Abstract

A new method to obtain the three-dimensional localization of fluorochrome distributions in micrometric samples is presented. It uses a microlens array coupled to the image port of a standard microscope to obtain tomographic data by a filtered back-projection algorithm. Scanning of the microlens array is proposed to obtain a dense data set for reconstruction. Simulation and experimental results are shown and the implications of this approach in fast 3D imaging are discussed.

© 2014 Optical Society of America

Full Article  |  PDF Article
OSA Recommended Articles
Development of a modular, high-speed plenoptic-camera for 3D flow-measurement

Zu Puayen Tan, Kyle Johnson, Chris Clifford, and Brian S. Thurow
Opt. Express 27(9) 13400-13415 (2019)

Enhancing the performance of the light field microscope using wavefront coding

Noy Cohen, Samuel Yang, Aaron Andalman, Michael Broxton, Logan Grosenick, Karl Deisseroth, Mark Horowitz, and Marc Levoy
Opt. Express 22(20) 24817-24839 (2014)

Wave optics theory and 3-D deconvolution for the light field microscope

Michael Broxton, Logan Grosenick, Samuel Yang, Noy Cohen, Aaron Andalman, Karl Deisseroth, and Marc Levoy
Opt. Express 21(21) 25418-25439 (2013)

References

  • View by:
  • |
  • |
  • |

  1. S. Kikuchi, K. Sonobe, and N. Ohyama, “Three-dimensional microscopic computed tomography based on generalized Radon transform for optical imaging systems,” Opt. Commun. 123(4-6), 725–733 (1996).
    [Crossref]
  2. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
    [Crossref] [PubMed]
  3. M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13(11), 4210–4223 (2005).
    [Crossref] [PubMed]
  4. M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
    [Crossref] [PubMed]
  5. M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
    [Crossref] [PubMed]
  6. P. Fei, Z. Yu, X. Wang, P. J. Lu, Y. Fu, Z. He, J. Xiong, and Y. Huang, “High dynamic range optical projection tomography (HDR-OPT),” Opt. Express 20(8), 8824–8836 (2012).
    [Crossref] [PubMed]
  7. E. H. Adelson and J. Y. Wang, “Single lens stereo with a plenoptic camera,” IEEE Trans. Pattern Anal. Mach. Intell. 14(2), 99–106 (1992).
    [Crossref]
  8. M. Levoy, M. Horowitz, R. Ng, A. Adams, and M. Footer, “Light field microscopy,” ACM Trans. Graph. Proc SIGGRAPH 2006 25, (2006).
    [Crossref]
  9. G. Saavedra, R. Martínez-Cuenca, M. Martínez-Corral, H. Navarro, M. Daneshpanah, and B. Javidi, “Digital slicing of 3D scenes by Fourier filtering of integral images,” Opt. Express 16(22), 17154–17160 (2008).
    [Crossref] [PubMed]
  10. M. Broxton, L. Grosenick, S. Yang, N. Cohen, A. Andalman, K. Deisseroth, and M. Levoy, “Wave optics theory and 3-D deconvolution for the light field microscope,” Opt. Express 21(21), 25418–25439 (2013).
    [Crossref] [PubMed]
  11. J.-S. Jang and B. Javidi, “Three-dimensional synthetic aperture integral imaging,” Opt. Lett. 27(13), 1144–1146 (2002).
    [Crossref] [PubMed]
  12. Y.-T. Lim, J.-H. Park, K.-C. Kwon, and N. Kim, “Resolution-enhanced integral imaging microscopy that uses lens array shifting,” Opt. Express 17(21), 19253–19263 (2009).
    [Crossref] [PubMed]
  13. L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745 (1974).
    [Crossref]
  14. W. H. Richardson, “Bayesian-Based Iterative Method of Image Restoration,” J. Opt. Soc. Am. 62(1), 55–59 (1972).
    [Crossref]
  15. J. Juskaitis, R., “Measuring the Real Point Spread Function of High Numerical Aperture Microscope Objective Lenses,” in Handbook of Biological Confocal Microscopy, Pawley, J.B., ed., 3rd ed. (Springer, 2010).
  16. J. W. Goodman, Fourier Optics, 2nd ed. (McGraw-Hill, 1996).
  17. F. O. Fahrbach, F. F. Voigt, B. Schmid, F. Helmchen, and J. Huisken, “Rapid 3D light-sheet microscopy with a tunable lens,” Opt. Express 21(18), 21010–21026 (2013).
    [Crossref] [PubMed]

2013 (2)

2012 (1)

2011 (1)

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

2009 (1)

2008 (2)

G. Saavedra, R. Martínez-Cuenca, M. Martínez-Corral, H. Navarro, M. Daneshpanah, and B. Javidi, “Digital slicing of 3D scenes by Fourier filtering of integral images,” Opt. Express 16(22), 17154–17160 (2008).
[Crossref] [PubMed]

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

2005 (1)

2002 (2)

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

J.-S. Jang and B. Javidi, “Three-dimensional synthetic aperture integral imaging,” Opt. Lett. 27(13), 1144–1146 (2002).
[Crossref] [PubMed]

1996 (1)

S. Kikuchi, K. Sonobe, and N. Ohyama, “Three-dimensional microscopic computed tomography based on generalized Radon transform for optical imaging systems,” Opt. Commun. 123(4-6), 725–733 (1996).
[Crossref]

1992 (1)

E. H. Adelson and J. Y. Wang, “Single lens stereo with a plenoptic camera,” IEEE Trans. Pattern Anal. Mach. Intell. 14(2), 99–106 (1992).
[Crossref]

1974 (1)

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745 (1974).
[Crossref]

1972 (1)

Adelson, E. H.

E. H. Adelson and J. Y. Wang, “Single lens stereo with a plenoptic camera,” IEEE Trans. Pattern Anal. Mach. Intell. 14(2), 99–106 (1992).
[Crossref]

Ahlgren, U.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Allan Johnson, G.

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

Andalman, A.

Baldock, R.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Birk, U. J.

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

Broxton, M.

Cohen, N.

Daneshpanah, M.

Davidson, D.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Deisseroth, K.

Dewhirst, M.

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

Fahrbach, F. O.

Fauver, M.

Fei, P.

Fu, Y.

Grosenick, L.

He, Z.

Hecksher-Sørensen, J.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Helmchen, F.

Hill, B.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Huang, Y.

Huisken, J.

Jang, J.-S.

Javidi, B.

Kikuchi, S.

S. Kikuchi, K. Sonobe, and N. Ohyama, “Three-dimensional microscopic computed tomography based on generalized Radon transform for optical imaging systems,” Opt. Commun. 123(4-6), 725–733 (1996).
[Crossref]

Kim, N.

Kwon, K.-C.

Levoy, M.

Lim, Y.-T.

Lu, P. J.

Lucy, L. B.

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745 (1974).
[Crossref]

Martínez-Corral, M.

Martínez-Cuenca, R.

Meyer, H.

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

Meyer, M. G.

Navarro, H.

Nelson, A. C.

Neumann, T.

Ohyama, N.

S. Kikuchi, K. Sonobe, and N. Ohyama, “Three-dimensional microscopic computed tomography based on generalized Radon transform for optical imaging systems,” Opt. Commun. 123(4-6), 725–733 (1996).
[Crossref]

Oldham, M.

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

Oliver, T.

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

Park, J.-H.

Patten, F. W.

Perry, P.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Rahn, J. R.

Richardson, W. H.

Rieckher, M.

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

Ripoll, J.

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

Ross, A.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Saavedra, G.

Sakhalkar, H.

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

Schmid, B.

Seibel, E. J.

Sharpe, J.

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Sonobe, K.

S. Kikuchi, K. Sonobe, and N. Ohyama, “Three-dimensional microscopic computed tomography based on generalized Radon transform for optical imaging systems,” Opt. Commun. 123(4-6), 725–733 (1996).
[Crossref]

Tavernarakis, N.

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

Voigt, F. F.

Wang, J. Y.

E. H. Adelson and J. Y. Wang, “Single lens stereo with a plenoptic camera,” IEEE Trans. Pattern Anal. Mach. Intell. 14(2), 99–106 (1992).
[Crossref]

Wang, X.

Xiong, J.

Yang, S.

Yu, Z.

Astron. J. (1)

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745 (1974).
[Crossref]

IEEE Trans. Pattern Anal. Mach. Intell. (1)

E. H. Adelson and J. Y. Wang, “Single lens stereo with a plenoptic camera,” IEEE Trans. Pattern Anal. Mach. Intell. 14(2), 99–106 (1992).
[Crossref]

J. Biomed. Opt. (1)

M. Oldham, H. Sakhalkar, T. Oliver, G. Allan Johnson, and M. Dewhirst, “Optical clearing of unsectioned specimens for three-dimensional imaging via optical transmission and emission tomography,” J. Biomed. Opt. 13(2), 021113 (2008).
[Crossref] [PubMed]

J. Opt. Soc. Am. (1)

Opt. Commun. (1)

S. Kikuchi, K. Sonobe, and N. Ohyama, “Three-dimensional microscopic computed tomography based on generalized Radon transform for optical imaging systems,” Opt. Commun. 123(4-6), 725–733 (1996).
[Crossref]

Opt. Express (6)

Opt. Lett. (1)

PLoS ONE (1)

M. Rieckher, U. J. Birk, H. Meyer, J. Ripoll, and N. Tavernarakis, “Microscopic Optical Projection Tomography In Vivo,” PLoS ONE 6(4), e18963 (2011).
[Crossref] [PubMed]

Science (1)

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, “Optical projection tomography as a tool for 3D microscopy and gene expression studies,” Science 296(5567), 541–545 (2002).
[Crossref] [PubMed]

Other (3)

M. Levoy, M. Horowitz, R. Ng, A. Adams, and M. Footer, “Light field microscopy,” ACM Trans. Graph. Proc SIGGRAPH 2006 25, (2006).
[Crossref]

J. Juskaitis, R., “Measuring the Real Point Spread Function of High Numerical Aperture Microscope Objective Lenses,” in Handbook of Biological Confocal Microscopy, Pawley, J.B., ed., 3rd ed. (Springer, 2010).

J. W. Goodman, Fourier Optics, 2nd ed. (McGraw-Hill, 1996).

Cited By

OSA participates in Crossref's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (8)

Fig. 1
Fig. 1 (a) OPT setup; S sample; MO microscope objective; P pinhole; TL tube lens; IS image sensor. (b) PI setup; MA microlens array.
Fig. 2
Fig. 2 (a) A plot describing the method of scanning the MA using a low resolution image sensor (IS) to increase the resolution of the angular detection. (b) A static equivalent to (a).
Fig. 3
Fig. 3 (a) The set of angular images of an ideal point source in focus for different pitch angles p ˜ . (b) After the focal plane. (c) Before the front focal plane. OA is the optical axis and FP is the front focal plane of the microscope objective.
Fig. 4
Fig. 4 (a-i) and (a-ii) the intensity on the MA plane for an emitter in-focus and out focus respectively. (b-i) and (b-ii) the intensity on the sensor plane for an emitter in-focus and out-focus respectively for the initial position of the MA. (c-i) and (c-ii) the average of the images for the different displacements of the MA for the in-focus and out-focus emitter. (d-i) and (d-ii) the average of the images corresponding to the different angles for the in-focus and out-focus case respectively. All the images have 200x200 px.
Fig. 5
Fig. 5 The reconstruction of the fluorochrome density distribution in the front focal volume of the microscope objective corresponding to two simulated point sources emitting simultaneously, one in-focus (at the cube center) and the other out-focus, obtained from the simulated MA image set of Fig. 4. Only the voxels with value higher than 0.7 of the normalized matrix ( 300 3 elements) of the reconstruction are represented. The arrow indicates the optical axis and the light propagation direction.
Fig. 6
Fig. 6 Scheme of the PI system coupled with an inverted microscope. L1 and L2 are lenses; MA is the microlens array; MT1 and MT2 are linear motorized translation stages; TS is a micrometric translation stage; F1 and F2 are filters.
Fig. 7
Fig. 7 (a) The reference image corresponding to the MA initial position. (b) The sample, imaged through the MA at the initial position. (c) The ensemble average of the scanning images; (d) One of the low resolution angular images. (e) The deconvolution of (d). (f) The average of the angular images. The bar represents the scale in the sample space.
Fig. 8
Fig. 8 (a) The reconstruction of the volume in front of the microscope objective of two fluorescent microspheres in agarose; (b) top projection with insets showing the signal on transversal planes at the marked axial positions; (c) the front projection. (d) The reconstruction of a single microsphere in different axial locations around the microscope front focal point (each color represents an independent measurement). The matrices were normalized and a threshold of 0.7 was applied before representation except in the insets in (b) where no threshold was applied.

Equations (3)

Equations on this page are rendered with MathJax. Learn more.

( p ˜ , y ˜ ) = ( tan 1 ( x cos y ˜ f ) , tan 1 ( y f ) )
W m = π ω 2 λ ( 1 Z 1 F )
Δ z = n Δ Z / G 2

Metrics