CLARITY for mapping the nervous system (original) (raw)
References
Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature advance online publication, doi:10.1038/nature12107 (10 April 2013).
Petersen, C.C.H. The functional organization of the barrel cortex. Neuron56, 339–355 (2007). CAS Google Scholar
Mombaerts, P. et al. Visualizing an olfactory sensory map. Cell87, 675–686 (1996). ArticleCAS Google Scholar
Deisseroth, K. Optogenetics and psychiatry: applications, challenges, and opportunities. Biol. Psychiatry71, 1030–1032 (2012). Article Google Scholar
Kasthuri, N. & Lichtman, J.W. The rise of the 'projectome'. Nat. Methods4, 307–308 (2007). ArticleCAS Google Scholar
Nicholson, C. Diffusion in brain extracellular space. Brain6, 1277–1340 (2008). Google Scholar
Cheong, W., Prahl, S. & Welch, A. A review of the optical properties of biological tissues. IEEE J. Quantum Electronics26, 2166–2185 (1990). Article Google Scholar
Helmchen, F. & Denk, W. Deep tissue two-photon microscopy. Nat. Methods2, 932–940 (2005). ArticleCAS Google Scholar
Rauschning, W. Surface cryoplanning: a technique for clinical anatomical correlations. Uppsala J. Med. Sci.91, 251–255 (1986). ArticleCAS Google Scholar
Toga, A.W., Ambach, K., Quinn, B., Hutchin, M. & Burton, J.S. Postmortem anatomy from cryosectioned whole human brain. J. Neurosci. Methods54, 239–252 (1994). ArticleCAS Google Scholar
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
McCormick, B.H. et al. Construction of anatomically correct models of mouse brain networks. Neurocomputing58–60, 379–386 (2004). Article Google Scholar
Li, A. et al. Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain. Science330, 1404–1408 (2010). ArticleCAS Google Scholar
Tsai, P. et al. All-optical histology using ultrashort laser pulses. Neuron39, 27–41 (2003). ArticleCAS Google Scholar
Ragan, T. et al. Serial two-photon tomography for automated ex vivo mouse brain imaging. Nat. Methods9, 255–258 (2012). ArticleCAS Google Scholar
Denk, W. & Horstmann, H. Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol.2, e329 (2004). Article Google Scholar
Micheva, K.D. & Smith, S.J. Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron55, 25–36 (2007). ArticleCAS Google Scholar
Osten, P. & Margrie, T.W. Mapping brain circuitry with a light microscope. Nat. Methods10, 515–523 (2013). ArticleCAS Google Scholar
Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature450, 56–62 (2007). ArticleCAS Google Scholar
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
Kleinfeld, D. et al. Large-scale automated histology in the pursuit of connectomes. J. Neurosci.31, 16125–16138 (2011). ArticleCAS Google Scholar
Bock, D.D. et al. Network anatomy and in vivo physiology of visual cortical neurons. Nature471, 177–182 (2011). ArticleCAS Google Scholar
Briggman, K.L., Helmstaedter, M. & Denk, W. Wiring specificity in the direction-selectivity circuit of the retina. Nature471, 183–188 (2011). ArticleCAS Google Scholar
Dodt, H., Leischner, U. & Schierloh, A. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods4, 331–336 (2007). ArticleCAS Google Scholar
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
Hama, H. et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci.14, 1481–1488 (2011). ArticleCAS Google Scholar
Keller, P.J. et al. Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy. Nat. Methods7, 637–642 (2010). ArticleCAS Google Scholar
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. Methods8, 757–760 (2011). ArticleCAS Google Scholar
Tomer, R., Khairy, K., Amat, F. & Keller, P.J. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat. Methods9, 755–763 (2012). ArticleCAS Google Scholar
Krzic, U., Gunther, S., Saunders, T.E., Streichan, S.J. & Hufnagel, L. Multiview light-sheet microscope for rapid in toto imaging. Nat. Methods9, 730–733 (2012). ArticleCAS Google Scholar
Keller, P.J., Schmidt, A.D., Wittbrodt, J. & Stelzer, E.H.K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science322, 1065–1069 (2008). ArticleCAS Google Scholar
Planchon, T.A. et al. Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat. Methods8, 417–423 (2011). ArticleCAS Google Scholar
Dani, A., Huang, B., Bergan, J., Dulac, C. & Zhuang, X. Superresolution imaging of chemical synapses in the brain. Neuron68, 843–856 (2010). ArticleCAS Google Scholar
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. Neuron68, 639–653 (2010). ArticleCAS Google Scholar
Wählby, C. & Erlandsson, F. Sequential immunofluorescence staining and image analysis for detection of large numbers of antigens in individual cell nuclei. Cytometry47, 32–41 (2002). Article Google Scholar
Feinberg, E.H. et al. GFP reconstitution across synaptic partners (GRASP) defines cell contacts and synapses in living nervous systems. Neuron57, 353–363 (2008). ArticleCAS Google Scholar
Wickersham, I.R. & Feinberg, E.H. New technologies for imaging synaptic partners. Curr. Opin. Neurobiol.22, 121–127 (2012). ArticleCAS Google Scholar
Gordon, M.D. & Scott, K. Motor control in a Drosophila taste circuit. Neuron61, 373–384 (2009). ArticleCAS Google Scholar
Kim, J. et al. mGRASP enables mapping mammalian synaptic connectivity with light microscopy. Nat. Methods9, 96–102 (2012). ArticleCAS Google Scholar
Wickersham, I. et al. Retrograde neuronal tracing with a deletion-mutant rabies virus. Nat. Methods4, 47–49 (2007). ArticleCAS Google Scholar
Miyamichi, K. et al. Cortical representations of olfactory input by trans-synaptic tracing. Nature472, 191–196 (2011). ArticleCAS Google Scholar
Liu, X. et al. Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature484, 381–385 (2012). ArticleCAS Google Scholar
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).
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. Development101, 697–713 (1987). CASPubMed Google Scholar
Helmstaedter, M. Cellular-resolution connectomics: challenges of dense neural circuit reconstruction. Nat. Methods10, 501–507 (2013). ArticleCAS Google Scholar
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). ArticleCAS Google Scholar
Ahrens, M.B. et al. Brain-wide neuronal dynamics during motor adaptation in zebrafish. Nature485, 471–477 (2012). ArticleCAS Google Scholar
Ziv, Y. et al. Long-term dynamics of CA1 hippocampal place codes. Nat. Neurosci.16, 264–266 (2013). ArticleCAS Google Scholar
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. Methods10, 413–420 (2013). ArticleCAS Google Scholar
Alivisatos, P. et al. The brain activity map. Science339, 1284–1285 (2013). ArticleCAS Google Scholar