Abstract

Elucidating the neural pathways that underlie brain function is one of the greatest challenges in neuroscience. Light sheet based microscopy is a cutting edge method to map cerebral circuitry through optical sectioning of cleared mouse brains. However, the image contrast provided by this method is not sufficient to resolve and reconstruct the entire neuronal network. Here we combined the advantages of light sheet illumination and confocal slit detection to increase the image contrast in real time, with a frame rate of 10 Hz. In fact, in confocal light sheet microscopy (CLSM), the out-of-focus and scattered light is filtered out before detection, without multiple acquisitions or any post-processing of the acquired data. The background rejection capabilities of CLSM were validated in cleared mouse brains by comparison with a structured illumination approach. We show that CLSM allows reconstructing macroscopic brain volumes with sub-cellular resolution. We obtained a comprehensive map of Purkinje cells in the cerebellum of L7-GFP transgenic mice. Further, we were able to trace neuronal projections across brain of thy1-GFP-M transgenic mice. The whole-brain high-resolution fluorescence imaging assured by CLSM may represent a powerful tool to navigate the brain through neuronal pathways. Although this work is focused on brain imaging, the macro-scale high-resolution tomographies affordable with CLSM are ideally suited to explore, at micron-scale resolution, the anatomy of different specimens like murine organs, embryos or flies.

©2012 Optical Society of America

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  1. C. Sotelo, “Viewing the brain through the master hand of Ramon y Cajal,” Nat. Rev. Neurosci. 4(1), 71–77 (2003).
    [Crossref] [PubMed]
  2. J. Huisken and D. Y. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
    [Crossref] [PubMed]
  3. P. J. Keller and H. U. Dodt, “Light sheet microscopy of living or cleared specimens,” Curr. Opin. Neurobiol. 22(1), 138–143 (2012).
    [Crossref] [PubMed]
  4. P. J. Keller, F. Pampaloni, and E. H. Stelzer, “Life sciences require the third dimension,” Curr. Opin. Cell Biol. 18(1), 117–124 (2006).
    [Crossref] [PubMed]
  5. J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
    [Crossref] [PubMed]
  6. J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
    [Crossref] [PubMed]
  7. H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
    [Crossref] [PubMed]
  8. C. Dunsby, “Optically sectioned imaging by oblique plane microscopy,” Opt. Express 16(25), 20306–20316 (2008).
    [Crossref] [PubMed]
  9. E. Fuchs, J. Jaffe, R. Long, and F. Azam, “Thin laser light sheet microscope for microbial oceanography,” Opt. Express 10(2), 145–154 (2002).
    [PubMed]
  10. T. F. Holekamp, D. Turaga, and T. E. Holy, “Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy,” Neuron 57(5), 661–672 (2008).
    [Crossref] [PubMed]
  11. J. Huisken and D. Y. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM),” Opt. Lett. 32(17), 2608–2610 (2007).
    [Crossref] [PubMed]
  12. J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
    [Crossref] [PubMed]
  13. P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
    [Crossref] [PubMed]
  14. H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Grössenbestimmung ultramikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Annalen der Physik 10, 1–39 (1903).
  15. M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5(2), 159–161 (2008).
    [Crossref] [PubMed]
  16. P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
    [PubMed]
  17. A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170(3), 229–236 (1993).
    [Crossref] [PubMed]
  18. S. Kalchmair, N. Jährling, K. Becker, and H. U. Dodt, “Image contrast enhancement in confocal ultramicroscopy,” Opt. Lett. 35(1), 79–81 (2010).
    [Crossref] [PubMed]
  19. P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
    [Crossref] [PubMed]
  20. J. Mertz and J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
    [Crossref] [PubMed]
  21. F. O. Fahrbach and A. Rohrbach, “Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media,” Nat Commun 3, 632 (2012).
    [Crossref] [PubMed]
  22. M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
    [Crossref] [PubMed]
  23. G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
    [Crossref] [PubMed]
  24. J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
    [Crossref] [PubMed]
  25. W. Spalteholz, Uber das Durchsichtigmachen von menschlichen und tierischen Präparaten und seine theoretischen Bedingungen, nebst Anhang: Uber Knochenfärbung. (S. Hirzel, Leipzig, 1914).
  26. M. J. Booth and T. Wilson, “Refractive-index-mismatch induced aberrations in single-photon and two-photon microscopy and the use of aberration correction,” J. Biomed. Opt. 6(3), 266–272 (2001).
    [Crossref] [PubMed]
  27. T. Wilson and A. R. Carlini, “Size of the detector in confocal imaging systems,” Opt. Lett. 12(4), 227–229 (1987).
    [Crossref] [PubMed]
  28. G. Cox and C. J. Sheppard, “Practical limits of resolution in confocal and non-linear microscopy,” Microsc. Res. Tech. 63(1), 18–22 (2004).
    [Crossref] [PubMed]
  29. J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
    [Crossref] [PubMed]
  30. J. Altman and S. A. Bayer, “Embryonic development of the rat cerebellum. III. Regional differences in the time of origin, migration, and settling of Purkinje cells,” J. Comp. Neurol. 231(1), 42–65 (1985).
    [Crossref] [PubMed]
  31. R. R. Buss, W. Sun, and R. W. Oppenheim, “Adaptive roles of programmed cell death during nervous system development,” Annu. Rev. Neurosci. 29(1), 1–35 (2006).
    [Crossref] [PubMed]
  32. M. Bauman and T. L. Kemper, “Histoanatomic observations of the brain in early infantile autism,” Neurology 35(6), 866–874 (1985).
    [Crossref] [PubMed]
  33. T. L. Kemper and M. Bauman, “Neuropathology of infantile autism,” J. Neuropathol. Exp. Neurol. 57(7), 645–652 (1998).
    [Crossref] [PubMed]
  34. E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
    [PubMed]
  35. M. Helmstaedter, K. L. Briggman, and W. Denk, “3D structural imaging of the brain with photons and electrons,” Curr. Opin. Neurobiol. 18(6), 633–641 (2008).
    [Crossref] [PubMed]
  36. J. W. Lichtman, J. Livet, and J. R. Sanes, “A technicolour approach to the connectome,” Nat. Rev. Neurosci. 9(6), 417–422 (2008).
    [Crossref] [PubMed]
  37. O. Sporns, G. Tononi, and R. Kötter, “The human connectome: A structural description of the human brain,” PLOS Comput. Biol. 1(4), e42 (2005).
    [Crossref] [PubMed]
  38. K. L. Briggman, M. Helmstaedter, and W. Denk, “Wiring specificity in the direction-selectivity circuit of the retina,” Nature 471(7337), 183–188 (2011).
    [Crossref] [PubMed]
  39. W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
    [Crossref] [PubMed]
  40. S. Mori, K. Oishi, and A. V. Faria, “White matter atlases based on diffusion tensor imaging,” Curr. Opin. Neurol. 22(4), 362–369 (2009).
    [Crossref] [PubMed]
  41. W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
    [Crossref] [PubMed]
  42. T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
    [Crossref] [PubMed]
  43. H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
    [Crossref] [PubMed]
  44. K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
    [Crossref] [PubMed]
  45. A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
    [Crossref] [PubMed]
  46. U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
    [Crossref] [PubMed]
  47. R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
    [Crossref] [PubMed]
  48. A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
    [Crossref] [PubMed]
  49. D. Mayerich, L. Abbott, and B. McCormick, “Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” J. Microsc. 231(1), 134–143 (2008).
    [Crossref] [PubMed]
  50. N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
    [PubMed]
  51. A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
    [Crossref] [PubMed]
  52. A. Bria, L. Silvestri, L. Sacconi, F. S. Pavone, and G. Iannello, “Stitching Terabyte-sized 3D images acquired in confocal ultramicroscopy,” presented at the IEEE International Symposium on Biomedical Imaging (ISBI 2012), Barcelona, Spain, 2–5 May 2012.
  53. P. J. Bex and W. Makous, “Spatial frequency, phase, and the contrast of natural images,” J. Opt. Soc. Am. A 19(6), 1096–1106 (2002).
    [Crossref] [PubMed]

2012 (5)

P. J. Keller and H. U. Dodt, “Light sheet microscopy of living or cleared specimens,” Curr. Opin. Neurobiol. 22(1), 138–143 (2012).
[Crossref] [PubMed]

F. O. Fahrbach and A. Rohrbach, “Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media,” Nat Commun 3, 632 (2012).
[Crossref] [PubMed]

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
[Crossref] [PubMed]

2011 (5)

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

K. L. Briggman, M. Helmstaedter, and W. Denk, “Wiring specificity in the direction-selectivity circuit of the retina,” Nature 471(7337), 183–188 (2011).
[Crossref] [PubMed]

J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
[Crossref] [PubMed]

2010 (7)

S. Kalchmair, N. Jährling, K. Becker, and H. U. Dodt, “Image contrast enhancement in confocal ultramicroscopy,” Opt. Lett. 35(1), 79–81 (2010).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

J. Mertz and J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[Crossref] [PubMed]

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
[Crossref] [PubMed]

2009 (3)

S. Mori, K. Oishi, and A. V. Faria, “White matter atlases based on diffusion tensor imaging,” Curr. Opin. Neurol. 22(4), 362–369 (2009).
[Crossref] [PubMed]

J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
[Crossref] [PubMed]

J. Huisken and D. Y. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

2008 (7)

C. Dunsby, “Optically sectioned imaging by oblique plane microscopy,” Opt. Express 16(25), 20306–20316 (2008).
[Crossref] [PubMed]

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5(2), 159–161 (2008).
[Crossref] [PubMed]

T. F. Holekamp, D. Turaga, and T. E. Holy, “Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy,” Neuron 57(5), 661–672 (2008).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

M. Helmstaedter, K. L. Briggman, and W. Denk, “3D structural imaging of the brain with photons and electrons,” Curr. Opin. Neurobiol. 18(6), 633–641 (2008).
[Crossref] [PubMed]

J. W. Lichtman, J. Livet, and J. R. Sanes, “A technicolour approach to the connectome,” Nat. Rev. Neurosci. 9(6), 417–422 (2008).
[Crossref] [PubMed]

D. Mayerich, L. Abbott, and B. McCormick, “Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” J. Microsc. 231(1), 134–143 (2008).
[Crossref] [PubMed]

2007 (4)

J. Huisken and D. Y. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM),” Opt. Lett. 32(17), 2608–2610 (2007).
[Crossref] [PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

2006 (2)

P. J. Keller, F. Pampaloni, and E. H. Stelzer, “Life sciences require the third dimension,” Curr. Opin. Cell Biol. 18(1), 117–124 (2006).
[Crossref] [PubMed]

R. R. Buss, W. Sun, and R. W. Oppenheim, “Adaptive roles of programmed cell death during nervous system development,” Annu. Rev. Neurosci. 29(1), 1–35 (2006).
[Crossref] [PubMed]

2005 (2)

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

O. Sporns, G. Tononi, and R. Kötter, “The human connectome: A structural description of the human brain,” PLOS Comput. Biol. 1(4), e42 (2005).
[Crossref] [PubMed]

2004 (2)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

G. Cox and C. J. Sheppard, “Practical limits of resolution in confocal and non-linear microscopy,” Microsc. Res. Tech. 63(1), 18–22 (2004).
[Crossref] [PubMed]

2003 (2)

C. Sotelo, “Viewing the brain through the master hand of Ramon y Cajal,” Nat. Rev. Neurosci. 4(1), 71–77 (2003).
[Crossref] [PubMed]

W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
[Crossref] [PubMed]

2002 (2)

2001 (2)

M. J. Booth and T. Wilson, “Refractive-index-mismatch induced aberrations in single-photon and two-photon microscopy and the use of aberration correction,” J. Biomed. Opt. 6(3), 266–272 (2001).
[Crossref] [PubMed]

M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
[Crossref] [PubMed]

2000 (1)

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

1998 (1)

T. L. Kemper and M. Bauman, “Neuropathology of infantile autism,” J. Neuropathol. Exp. Neurol. 57(7), 645–652 (1998).
[Crossref] [PubMed]

1993 (1)

A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170(3), 229–236 (1993).
[Crossref] [PubMed]

1987 (1)

1986 (1)

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

1985 (2)

M. Bauman and T. L. Kemper, “Histoanatomic observations of the brain in early infantile autism,” Neurology 35(6), 866–874 (1985).
[Crossref] [PubMed]

J. Altman and S. A. Bayer, “Embryonic development of the rat cerebellum. III. Regional differences in the time of origin, migration, and settling of Purkinje cells,” J. Comp. Neurol. 231(1), 42–65 (1985).
[Crossref] [PubMed]

1903 (1)

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Grössenbestimmung ultramikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Annalen der Physik 10, 1–39 (1903).

Abbott, L.

D. Mayerich, L. Abbott, and B. McCormick, “Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” J. Microsc. 231(1), 134–143 (2008).
[Crossref] [PubMed]

Altman, J.

J. Altman and S. A. Bayer, “Embryonic development of the rat cerebellum. III. Regional differences in the time of origin, migration, and settling of Purkinje cells,” J. Comp. Neurol. 231(1), 42–65 (1985).
[Crossref] [PubMed]

Amat, F.

R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
[Crossref] [PubMed]

Ando, R.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Arrenberg, A. B.

A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
[Crossref] [PubMed]

Azam, F.

Baader, S. L.

J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
[Crossref] [PubMed]

Baier, H.

A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
[Crossref] [PubMed]

Bao, Z.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Bauman, M.

T. L. Kemper and M. Bauman, “Neuropathology of infantile autism,” J. Neuropathol. Exp. Neurol. 57(7), 645–652 (1998).
[Crossref] [PubMed]

M. Bauman and T. L. Kemper, “Histoanatomic observations of the brain in early infantile autism,” Neurology 35(6), 866–874 (1985).
[Crossref] [PubMed]

Bayer, S. A.

J. Altman and S. A. Bayer, “Embryonic development of the rat cerebellum. III. Regional differences in the time of origin, migration, and settling of Purkinje cells,” J. Comp. Neurol. 231(1), 42–65 (1985).
[Crossref] [PubMed]

Becker, K.

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

S. Kalchmair, N. Jährling, K. Becker, and H. U. Dodt, “Image contrast enhancement in confocal ultramicroscopy,” Opt. Lett. 35(1), 79–81 (2010).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Bernstein, M.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Betzig, E.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Bex, P. J.

Booth, M. J.

M. J. Booth and T. Wilson, “Refractive-index-mismatch induced aberrations in single-photon and two-photon microscopy and the use of aberration correction,” J. Biomed. Opt. 6(3), 266–272 (2001).
[Crossref] [PubMed]

Bradke, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Briggman, K. L.

K. L. Briggman, M. Helmstaedter, and W. Denk, “Wiring specificity in the direction-selectivity circuit of the retina,” Nature 471(7337), 183–188 (2011).
[Crossref] [PubMed]

M. Helmstaedter, K. L. Briggman, and W. Denk, “3D structural imaging of the brain with photons and electrons,” Curr. Opin. Neurobiol. 18(6), 633–641 (2008).
[Crossref] [PubMed]

Burns, D. H.

A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170(3), 229–236 (1993).
[Crossref] [PubMed]

Buss, R. R.

R. R. Buss, W. Sun, and R. W. Oppenheim, “Adaptive roles of programmed cell death during nervous system development,” Annu. Rev. Neurosci. 29(1), 1–35 (2006).
[Crossref] [PubMed]

Buytaert, J. A.

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

Carlini, A. R.

Conchello, J. A.

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

Cox, G.

G. Cox and C. J. Sheppard, “Practical limits of resolution in confocal and non-linear microscopy,” Microsc. Res. Tech. 63(1), 18–22 (2004).
[Crossref] [PubMed]

Davidson, M. W.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Deininger, K.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Denk, W.

K. L. Briggman, M. Helmstaedter, and W. Denk, “Wiring specificity in the direction-selectivity circuit of the retina,” Nature 471(7337), 183–188 (2011).
[Crossref] [PubMed]

M. Helmstaedter, K. L. Briggman, and W. Denk, “3D structural imaging of the brain with photons and electrons,” Curr. Opin. Neurobiol. 18(6), 633–641 (2008).
[Crossref] [PubMed]

Deussing, J. M.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Dirckx, J. J.

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

Dodt, H. U.

P. J. Keller and H. U. Dodt, “Light sheet microscopy of living or cleared specimens,” Curr. Opin. Neurobiol. 22(1), 138–143 (2012).
[Crossref] [PubMed]

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

S. Kalchmair, N. Jährling, K. Becker, and H. U. Dodt, “Image contrast enhancement in confocal ultramicroscopy,” Opt. Lett. 35(1), 79–81 (2010).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Dunsby, C.

Duong, T.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Eder, M.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Ertürk, A.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Fahrbach, F. O.

F. O. Fahrbach and A. Rohrbach, “Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media,” Nat Commun 3, 632 (2012).
[Crossref] [PubMed]

Faria, A. V.

S. Mori, K. Oishi, and A. V. Faria, “White matter atlases based on diffusion tensor imaging,” Curr. Opin. Neurol. 22(4), 362–369 (2009).
[Crossref] [PubMed]

Faulkner-Jones, B. E.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Feng, G.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Förstner, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Freeman, B. J.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Fuchs, E.

Fukami, K.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Galbraith, C. G.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Galbraith, J. A.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Gao, L.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Gong, H.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Greger, K.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

Gunther, S.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Guthrie, D.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Hama, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Hellal, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Helmstaedter, M.

K. L. Briggman, M. Helmstaedter, and W. Denk, “Wiring specificity in the direction-selectivity circuit of the retina,” Nature 471(7337), 183–188 (2011).
[Crossref] [PubMed]

M. Helmstaedter, K. L. Briggman, and W. Denk, “3D structural imaging of the brain with photons and electrons,” Curr. Opin. Neurobiol. 18(6), 633–641 (2008).
[Crossref] [PubMed]

Holekamp, T. F.

T. F. Holekamp, D. Turaga, and T. E. Holy, “Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy,” Neuron 57(5), 661–672 (2008).
[Crossref] [PubMed]

Holy, T. E.

T. F. Holekamp, D. Turaga, and T. E. Holy, “Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy,” Neuron 57(5), 661–672 (2008).
[Crossref] [PubMed]

Hübener, M.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Hufnagel, L.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Huisken, J.

A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
[Crossref] [PubMed]

J. Huisken and D. Y. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

J. Huisken and D. Y. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM),” Opt. Lett. 32(17), 2608–2610 (2007).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Imamoto, N.

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5(2), 159–161 (2008).
[Crossref] [PubMed]

Jaffe, J.

Jährling, N.

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

S. Kalchmair, N. Jährling, K. Becker, and H. U. Dodt, “Image contrast enhancement in confocal ultramicroscopy,” Opt. Lett. 35(1), 79–81 (2010).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Jankowski, J.

J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
[Crossref] [PubMed]

Jeong, W. K.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Kalchmair, S.

Kawano, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Keck, T.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Keller, P. J.

R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
[Crossref] [PubMed]

P. J. Keller and H. U. Dodt, “Light sheet microscopy of living or cleared specimens,” Curr. Opin. Neurobiol. 22(1), 138–143 (2012).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

P. J. Keller, F. Pampaloni, and E. H. Stelzer, “Life sciences require the third dimension,” Curr. Opin. Cell Biol. 18(1), 117–124 (2006).
[Crossref] [PubMed]

Keller-Peck, C.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Kemper, T. L.

T. L. Kemper and M. Bauman, “Neuropathology of infantile autism,” J. Neuropathol. Exp. Neurol. 57(7), 645–652 (1998).
[Crossref] [PubMed]

M. Bauman and T. L. Kemper, “Histoanatomic observations of the brain in early infantile autism,” Neurology 35(6), 866–874 (1985).
[Crossref] [PubMed]

Khairy, K.

R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Kim, J.

J. Mertz and J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[Crossref] [PubMed]

Kirchhoff, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Kötter, R.

O. Sporns, G. Tononi, and R. Kötter, “The human connectome: A structural description of the human brain,” PLOS Comput. Biol. 1(4), e42 (2005).
[Crossref] [PubMed]

Kramer, E.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Krzic, U.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Kurokawa, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Leischner, U.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Li, A.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Lichtman, J.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Lichtman, J. W.

J. W. Lichtman, J. Livet, and J. R. Sanes, “A technicolour approach to the connectome,” Nat. Rev. Neurosci. 9(6), 417–422 (2008).
[Crossref] [PubMed]

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Liu, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Livet, J.

J. W. Lichtman, J. Livet, and J. R. Sanes, “A technicolour approach to the connectome,” Nat. Rev. Neurosci. 9(6), 417–422 (2008).
[Crossref] [PubMed]

Long, R.

Luo, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Makous, W.

Marcello, M.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

Mauch, C. P.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Mayerich, D.

D. Mayerich, L. Abbott, and B. McCormick, “Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” J. Microsc. 231(1), 134–143 (2008).
[Crossref] [PubMed]

McCormick, B.

D. Mayerich, L. Abbott, and B. McCormick, “Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” J. Microsc. 231(1), 134–143 (2008).
[Crossref] [PubMed]

Mellor, R. H.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Mertz, J.

J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
[Crossref] [PubMed]

J. Mertz and J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[Crossref] [PubMed]

Meyer, D.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Miething, A.

J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
[Crossref] [PubMed]

Milkie, D. E.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Miyawaki, A.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Morgan, J. I.

M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
[Crossref] [PubMed]

Mori, S.

S. Mori, K. Oishi, and A. V. Faria, “White matter atlases based on diffusion tensor imaging,” Curr. Opin. Neurol. 22(4), 362–369 (2009).
[Crossref] [PubMed]

Nerbonne, J. M.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Nguyen, Q. T.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Noda, H.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Oishi, K.

S. Mori, K. Oishi, and A. V. Faria, “White matter atlases based on diffusion tensor imaging,” Curr. Opin. Neurol. 22(4), 362–369 (2009).
[Crossref] [PubMed]

Oppenheim, R. W.

R. R. Buss, W. Sun, and R. W. Oppenheim, “Adaptive roles of programmed cell death during nervous system development,” Annu. Rev. Neurosci. 29(1), 1–35 (2006).
[Crossref] [PubMed]

Pampaloni, F.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

P. J. Keller, F. Pampaloni, and E. H. Stelzer, “Life sciences require the third dimension,” Curr. Opin. Cell Biol. 18(1), 117–124 (2006).
[Crossref] [PubMed]

Pfister, H.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Planchon, T. A.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Reid, R. C.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Rice, D. S.

M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
[Crossref] [PubMed]

Richter, M.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Ritvo, A.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Ritvo, E. R.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Robinson, H.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Rohrbach, A.

F. O. Fahrbach and A. Rohrbach, “Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media,” Nat Commun 3, 632 (2012).
[Crossref] [PubMed]

Saghafi, S.

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

Sakata-Sogawa, K.

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5(2), 159–161 (2008).
[Crossref] [PubMed]

Sakaue-Sawano, A.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Sanes, J. R.

J. W. Lichtman, J. Livet, and J. R. Sanes, “A technicolour approach to the connectome,” Nat. Rev. Neurosci. 9(6), 417–422 (2008).
[Crossref] [PubMed]

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Santella, A.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Saunders, T. E.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Scheibel, A. B.

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Schierloh, A.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Schilling, K.

J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
[Crossref] [PubMed]

Schmidt, A. D.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

Schneider, J.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Schnorrer, F.

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

Schönbauer, C.

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

Sheppard, C. J.

G. Cox and C. J. Sheppard, “Practical limits of resolution in confocal and non-linear microscopy,” Microsc. Res. Tech. 63(1), 18–22 (2004).
[Crossref] [PubMed]

Shimogori, T.

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Siedentopf, H.

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Grössenbestimmung ultramikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Annalen der Physik 10, 1–39 (1903).

Sotelo, C.

C. Sotelo, “Viewing the brain through the master hand of Ramon y Cajal,” Nat. Rev. Neurosci. 4(1), 71–77 (2003).
[Crossref] [PubMed]

Spelman, F. A.

A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170(3), 229–236 (1993).
[Crossref] [PubMed]

Sporns, O.

O. Sporns, G. Tononi, and R. Kötter, “The human connectome: A structural description of the human brain,” PLOS Comput. Biol. 1(4), e42 (2005).
[Crossref] [PubMed]

Stainier, D. Y.

A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
[Crossref] [PubMed]

J. Huisken and D. Y. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

J. Huisken and D. Y. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM),” Opt. Lett. 32(17), 2608–2610 (2007).
[Crossref] [PubMed]

Steffens, H.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Stelzer, E. H.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

P. J. Keller, F. Pampaloni, and E. H. Stelzer, “Life sciences require the third dimension,” Curr. Opin. Cell Biol. 18(1), 117–124 (2006).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Streichan, S. J.

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

Sun, W.

R. R. Buss, W. Sun, and R. W. Oppenheim, “Adaptive roles of programmed cell death during nervous system development,” Annu. Rev. Neurosci. 29(1), 1–35 (2006).
[Crossref] [PubMed]

Swoger, J.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Tokunaga, M.

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5(2), 159–161 (2008).
[Crossref] [PubMed]

Tomer, R.

R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
[Crossref] [PubMed]

Tomomura, M.

M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
[Crossref] [PubMed]

Tononi, G.

O. Sporns, G. Tononi, and R. Kötter, “The human connectome: A structural description of the human brain,” PLOS Comput. Biol. 1(4), e42 (2005).
[Crossref] [PubMed]

Turaga, D.

T. F. Holekamp, D. Turaga, and T. E. Holy, “Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy,” Neuron 57(5), 661–672 (2008).
[Crossref] [PubMed]

Turney, S. G.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Verveer, P. J.

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

Voie, A. H.

A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170(3), 229–236 (1993).
[Crossref] [PubMed]

Wallace, M.

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

Wang, Q.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Webb, W. W.

W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
[Crossref] [PubMed]

Weiler, R.

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

Westermann, R.

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

Williams, R. M.

W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
[Crossref] [PubMed]

Wilson, T.

M. J. Booth and T. Wilson, “Refractive-index-mismatch induced aberrations in single-photon and two-photon microscopy and the use of aberration correction,” J. Biomed. Opt. 6(3), 266–272 (2001).
[Crossref] [PubMed]

T. Wilson and A. R. Carlini, “Size of the detector in confocal imaging systems,” Opt. Lett. 12(4), 227–229 (1987).
[Crossref] [PubMed]

Wittbrodt, J.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Wu, J.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Yan, C.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Yuzaki, M.

M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
[Crossref] [PubMed]

Zeng, S.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Zhang, B.

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

Zieglgänsberger, W.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Zipfel, W. R.

W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
[Crossref] [PubMed]

Zsigmondy, R.

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Grössenbestimmung ultramikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Annalen der Physik 10, 1–39 (1903).

Am. J. Psychiatry (1)

E. R. Ritvo, B. J. Freeman, A. B. Scheibel, T. Duong, H. Robinson, D. Guthrie, and A. Ritvo, “Lower Purkinje cell counts in the cerebella of four autistic subjects: initial findings of the UCLA-NSAC Autopsy Research Report,” Am. J. Psychiatry 143(7), 862–866 (1986).
[PubMed]

Annalen der Physik (1)

H. Siedentopf and R. Zsigmondy, “Uber Sichtbarmachung und Grössenbestimmung ultramikroskopischer Teilchen, mit besonderer Anwendung auf Goldrubingläser,” Annalen der Physik 10, 1–39 (1903).

Annu. Rev. Neurosci. (1)

R. R. Buss, W. Sun, and R. W. Oppenheim, “Adaptive roles of programmed cell death during nervous system development,” Annu. Rev. Neurosci. 29(1), 1–35 (2006).
[Crossref] [PubMed]

Cerebellum (1)

J. Jankowski, A. Miething, K. Schilling, and S. L. Baader, “Physiological purkinje cell death is spatiotemporally organized in the developing mouse cerebellum,” Cerebellum 8(3), 277–290 (2009).
[Crossref] [PubMed]

Curr. Opin. Cell Biol. (1)

P. J. Keller, F. Pampaloni, and E. H. Stelzer, “Life sciences require the third dimension,” Curr. Opin. Cell Biol. 18(1), 117–124 (2006).
[Crossref] [PubMed]

Curr. Opin. Neurobiol. (2)

P. J. Keller and H. U. Dodt, “Light sheet microscopy of living or cleared specimens,” Curr. Opin. Neurobiol. 22(1), 138–143 (2012).
[Crossref] [PubMed]

M. Helmstaedter, K. L. Briggman, and W. Denk, “3D structural imaging of the brain with photons and electrons,” Curr. Opin. Neurobiol. 18(6), 633–641 (2008).
[Crossref] [PubMed]

Curr. Opin. Neurol. (1)

S. Mori, K. Oishi, and A. V. Faria, “White matter atlases based on diffusion tensor imaging,” Curr. Opin. Neurol. 22(4), 362–369 (2009).
[Crossref] [PubMed]

Development (1)

J. Huisken and D. Y. Stainier, “Selective plane illumination microscopy techniques in developmental biology,” Development 136(12), 1963–1975 (2009).
[Crossref] [PubMed]

Eur. J. Neurosci. (1)

M. Tomomura, D. S. Rice, J. I. Morgan, and M. Yuzaki, “Purification of Purkinje cells by fluorescence-activated cell sorting from transgenic mice that express green fluorescent protein,” Eur. J. Neurosci. 14(1), 57–63 (2001).
[Crossref] [PubMed]

Front Syst Neurosci (1)

N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, and H. U. Dodt, “Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy,” Front Syst Neurosci 4, 1 (2010).
[PubMed]

IEEE Trans. Vis. Comput. Graph. (1)

W. K. Jeong, J. Schneider, S. G. Turney, B. E. Faulkner-Jones, D. Meyer, R. Westermann, R. C. Reid, J. Lichtman, and H. Pfister, “Interactive histology of large-scale biomedical image stacks,” IEEE Trans. Vis. Comput. Graph. 16(6), 1386–1395 (2010).
[Crossref] [PubMed]

J. Biomed. Opt. (3)

J. Mertz and J. Kim, “Scanning light-sheet microscopy in the whole mouse brain with HiLo background rejection,” J. Biomed. Opt. 15(1), 016027 (2010).
[Crossref] [PubMed]

M. J. Booth and T. Wilson, “Refractive-index-mismatch induced aberrations in single-photon and two-photon microscopy and the use of aberration correction,” J. Biomed. Opt. 6(3), 266–272 (2001).
[Crossref] [PubMed]

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

J. Comp. Neurol. (1)

J. Altman and S. A. Bayer, “Embryonic development of the rat cerebellum. III. Regional differences in the time of origin, migration, and settling of Purkinje cells,” J. Comp. Neurol. 231(1), 42–65 (1985).
[Crossref] [PubMed]

J. Microsc. (2)

A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc. 170(3), 229–236 (1993).
[Crossref] [PubMed]

D. Mayerich, L. Abbott, and B. McCormick, “Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” J. Microsc. 231(1), 134–143 (2008).
[Crossref] [PubMed]

J. Neuropathol. Exp. Neurol. (1)

T. L. Kemper and M. Bauman, “Neuropathology of infantile autism,” J. Neuropathol. Exp. Neurol. 57(7), 645–652 (1998).
[Crossref] [PubMed]

J. Opt. Soc. Am. A (1)

Microsc. Res. Tech. (1)

G. Cox and C. J. Sheppard, “Practical limits of resolution in confocal and non-linear microscopy,” Microsc. Res. Tech. 63(1), 18–22 (2004).
[Crossref] [PubMed]

Nat Commun (1)

F. O. Fahrbach and A. Rohrbach, “Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media,” Nat Commun 3, 632 (2012).
[Crossref] [PubMed]

Nat. Biotechnol. (1)

W. R. Zipfel, R. M. Williams, and W. W. Webb, “Nonlinear magic: multiphoton microscopy in the biosciences,” Nat. Biotechnol. 21(11), 1369–1377 (2003).
[Crossref] [PubMed]

Nat. Med. (1)

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2011).
[Crossref] [PubMed]

Nat. Methods (9)

U. Krzic, S. Gunther, T. E. Saunders, S. J. Streichan, and L. Hufnagel, “Multiview light-sheet microscope for rapid in toto imaging,” Nat. Methods 9(7), 730–733 (2012).
[Crossref] [PubMed]

R. Tomer, K. Khairy, F. Amat, and P. J. Keller, “Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy,” Nat. Methods 9(7), 755–763 (2012).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

J. A. Conchello and J. W. Lichtman, “Optical sectioning microscopy,” Nat. Methods 2(12), 920–931 (2005).
[Crossref] [PubMed]

M. Tokunaga, N. Imamoto, and K. Sakata-Sogawa, “Highly inclined thin illumination enables clear single-molecule imaging in cells,” Nat. Methods 5(2), 159–161 (2008).
[Crossref] [PubMed]

P. J. Verveer, J. Swoger, F. Pampaloni, K. Greger, M. Marcello, and E. H. Stelzer, “High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy,” Nat. Methods 4(4), 311–313 (2007).
[PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
[Crossref] [PubMed]

Nat. Neurosci. (1)

H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, and A. Miyawaki, “Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain,” Nat. Neurosci. 14(11), 1481–1488 (2011).
[Crossref] [PubMed]

Nat. Rev. Neurosci. (2)

J. W. Lichtman, J. Livet, and J. R. Sanes, “A technicolour approach to the connectome,” Nat. Rev. Neurosci. 9(6), 417–422 (2008).
[Crossref] [PubMed]

C. Sotelo, “Viewing the brain through the master hand of Ramon y Cajal,” Nat. Rev. Neurosci. 4(1), 71–77 (2003).
[Crossref] [PubMed]

Nature (1)

K. L. Briggman, M. Helmstaedter, and W. Denk, “Wiring specificity in the direction-selectivity circuit of the retina,” Nature 471(7337), 183–188 (2011).
[Crossref] [PubMed]

Neurology (1)

M. Bauman and T. L. Kemper, “Histoanatomic observations of the brain in early infantile autism,” Neurology 35(6), 866–874 (1985).
[Crossref] [PubMed]

Neuron (2)

G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP,” Neuron 28(1), 41–51 (2000).
[Crossref] [PubMed]

T. F. Holekamp, D. Turaga, and T. E. Holy, “Fast three-dimensional fluorescence imaging of activity in neural populations by objective-coupled planar illumination microscopy,” Neuron 57(5), 661–672 (2008).
[Crossref] [PubMed]

Opt. Express (2)

Opt. Lett. (3)

PLOS Comput. Biol. (1)

O. Sporns, G. Tononi, and R. Kötter, “The human connectome: A structural description of the human brain,” PLOS Comput. Biol. 1(4), e42 (2005).
[Crossref] [PubMed]

PLoS ONE (1)

K. Becker, N. Jährling, S. Saghafi, R. Weiler, and H. U. Dodt, “Chemical clearing and dehydration of GFP expressing mouse brains,” PLoS ONE 7(3), e33916 (2012).
[Crossref] [PubMed]

Science (4)

A. B. Arrenberg, D. Y. Stainier, H. Baier, and J. Huisken, “Optogenetic control of cardiac function,” Science 330(6006), 971–974 (2010).
[Crossref] [PubMed]

A. Li, H. Gong, B. Zhang, Q. Wang, C. Yan, J. Wu, Q. Liu, S. Zeng, and Q. Luo, “Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain,” Science 330(6009), 1404–1408 (2010).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy,” Science 322(5904), 1065–1069 (2008).
[Crossref] [PubMed]

Other (2)

W. Spalteholz, Uber das Durchsichtigmachen von menschlichen und tierischen Präparaten und seine theoretischen Bedingungen, nebst Anhang: Uber Knochenfärbung. (S. Hirzel, Leipzig, 1914).

A. Bria, L. Silvestri, L. Sacconi, F. S. Pavone, and G. Iannello, “Stitching Terabyte-sized 3D images acquired in confocal ultramicroscopy,” presented at the IEEE International Symposium on Biomedical Imaging (ISBI 2012), Barcelona, Spain, 2–5 May 2012.

Supplementary Material (3)

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Figures (7)

Fig. 1
Fig. 1 Confocal light sheet microscopy (CLSM). (a) Side (upper panel) and top (lower panel) views of the spatial filter operation scheme. The diffraction limited excitation beam (black dashed line) is blurred (blue area) because of sample-induced scattering. The fluorescence light is then emitted both in-focus (green continuous lines) and out-of-focus (green dashed lines): only the in-focus ballistic photons are properly focused in the aperture of the spatial filter (Slit) by the first 4f optical system (objective, Obj and tube lens, TL). The second 4f system (L1, L2) images ballistic photons on the EM-CCD sensor. In the top view, rays originating from different positions are depicted with different hues of green. (b) CLSM optical scheme. The excitation laser beam is scanned by a first galvo mirror (GM1) and focused by a scanning lens (SL) on the specimen. The fluorescence emission orthogonally collected by Obj is de-scanned by a second galvo (GM2) pivoting the linear image onto the slit aperture. A third scanning mirror (GM3) recreates the wide field-like image on the EM-CCD sensor after filtering out of the excitation light by a fluorescence filter (FF). Precision micro-translators allow both 3D motion of the specimen chamber (3D stage) and the movement of excitation (SL) and detection (Obj) optics.

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Fig. 2
Fig. 2 Measurement of radial and axial CLSM point spread functions. Axial (purple circles) and radial (green circles) point spread functions (PSFs) measured in conventional (a) and in confocal modality (b). The best Gaussian fits for axial and radial PSFs are shown by the blue and red lines, respectively. Experimental data have been normalized in area.

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Fig. 3
Fig. 3 Background rejection. (a) Comparison between LSM, SI-LSM and CLSM performed in: excised hippocampus (EH) of a thy1-GFP-M mouse, cerebellum (C) of a L7-GFP mouse and whole brain (WB) of a thy1-GFP-M mouse; post natal day (PND) 15 for all samples. Images are maximum intensity projections of 40 sections (z-step 1 µm). The lookup table saturates 4% of pixels for better visibility and comparison. Scale bars, 100 µm. (b) Intensity profiles (green: LSM; blue: SI-LSM; red: CLSM) along the dotted purple lines highlighted in panel (a). The profiles are normalized with respect to their maximum intensity value. (c) Contrast enhancement of SI-LSM (in blue) and CLSM (in red) with respect to LSM, calculated from data acquired in EH, C, WB. Each bar represents the mean and standard error of the mean. The green line refers to no contrast enhancement.

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Fig. 4
Fig. 4 Background rejection using higher NA optics. Purkinje cells in the cerebellum of a PND 15 L7-GFP mouse, imaged with LSM (a) and CLSM (b) using an objective with higher numerical aperture (Nikon 50 × , NA = 0.45). Slit width was 15 µm, corresponding to 0.6 µm in object space. Images are maximum intensity projections of 160 sections (z-step 1 µm). For better visibility and comparison a nonlinear gamma transformation (γ = 0.35) was applied to the images, and the lookup table was linearly modified to eliminate 4% outliers. Scale bars, 100 µm

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Fig. 5
Fig. 5 Purkinje cells micron-scale neuroanatomy in the whole cerebellum. (a) 3D volume rendering of a PND-10 L7-GFP mouse cerebellum. The superimposed planes refer to transverse (red), sagittal (green) and coronal (blue) digital sections shown in panel (b), (c) and (d) respectively. (b-d) Maximum intensity projections of 40 µm thick slabs. Scale bars, 1 mm. (e, f) 10 × magnification of the regions highlighted by the yellow boxes in panels (b) and (d). The lookup table saturates 2% of pixels for better visibility.

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Fig. 6
Fig. 6 Micron-scale neuroanatomy of a whole thy1-GFP-M brain. (a) Isosurface perspective (P) and transverse (T), coronal (C) and sagittal (S) contours of an entire PND-15 mouse brain. The volumes highlighted by the blue and red boxes are magnified in panel (b) and (c) respectively. (b) Volume rendering of a portion of hippocampus. (c) Volume rendering of a portion of superior colliculus. (d) Soma segmentation and process tracing of selected fluorescent neurons present in the red box (c). For clarity, each neuron was drawn with a different color. Scale bars, 200 µm.

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Fig. 7
Fig. 7 Stitching processing pipeline. All the processing steps and their action on both data and metadata are illustrated. On the right, for each step, it is indicated the number of reading and writing operations. Steps that are performed at the same time are connected with arrowless lines.

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Tables (1)

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Table 1 Comparison of Different Techniques for the Study of Neuronal Anatomy

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Equations (2)

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f'−f=d'−d≈ d'( 1−1/n )≈ 0.36 d'
I( x,y ) = i=1,...,20 max I i ( x,y )− γ i=1,...,20 min I i ( x,y )

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