CLARITY for mapping the nervous system (original) (raw)

References

  1. Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature advance online publication, doi:10.1038/nature12107 (10 April 2013).
  2. Petersen, C.C.H. The functional organization of the barrel cortex. Neuron 56, 339–355 (2007).
    CAS Google Scholar
  3. Mombaerts, P. et al. Visualizing an olfactory sensory map. Cell 87, 675–686 (1996).
    Article CAS Google Scholar
  4. Deisseroth, K. Optogenetics and psychiatry: applications, challenges, and opportunities. Biol. Psychiatry 71, 1030–1032 (2012).
    Article Google Scholar
  5. Kasthuri, N. & Lichtman, J.W. The rise of the 'projectome'. Nat. Methods 4, 307–308 (2007).
    Article CAS Google Scholar
  6. Nicholson, C. Diffusion in brain extracellular space. Brain 6, 1277–1340 (2008).
    Google Scholar
  7. Cheong, W., Prahl, S. & Welch, A. A review of the optical properties of biological tissues. IEEE J. Quantum Electronics 26, 2166–2185 (1990).
    Article Google Scholar
  8. Helmchen, F. & Denk, W. Deep tissue two-photon microscopy. Nat. Methods 2, 932–940 (2005).
    Article CAS Google Scholar
  9. Rauschning, W. Surface cryoplanning: a technique for clinical anatomical correlations. Uppsala J. Med. Sci. 91, 251–255 (1986).
    Article CAS Google Scholar
  10. Toga, A.W., Ambach, K., Quinn, B., Hutchin, M. & Burton, J.S. Postmortem anatomy from cryosectioned whole human brain. J. Neurosci. Methods 54, 239–252 (1994).
    Article CAS Google Scholar
  11. Ewald, A.J., McBride, H., Reddington, M., Fraser, S.E. & Kerschmann, R. Surface imaging microscopy, an automated method for visualizing whole embryo samples in three dimensions at high resolution. Dev. Dyn. 225, 369–375 (2002).
    Article Google Scholar
  12. McCormick, B.H. et al. Construction of anatomically correct models of mouse brain networks. Neurocomputing 58–60, 379–386 (2004).
    Article Google Scholar
  13. Li, A. et al. Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain. Science 330, 1404–1408 (2010).
    Article CAS Google Scholar
  14. Tsai, P. et al. All-optical histology using ultrashort laser pulses. Neuron 39, 27–41 (2003).
    Article CAS Google Scholar
  15. Ragan, T. et al. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat. Methods 9, 255–258 (2012).
    Article CAS Google Scholar
  16. Denk, W. & Horstmann, H. Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2, e329 (2004).
    Article Google Scholar
  17. Micheva, K.D. & Smith, S.J. Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 55, 25–36 (2007).
    Article CAS Google Scholar
  18. Osten, P. & Margrie, T.W. Mapping brain circuitry with a light microscope. Nat. Methods 10, 515–523 (2013).
    Article CAS Google Scholar
  19. Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56–62 (2007).
    Article CAS Google Scholar
  20. Tsai, P. et al. Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of cell nuclei and microvessels. J. Neurosci. 18, 14553–14570 (2009).
    Article Google Scholar
  21. Kleinfeld, D. et al. Large-scale automated histology in the pursuit of connectomes. J. Neurosci. 31, 16125–16138 (2011).
    Article CAS Google Scholar
  22. Bock, D.D. et al. Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177–182 (2011).
    Article CAS Google Scholar
  23. Briggman, K.L., Helmstaedter, M. & Denk, W. Wiring specificity in the direction-selectivity circuit of the retina. Nature 471, 183–188 (2011).
    Article CAS Google Scholar
  24. Dodt, H., Leischner, U. & Schierloh, A. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331–336 (2007).
    Article CAS Google Scholar
  25. Ertürk, A., Mauch, C., Hellal, F. & Förstner, F. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat. Med. 18, 166–171 (2012).
    Article Google Scholar
  26. Hama, H. et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14, 1481–1488 (2011).
    Article CAS Google Scholar
  27. Keller, P.J. et al. Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat. Methods 7, 637–642 (2010).
    Article CAS Google Scholar
  28. Truong, T.V., Supatto, W., Koos, D.S., Choi, J.M. & Fraser, S.E. Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nat. Methods 8, 757–760 (2011).
    Article CAS Google Scholar
  29. Tomer, R., Khairy, K., Amat, F. & Keller, P.J. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat. Methods 9, 755–763 (2012).
    Article CAS Google Scholar
  30. Krzic, U., Gunther, S., Saunders, T.E., Streichan, S.J. & Hufnagel, L. Multiview light-sheet microscope for rapid in toto imaging. Nat. Methods 9, 730–733 (2012).
    Article CAS Google Scholar
  31. Keller, P.J., Schmidt, A.D., Wittbrodt, J. & Stelzer, E.H.K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065–1069 (2008).
    Article CAS Google Scholar
  32. Planchon, T.A. et al. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods 8, 417–423 (2011).
    Article CAS Google Scholar
  33. Dani, A., Huang, B., Bergan, J., Dulac, C. & Zhuang, X. Superresolution imaging of chemical synapses in the brain. Neuron 68, 843–856 (2010).
    Article CAS Google Scholar
  34. Micheva, K.D., Busse, B., Weiler, N.C., O'Rourke, N. & Smith, S.J. Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron 68, 639–653 (2010).
    Article CAS Google Scholar
  35. Wählby, C. & Erlandsson, F. Sequential immunofluorescence staining and image analysis for detection of large numbers of antigens in individual cell nuclei. Cytometry 47, 32–41 (2002).
    Article Google Scholar
  36. Feinberg, E.H. et al. GFP reconstitution across synaptic partners (GRASP) defines cell contacts and synapses in living nervous systems. Neuron 57, 353–363 (2008).
    Article CAS Google Scholar
  37. Wickersham, I.R. & Feinberg, E.H. New technologies for imaging synaptic partners. Curr. Opin. Neurobiol. 22, 121–127 (2012).
    Article CAS Google Scholar
  38. Gordon, M.D. & Scott, K. Motor control in a Drosophila taste circuit. Neuron 61, 373–384 (2009).
    Article CAS Google Scholar
  39. Kim, J. et al. mGRASP enables mapping mammalian synaptic connectivity with light microscopy. Nat. Methods 9, 96–102 (2012).
    Article CAS Google Scholar
  40. Wickersham, I. et al. Retrograde neuronal tracing with a deletion-mutant rabies virus. Nat. Methods 4, 47–49 (2007).
    Article CAS Google Scholar
  41. Miyamichi, K. et al. Cortical representations of olfactory input by trans-synaptic tracing. Nature 472, 191–196 (2011).
    Article CAS Google Scholar
  42. Liu, X. et al. Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature 484, 381–385 (2012).
    Article CAS Google Scholar
  43. Guenthner, C.J., Miyamichi, K., Yang, H., Heller, H.C. & Luo, L. Permanent genetic access to transiently active neurons using targeted recombination in active populations (TRAP). Neuron (in the press).
  44. Godement, P., Vanselow, J., Thanos, S. & Bonhoeffer, F. A study in developing visual systems with a new method of staining neurones and their processes in fixed tissue. Development 101, 697–713 (1987).
    CAS PubMed Google Scholar
  45. Helmstaedter, M. Cellular-resolution connectomics: challenges of dense neural circuit reconstruction. Nat. Methods 10, 501–507 (2013).
    Article CAS Google Scholar
  46. Dombeck, D.A., Graziano, M.S. & Tank, D.W. Functional clustering of neurons in motor cortex determined by cellular resolution imaging in awake behaving mice. J. Neurosci. 29, 13751–13760 (2009).
    Article CAS Google Scholar
  47. Ahrens, M.B. et al. Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature 485, 471–477 (2012).
    Article CAS Google Scholar
  48. Ziv, Y. et al. Long-term dynamics of CA1 hippocampal place codes. Nat. Neurosci. 16, 264–266 (2013).
    Article CAS Google Scholar
  49. Ahrens, M.B., Orger, M.B., Robson, D.N., Li, J.M. & Keller, P.J. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat. Methods 10, 413–420 (2013).
    Article CAS Google Scholar
  50. Alivisatos, P. et al. The brain activity map. Science 339, 1284–1285 (2013).
    Article CAS Google Scholar

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