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Light-Sheet Microscopy for Whole-Brain Imaging

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Advanced Optical Methods for Brain Imaging

Part of the book series: Progress in Optical Science and Photonics ((POSP,volume 5))

Abstract

The brain is a complex system of interconnected and interacting structures. To fully understand its architecture, we need an imaging method that is capable of imaging the entire brain at sufficient resolution to capture single cells and projections and discriminate between cells with different functions. This has been made possible by the combination of light-sheet fluorescence microscopy with optical tissue clearing. In this chapter, we briefly describe the currently known methods of tissue clearing, discussing the advantages and disadvantages of different approaches. Next, we explain the principles of light-sheet fluorescence microscopy focusing on its application, the whole-brain imaging. We discuss the technical challenges specific to this approach, in particular those resulting from high refractive index of cleared tissue as well as from the large size of collected data. Finally, we list some of the recent papers which make use of light-sheet imaging of cleared tissue.

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References

  1. A.H. Voie, D.H. Burns, F.A. Spelman, J. Microsc. 170, 229 (1993)

    Article  Google Scholar 

  2. H. Siedentopf, R. Zsigmondy, Ann. Physik 4, 1 (1903)

    Google Scholar 

  3. W. Spalteholz, Über Das Durchsichtigmachen von Menschlichen Und Tierischen Präparaten (S. Hirzel, Leipzig, 1914)

    Google Scholar 

  4. H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C.P. Mauch, K. Deininger, J.M. Deussing, M. Eder, W. Zieglgänsberger, K. Becker, Nat. Meth. 4, 331 (2007)

    Article  Google Scholar 

  5. D.S. Richardson, J.W. Lichtman, Cell 162, 246 (2015)

    Article  Google Scholar 

  6. E.A. Susaki, H.R. Ueda, Cell Chem. Biol. 23, 137 (2016)

    Article  Google Scholar 

  7. L. Silvestri, I. Costantini, L. Sacconi, F.S. Pavone, J. Biomed. Opt. 21, 081205 (2016)

    Article  Google Scholar 

  8. T. Yu, Y. Qi, H. Gong, Q. Luo, and D. Zhu, J Biophotonics (2017)

    Google Scholar 

  9. H. Hama, H. Kurokawa, H. Kawano, R. Ando, T. Shimogori, H. Noda, K. Fukami, A. Sakaue-Sawano, A. Miyawaki, Nat. Neurosci. 14, 1481 (2011)

    Article  Google Scholar 

  10. E.A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T.M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, H.R. Ueda, Cell 157, 726 (2014)

    Article  Google Scholar 

  11. K. Chung, K. Deisseroth, Nat. Meth. 10, 508 (2013)

    Article  Google Scholar 

  12. B. Yang, J.B. Treweek, R.P. Kulkarni, B.E. Deverman, C.-K. Chen, E. Lubeck, S. Shah, L. Cai, V. Gradinaru, Cell 158, 945 (2014)

    Article  Google Scholar 

  13. M.K. Schwarz, A. Scherbarth, R. Sprengel, J. Engelhardt, P. Theer, G. Giese, PLoS ONE 10, e0124650 (2015)

    Article  Google Scholar 

  14. C. Pan, R. Cai, F.P. Quacquarelli, A. Ghasemigharagoz, A. Lourbopoulos, P. Matryba, N. Plesnila, M. Dichgans, F. Hellal, A. Ertürk, Nat. Meth. 13, 859 (2016)

    Article  Google Scholar 

  15. M. Stefaniuk, E.J. Gualda, M. Pawlowska, D. Legutko, P. Matryba, P. Koza, W. Konopka, D. Owczarek, M. Wawrzyniak, P. Loza-Alvarez, L. Kaczmarek, Sci. Rep. 6, 28209 (2016)

    Article  Google Scholar 

  16. M.-T. Ke, Y. Nakai, S. Fujimoto, R. Takayama, S. Yoshida, T.S. Kitajima, M. Sato, T. Imai, Cell Rep. 14, 2718 (2016)

    Article  Google Scholar 

  17. H. Hama, H. Hioki, K. Namiki, T. Hoshida, H. Kurokawa, F. Ishidate, T. Kaneko, T. Akagi, T. Saito, T. Saido, A. Miyawaki, Nat. Neurosci. 18, 1518 (2015)

    Article  Google Scholar 

  18. K. Tainaka, S.I. Kubota, T.Q. Suyama, E.A. Susaki, D. Perrin, M. Ukai-Tadenuma, H. Ukai, H.R. Ueda, Cell 159, 911 (2014)

    Article  Google Scholar 

  19. P. Matryba, L. Bozycki, M. Pawłowska, L. Kaczmarek, M. Stefaniuk, J. Biophotonics (2017)

    Google Scholar 

  20. N. Renier, Z. Wu, D.J. Simon, J. Yang, P. Ariel, M. Tessier-Lavigne, Cell 159, 896 (2014)

    Article  Google Scholar 

  21. N. Renier, E.L. Adams, C. Kirst, Z. Wu, R. Azevedo, J. Kohl, A.E. Autry, L. Kadiri, K. Umadevi Venkataraju, Y. Zhou, V.X. Wang, C.Y. Tang, O. Olsen, C. Dulac, P. Osten, M. Tessier-Lavigne, Cell 165, 1789 (2016)

    Article  Google Scholar 

  22. F. Chen, P.W. Tillberg, E.S. Boyden, Science 347, 543 (2015)

    Article  Google Scholar 

  23. J. Huisken, J. Swoger, F.D. Bene, J. Wittbrodt, E.H.K. Stelzer, Science 305, 1007 (2004)

    Article  Google Scholar 

  24. K. Greger, J. Swoger, E.H.K. Stelzer, Rev. Sci. Instrum. 78, 023705 (2007)

    Article  Google Scholar 

  25. P.J. Keller, A.D. Schmidt, J. Wittbrodt, E.H.K. Stelzer, Science 322, 1065 (2008)

    Article  Google Scholar 

  26. L. Silvestri, A. Bria, L. Sacconi, G. Iannello, F. Pavone, Opt. Express 20, 20582 (2012)

    Article  Google Scholar 

  27. E. Baumgart, U. Kubitscheck, Opt. Express OE 20, 21805 (2012)

    Article  Google Scholar 

  28. C.J. Engelbrecht, E.H. Stelzer, Opt. Lett. OL 31, 1477 (2006)

    Article  Google Scholar 

  29. T.A. Planchon, L. Gao, D.E. Milkie, M.W. Davidson, J.A. Galbraith, C.G. Galbraith, E. Betzig, Nat. Meth. 8, 417 (2011)

    Article  Google Scholar 

  30. K.M. Dean, R. Fiolka, Opt. Express 22, 26141 (2014)

    Article  Google Scholar 

  31. R. Tomer, L. Ye, B. Hsueh, K. Deisseroth, Nat. Protoc. 9, 1682 (2014)

    Article  Google Scholar 

  32. D.P. Ryan, E.A. Gould, G.J. Seedorf, O. Masihzadeh, S.H. Abman, S. Vijayaraghavan, W.B. Macklin, D. Restrepo, D.P. Shepherd, Nat. Commun. 8, 612 (2017)

    Article  Google Scholar 

  33. J. Huisken, D.Y.R. Stainier, Opt. Lett. 32, 2608 (2007)

    Article  Google Scholar 

  34. J. Fehrenbach, P. Weiss, C. Lorenzo, IEEE Trans. Image Process. 21, 4420 (2012)

    Article  MathSciNet  Google Scholar 

  35. X. Liang, Y. Zang, D. Dong, L. Zhang, M. Fang, X. Yang, A. Arranz, J. Ripoll, H. Hui, J. Tian, J. Biomed. Opt. 21, 106005 (2016)

    Article  Google Scholar 

  36. L. Silvestri, L. Sacconi, F.S. Pavone, Microsc. Res. Tech. 77, 483 (2014)

    Article  Google Scholar 

  37. V. Marx, Nat. Meth. 11, 1209 (2014)

    Article  Google Scholar 

  38. L. Silvestri, M. Paciscopi, P. Soda, F. Biamonte, G. Iannello, P. Frasconi, F.S. Pavone, Front. Neuroanat. 9, 68 (2015)

    Article  Google Scholar 

  39. J. Doerr, M.K. Schwarz, D. Wiedermann, A. Leinhaas, A. Jakobs, F. Schloen, I. Schwarz, M. Diedenhofen, N.C. Braun, P. Koch, D.A. Peterson, U. Kubitscheck, M. Hoehn, O. Brüstle, Nat. Commun. 8, 14162 (2017)

    Article  Google Scholar 

  40. Y. Ding, J. Lee, J. Ma, K. Sung, T. Yokota, N. Singh, M. Dooraghi, P. Abiri, Y. Wang, R.P. Kulkarni, A. Nakano, T.P. Nguyen, P. Fei, T.K. Hsiai, Sci. Rep. 7, 42209 (2017)

    Article  Google Scholar 

  41. E.J. Gualda, T. Vale, P. Almada, J.A. Feijó, G.G. Martins, N. Moreno, Nat. Meth. 10, 599 (2013)

    Article  Google Scholar 

  42. P.G. Pitrone, J. Schindelin, L. Stuyvenberg, S. Preibisch, M. Weber, K.W. Eliceiri, J. Huisken, P. Tomancak, Nat. Meth. 10, 598 (2013)

    Article  Google Scholar 

  43. A.D. Edelstein, M.A. Tsuchida, N. Amodaj, H. Pinkard, R.D. Vale, N. Stuurman, J. Biol. Methods 1, e10 (2014)

    Article  Google Scholar 

  44. L. Ye, W.E. Allen, K.R. Thompson, Q. Tian, B. Hsueh, C. Ramakrishnan, A.-C. Wang, J.H. Jennings, A. Adhikari, C.H. Halpern, I.B. Witten, A.L. Barth, L. Luo, J.A. McNab, K. Deisseroth, Cell 165, 1776 (2016)

    Article  Google Scholar 

  45. A. Bria, G. Iannello, BMC Bioinform. 13, 316 (2012)

    Article  Google Scholar 

  46. S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, IEEE Trans. Med. Imaging 29, 196 (2010)

    Article  Google Scholar 

  47. M. Paciscopi, L. Silvestri, F.S. Pavone, P. Frasconi, arXiv:1511.01168 [Cs] (2015)

    Google Scholar 

  48. W. Menegas, J.F. Bergan, S.K. Ogawa, Y. Isogai, K.U. Venkataraju, P. Osten, N. Uchida, M. Watabe-Uchida, ELife Sci. 4, e10032 (2015)

    Google Scholar 

  49. A. Ertürk, K. Becker, N. Jährling, C.P. Mauch, C.D. Hojer, J.G. Egen, F. Hellal, F. Bradke, M. Sheng, H.-U. Dodt, Nat. Protoc. 7, 1983 (2012)

    Article  Google Scholar 

  50. K. Chung, J. Wallace, S.-Y. Kim, S. Kalyanasundaram, A.S. Andalman, T.J. Davidson, J.J. Mirzabekov, K.A. Zalocusky, J. Mattis, A.K. Denisin, S. Pak, H. Bernstein, C. Ramakrishnan, L. Grosenick, V. Gradinaru, K. Deisseroth, Nature 497, 332 (2013)

    Article  Google Scholar 

  51. H.-L. (Liz) Hsiang, J.R. Epp, M.C. van den Oever, C. Yan, A.J. Rashid, N. Insel, L. Ye, Y. Niibori, K. Deisseroth, P.W. Frankland, S.A. Josselyn, J. Neurosci. 34, 14115 (2014)

    Google Scholar 

  52. P. Osten, T.W. Margrie, Nat. Methods 10, 515 (2013)

    Article  Google Scholar 

  53. T. Ragan, L.R. Kadiri, K.U. Venkataraju, K. Bahlmann, J. Sutin, J. Taranda, I. Arganda-Carreras, Y. Kim, H.S. Seung, P. Osten, Nat. Meth. 9, 255 (2012)

    Article  Google Scholar 

  54. Y. Kim, K.U. Venkataraju, K. Pradhan, C. Mende, J. Taranda, S.C. Turaga, I. Arganda-Carreras, L. Ng, M.J. Hawrylycz, K.S. Rockland, H.S. Seung, P. Osten, Cell Rep. 10, 292 (2015)

    Article  Google Scholar 

  55. A.R. Nectow, M. Schneeberger, H. Zhang, B.C. Field, N. Renier, E. Azevedo, B. Patel, Y. Liang, S. Mitra, M. Tessier-Lavigne, M.-H. Han, J.M. Friedman, Cell 170, 429 (2017)

    Article  Google Scholar 

  56. N. Renier, C. Dominici, R.S. Erzurumlu, C.F. Kratochwil, F.M. Rijli, P. Gaspar, A. Chédotal, ELife Sci. 6, e23494 (2017)

    Google Scholar 

  57. E.L. Sylwestrak, P. Rajasethupathy, M.A. Wright, A. Jaffe, K. Deisseroth, Cell 164, 792 (2016)

    Article  Google Scholar 

  58. M.B. Ahrens, M.B. Orger, D.N. Robson, J.M. Li, P.J. Keller, Nat. Meth. 10, 413 (2013)

    Article  Google Scholar 

  59. T. Panier, S.A. Romano, R. Olive, T. Pietri, G. Sumbre, R. Candelier, G. Debrégeas, Front. Neural Circuits 7, 65 (2013)

    Article  Google Scholar 

  60. N. Vladimirov, Y. Mu, T. Kawashima, D.V. Bennett, C.-T. Yang, L.L. Looger, P.J. Keller, J. Freeman, M.B. Ahrens, Nat. Meth. 11, 883 (2014)

    Article  Google Scholar 

  61. Z. Yang, P. Haslehurst, S. Scott, N. Emptage, K. Dholakia, Sci Rep 6, (2016)

    Google Scholar 

  62. Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, H. Shroff, PNAS 108, 17708 (2011)

    Article  Google Scholar 

  63. K. Ando, Q. Laborde, A. Lazar, D. Godefroy, I. Youssef, M. Amar, A. Pooler, M.-C. Potier, B. Delatour, C. Duyckaerts, Acta Neuropathol. 128, 457 (2014)

    Article  Google Scholar 

  64. T. Liebmann, N. Renier, K. Bettayeb, P. Greengard, M. Tessier-Lavigne, M. Flajolet, Cell Rep. 16, 1138 (2016)

    Article  Google Scholar 

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Acknowledgements

M. P. and D. L. received support from NCN Grant UMO-2015/17/B/NZ4/02631. M. S. and L. K. acknowledge TEAM Grant FNP (FNP).

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Authors and Affiliations

  1. Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093, Warsaw, Poland

    Monika Pawłowska, Marzena Stefaniuk, Diana Legutko & Leszek Kaczmarek

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  1. Monika Pawłowska
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  2. Marzena Stefaniuk
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  3. Diana Legutko
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  4. Leszek Kaczmarek
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Correspondence to Monika Pawłowska .

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Editors and Affiliations

  1. Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan

    Fu-Jen Kao

  2. Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA

    Gerd Keiser

  3. Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan

    Ankur Gogoi

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Pawłowska, M., Stefaniuk, M., Legutko, D., Kaczmarek, L. (2019). Light-Sheet Microscopy for Whole-Brain Imaging. In: Kao, FJ., Keiser, G., Gogoi, A. (eds) Advanced Optical Methods for Brain Imaging. Progress in Optical Science and Photonics, vol 5. Springer, Singapore. https://doi.org/10.1007/978-981-10-9020-2_3

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  • DOI: https://doi.org/10.1007/978-981-10-9020-2_3

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