Array tomography (AT) is a new high-throughput proteometric imaging method offering unprecedented capabilities for high-resolution imaging of tissue molecular architectures.  AT is based on (1) automated physical, ultrathin sectioning of tissue specimens embedded in hydrophilic resin, (2)  construction of planar arrays of such serial sections on optical coverslips, (3) staining and imaging of these  arrays, and (4) computational reconstruction into three dimensions, followed by (5) volumetric image analysis.  Because these arrays are very effectively stabilized by the glass substrate, they can withstand many repeated cycles of antibody staining, imaging and elution.  This permits the imaging of large numbers (i.e., 20 or more) of antibodies on each individual section.

Methodology:

Micheva, K.D., and Smith, S.J (2007)  Array tomography: A new tool for imaging the molecular architecture and ultrastructure of neural circuits.  Neuron 55:25-36.

Micheva, K.D., Busse, B.L., Weiler, N.C., O'Rourke, N., Smith, S.J (2010) Single-synapse analysis of a diverse synapse population: Proteomic imaging methods and markers. Neuron 68:639-653 

Micheva, K.D., O’Rourke, N., Busse, B., and Smith, S.J (2010) Array Tomography: High-Resolution Three-Dimensional Immunofluorescence.  In: Imaging: A Laboratory Manual, 3rd Ed.  Cold Spring Harbor Press, Ch. 45, pp. 697-719. 

Applications:

Appelbaum, L., Wang, G., Yokogawa, T., Skariah, G.M., Smith, S.J, Mourrain, P. and Mignot, E. (2010) Circadian and homeostatic regulation of structural synaptic plasticity in hypocretin neurons. Neuron 68:87-98.

Li, L., Tasic, B., Micheva, K.D., Ivanov, V.M., Spletter, M.L., Smith, S.J, Luo, L. (2010) Visualizing the distribution of synapses from individual neurons in the mouse brain.  PLoS One 5(7):e11503.

Appelbaum, L., Wang, G.X., Maro, G.S., Mori, R., Tovin, A., Marin, W., Yokogawa, T., Kawakami, K., Smith, S.J., Gothilf, Y., Mignot, E. and Mourrain, P. (2009) Sleep-wake regulation and hypocretin-melatonin interaction in zebrafish. Proc Natl Acad Sci U S A 106(51):21942-7.

Datwani, A., McConnell, M.J., Kanold, P.O., Micheva, K.D., Busse, B., Shamloo, M., Smith, S.J and Shatz, C.J. (2009)  Classical MHCI molecules regulate retinogeniculate refinement and limit ocular dominance plasticity. Neuron 64:463-70.

Eroglu, C., Allen, N.J., Susman, MW, O'Rourke, N.A., Park, C.Y., Ozkan, E., Chakraborty, C., Mulinyawe, S.B., Annis, D.S., Huberman, A.D., Green, E.M., Lawler, J., Dolmetsch, R., Garcia, K.C., Smith, S.J, Luo, Z.D., Rosenthal, A., Mosher, D.F. and Barres, B.A. (2009) Gabapentin receptor alpha2delta-1 is a neuronal thrombospondin receptor responsible for excitatory CNS synaptogenesis. Cell 139:380-92.

Koffie, R.M., Meyer-Luehmann, M., Hashimoto, T., Adams, K.W., Mielke, M.L., Garcia-Alloza, M., Micheva, K.D., Smith, S.J, Kim, M.L., Lee, V.M., Hyman, B.T., and Spires-Jones, T.L. (2009) Oligomeric amyloid beta associates with postsynaptic densities and correlates with excitatory synapse loss near senile plaques.  Proc. Natl. Acad. Sci., USA 106: 4012-7.

Stevens, B., Allen, N.J., Vazquez, L.E,. Howell, G.R.,Christopherson, K.S., Nouri, N., Micheva, K.D., Mehalow, A., Huberman, A.D., Stafford, B., Sher, A., Litke, A.M., Lambris, J.D., Smith, S.J., John, S.W.M., & Barres, B.A. (2007) The classical complement cascade mediates CNS synapse elimination. Cell 131:1164-78.

Commentaries:

Smith, S.J (2007) Circuit Reconstruction Tools Today.  Curr. Opin. In Neurobiol. 17:601-608.

Lichtman, J.W. and Smith, S.J (2008)  Seeing Circuits Assemble.  Neuron 60:441-448.