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Light field microscopy

Published:01 July 2006Publication History
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Abstract

By inserting a microlens array into the optical train of a conventional microscope, one can capture light fields of biological specimens in a single photograph. Although diffraction places a limit on the product of spatial and angular resolution in these light fields, we can nevertheless produce useful perspective views and focal stacks from them. Since microscopes are inherently orthographic devices, perspective views represent a new way to look at microscopic specimens. The ability to create focal stacks from a single photograph allows moving or light-sensitive specimens to be recorded. Applying 3D deconvolution to these focal stacks, we can produce a set of cross sections, which can be visualized using volume rendering. In this paper, we demonstrate a prototype light field microscope (LFM), analyze its optical performance, and show perspective views, focal stacks, and reconstructed volumes for a variety of biological specimens. We also show that synthetic focusing followed by 3D deconvolution is equivalent to applying limited-angle tomography directly to the 4D light field.

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References

  1. Adelson, T., Wang, J. Y. A. 1992. Single lens stereo with a plenoptic camera. IEEE Transactions on Pattern Analysis and Machine Intelligence 14, 2, 99--106. Google ScholarGoogle ScholarDigital LibraryDigital Library
  2. Agard, D. A. 1984. Optical sectioning microscopy: Cellular architecture in three dimensions. Ann. Rev. Biophys. Bioeng 13, 191--219.Google ScholarGoogle ScholarCross RefCross Ref
  3. Andersen, A. H., Kak, A. C., 1984. Simultaneous algebraic reconstruction technique (SART): A superior implementation of the ART algorithm. Ultrasonic Imaging 6, 81--94.Google ScholarGoogle ScholarCross RefCross Ref
  4. Arridge, S. R. 2001. Methods for the inverse problem in optical tomography. Proc. Waves and Imaging Through Complex Media. Kluwer, 307--329.Google ScholarGoogle ScholarCross RefCross Ref
  5. Castleman, K. R. 1979. Digital Image Processing. Prentice Hall. Google ScholarGoogle ScholarDigital LibraryDigital Library
  6. Chamgoulov, R. O., Lane, P. M., Macaulay, C. E. 2004. Optical computed-tomography microscope using digital spatial light modulation. Proc. SPIE 5324, 182--190.Google ScholarGoogle Scholar
  7. Colsher, J. G. 1980. Fully three-dimensional positron emission tomography. Phys. Med. Biol. 25, 1, 103--115.Google ScholarGoogle ScholarCross RefCross Ref
  8. Corle, T. R., Kino, G. S. 1996. Confocal Scanning Optical Microscopy and Related Imaging Systems. Academic Press.Google ScholarGoogle Scholar
  9. Ellis, G. W. 1966. Holomicrography: transformation of image during reconstruction a posteriori. Science 143, 1195--1196.Google ScholarGoogle ScholarCross RefCross Ref
  10. Goldberg, N. 1992. Camera technology: the dark side of the lens. Academic Press.Google ScholarGoogle Scholar
  11. Goodman, J. 1996. Introduction to Fourier optics. 2nd edition, McGraw-Hill.Google ScholarGoogle Scholar
  12. Gustafsson, M. G. L. 2005. Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution. Proc. National Academy of Sciences 102, 37.Google ScholarGoogle ScholarCross RefCross Ref
  13. Holmes, T. J., Bhattacharyya, S., et al. 1995. Light microscopic images reconstructed by maximum likelihood deconvolution. In Handbook of Biological Confocal Microscopy, ed. J. B. Pawley, Plenum Press, 389--402.Google ScholarGoogle Scholar
  14. Inoue, S., Oldenbourg, R. 1995. Microscopes. In Handbook of Optics, 2nd edition, McGraw-Hill.Google ScholarGoogle Scholar
  15. Inoue, S. and Spring, K. R. 1997. Video Microscopy. 2nd edition, Plenum Press.Google ScholarGoogle Scholar
  16. Gabor, D. 1948. A new microscopic principle. Nature 161, 777--778.Google ScholarGoogle ScholarCross RefCross Ref
  17. Isaksen, A., Mcmillan, L., Gortler, S. J. 2000. Dynamically reparameterized light fields. Proc. SIGGRAPH 2000. Google ScholarGoogle ScholarDigital LibraryDigital Library
  18. Javidi, B., Okano, F., eds. 2002. Three-Dimensional Television, Video and Display Technologies. Springer-Verlag. Google ScholarGoogle ScholarDigital LibraryDigital Library
  19. Kak, A. C., Slaney, M. 1988. Principles of Computerized Tomographic Imaging. IEEE Press.Google ScholarGoogle Scholar
  20. Kawata, S., Nakamura, 0., Minami, S. 1987. Optical microscope tomography. I. Support constraint. J. Opt. Soc. Am. A 4, 1, 292--297.Google ScholarGoogle ScholarCross RefCross Ref
  21. Kingslake, R. 1983. Optical system design. Academic Press.Google ScholarGoogle Scholar
  22. Levoy, M., Hanrahan, P. 1996. Light field rendering. Proc. SIGGRAPH 1996. Google ScholarGoogle ScholarDigital LibraryDigital Library
  23. Levoy, M., Chen, B., Vaish, V., Horowitz, M., Mcdowall, I., Bolas, M. 2004. Synthetic aperture confocal imaging. ACM Transactions on Graphics (Proc. SIGGRAPH) 23, 3, 825--834. Google ScholarGoogle ScholarDigital LibraryDigital Library
  24. Markham, J., Conchello, J.-A. 2001. Artefacts in restored images due to intensity loss in three-dimensional fluorescence microscopy. J. Microscopy 204, 2, 93--98.Google ScholarGoogle ScholarCross RefCross Ref
  25. Mcnally, J. G., Preza, C., Conchello, J. A., Thomas, L. J. Jr. 1994. Artifacts in computational optical-sectioning microscopy. J. Opt. Soc. Am. A 11, 3, 1056--67.Google ScholarGoogle ScholarCross RefCross Ref
  26. Nayar, S. K., Nakagawa, Y. 1990. Shape from focus: An effective approach for rough surfaces. Proc. International Conference on Robotics and Automation (ICRA), Vol. 2, 218--225.Google ScholarGoogle ScholarCross RefCross Ref
  27. Nayar, S. K., Narasimhan, S. G. 2002. Assorted pixels: Multi-sampled imaging with structural models. Proc. ECCV. Google ScholarGoogle ScholarDigital LibraryDigital Library
  28. Ng, R. 2005. Fourier slice photography. ACM Transactions on Graphics (Proc. SIGGRAPH) 24, 3, 735--744. Google ScholarGoogle ScholarDigital LibraryDigital Library
  29. Ng, R., Levoy, M., Bredif, M., Duval, G., Horowitz, M., Hanrahan, P. 2005. Light Field Photography with a Hand-Held Plenoptic Camera. Stanford Tech Report CTSR 2005-02.Google ScholarGoogle Scholar
  30. Ng, R. 2006. Digital Light Field Photography. PhD dissertation, Stanford University. Google ScholarGoogle ScholarDigital LibraryDigital Library
  31. Noguchi, M., Nayar, S. 1994. Microscopic shape from focus using active illumination. Proc. IAPR International Conference on Pattern Recognition (ICPR), Vol. A, 147--152.Google ScholarGoogle ScholarCross RefCross Ref
  32. Okoshi, T. 1976. Three-Dimensional Imaging Techniques. Academic Press.Google ScholarGoogle Scholar
  33. Piller, H. 1977. Microscope Photometry. Springer-Verlag.Google ScholarGoogle Scholar
  34. Pluta, M. 1988. Advanced Light Microscopy (in 3 volumes). Elsevier.Google ScholarGoogle Scholar
  35. Schechner, Y., Kiryati, N. 1999. The optimal axial interval for estimating depth from defocus. Proc. ICCV. Google ScholarGoogle ScholarDigital LibraryDigital Library
  36. Schechner, Y., Kiryati, N. 2000. Depth from defocus vs. stereo: How different really are they? IJCV 39, 2, 141--162. Google ScholarGoogle ScholarDigital LibraryDigital Library
  37. Schechner, Y. Y., Kiryati, N., Basri, R. 2000. Separation of transparent layers using focus. IJCV 39, 1, 25--39. Google ScholarGoogle ScholarDigital LibraryDigital Library
  38. Schechner, Y., Nayar, S. 2001. Generalized Mosaicing. Proc. ICCV.Google ScholarGoogle Scholar
  39. Shah, U. B., Nayar, S. K. 1992. Extracting 3-D structure and focused images using an optical microscope. Proc. IEEE Symposium on Computer-Based Medical Systems.Google ScholarGoogle ScholarCross RefCross Ref
  40. Streibl, N. 1984. Depth transfer by an imaging system. Optica Acta 31, 11, 1233--1241.Google ScholarGoogle ScholarCross RefCross Ref
  41. Streibl, N. 1985. Three-dimensional imaging by a microscope. J. Opt. Soc. Am. A 2, 2, 121--127.Google ScholarGoogle ScholarCross RefCross Ref
  42. Swedlow, J. R., Sedat, J. W., Agard, D. A. 1997. Deconvolution in optical microscopy. In Deconvolution of Images and Spectra, ed. P. A. Jansson, Academic Press, 284--309. Google ScholarGoogle ScholarDigital LibraryDigital Library
  43. Vaish, V., Garg, G., Talvala, E., Antunez, E., Wilburn, B., Horowitz, M., Levoy, M., Synthetic aperture focusing using a shear-warp factorization of the viewing transform. Proc. Workshop on Advanced 3D Imaging for Safety and Security, in conjunction with CVPR 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  44. Weinstein, R. S., Descour, M. R., et al. 2004. An array microscope for ultrarapid virtual slide processing and telepathology. Design, fabrication, and validation study. Human Pathology 35, 11, 1303--1314.Google ScholarGoogle ScholarCross RefCross Ref

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  1. Light field microscopy

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      cover image ACM Transactions on Graphics
      ACM Transactions on Graphics  Volume 25, Issue 3
      July 2006
      742 pages
      ISSN:0730-0301
      EISSN:1557-7368
      DOI:10.1145/1141911
      Issue’s Table of Contents

      Copyright © 2006 ACM

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      Publication History

      • Published: 1 July 2006
      Published in tog Volume 25, Issue 3

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