This protocol details how to quantify synapse number both in dissociated neuronal culture and in brain sections using immunocytochemistry. Using compartment-specific antibodies, we label presynaptic terminals as well as sites of postsynaptic specialization. We define synapses as points of colocalization between the signals generated by these markers.
Ippolito, D. M., Eroglu, C. Quantifying Synapses: an Immunocytochemistry-based Assay to Quantify Synapse Number. J. Vis. Exp. (45), e2270, doi:10.3791/2270 (2010).