detector, and wherein each fiber in said first predetermined group is associated with a predetermined different second portion of said sample wherein each of said predetermined different second portions is smaller than said first portion; and detecting said second photons using said photon detector.

36. The method of claim 35 wherein a number of fibers in said predetermined group is less than or equal to twenty-five percent of a total number of fibers in said fiber array spectral translator.

37. The method of claim 35 wherein a number of fibers in said predetermined group is less than or equal to ten percent of a total number of fibers in said fiber array spectral translator.

38. The method of claim 35 wherein a number of fibers in said predetermined group is less than or equal to one percent of a total number of fibers in said fiber array spectral translator.

39. The method of claim 35 wherein ones of said predetermined different second portions overlap.

40. The method of claim 35 wherein said photon detector is selected from the group consisting of: charge-coupled device (“CCD”), complementary metal oxide semiconductor (“CMOS”) detector, and focal plane array sensor.

41. The method of claim 35 wherein said photon source is a laser.

42. The method of claim 35 wherein said second photons are selected from the group consisting of: fluorescence photons from said sample, photons emitted by said sample, photons reflected from said sample, and photons refracted by said sample.

43. The method of claim 35 wherein said second photons are scattered photons.

44. The method of claim 35 wherein said second photons are Raman scattered photons.

45. The method of claim 35 wherein a number of fibers in said predetermined group is one.

46. The method of claim 35 wherein said photon source illuminates said first portion of the sample with first photons via a second predetermined group of said plural fibers.

47. The method of claim 46 wherein said first and second predetermined groups are the same and said first and second portions of the sample are substantially the same.

48. The method of claim 46 wherein said first predetermined group is a first predetermined one of said plural fibers.

49. The method of claim 48 wherein said first portion is smaller than said second portion.

50. The method of claim 46 wherein said second predetermined group is a second predetermined one of said plural fibers.

51. The method of claim 50 wherein said second portion is smaller than said first portion.

52. The method of claim 46 wherein said first predetermined group is a first predetermined one of said plural fibers and wherein said second predetermined group is a second predetermined one of said plural fibers.

53. The method of claim 35 further comprising: sending a first signal representative of said second photons to a microprocessor unit, wherein said microprocessor unit forms a second signal from said first signal; sending said second signal from said microprocessor unit to a display device, and displaying a first visual representation of said second signal.

54. The method of claim 53 wherein said first visual representation is a spectrum.

55. The method of claim 54 wherein said spectrum is a Raman spectrum.

56. The method of 53 wherein said first visual representation is an image.

57. The method of claim 56 wherein said image is a Raman image.

58. The method of claim 56 wherein said microprocessor unit runs a software program for forming said second signal from said first signal.

59. The method of claim 53 further comprising receiving input from a user on said display device comprising a user-input screen, wherein said user selects a portion of said first visual representation.

60. The method of claim 53 wherein said user-input screen is a touch-screen.

61. The method of claim 53 further comprising a receiving input from a user input device operatively connected to said microprocessor unit, wherein said user selects a portion of said first visual representation.

62. The method of claim 61 wherein said user input device is a computer mouse.

63. The method of claim 53 further comprising storing a second visual representation in a memory device, and overlaying said first visual representation on said second visual representation.

64. The method of claim 63 wherein said second visual representation is an optical image of said sample.

65. The method of claim 64 wherein said second visual representation is an optical image of a third portion of said sample.

66. The method of claim 65 wherein said third portion of said sample is substantially the same as said first portion of said sample.

67. The method of claim 35 wherein said first photons have a wavelength selected from the group of wavelengths consisting of: ultraviolet light, visible light, near infrared light, infrared light, and combinations thereof.

68. The method of claim 35 wherein said second photons are fluorescence emission photons from said sample.