A fundamental objective in neurobiology is to understand the neuronal circuitry that underlies different aspects of behavior (sensory integration, decision making, motor control, learning, and memory formation). In invertebrates, neural circuitry is classically analyzed at the cellular level using sparse reconstruction based on single cell staining techniques (Golgi and intracellular staining) in conjunction with functional and correlative studies using immunohistology and ultrastructure analysis. These approaches led to the identification of complete circuits at the synaptic level in small invertebrates (e.g., Caenorhabditis elegans) and in small parts of the brain (e.g., fly lamina). Advances in light microscopy techniques and the use of targeted expression of neuronal and molecular markers in transgenic animals allow more elaborate circuit mapping. High-throughput techniques in electron microscopy, genetic engineering (‘brainbow’), and three-dimensional microscopy of global brain circuitry allow the establishment of the connectome and complete wiring diagrams of dense neuropils, including synaptic connections. This chapter focuses on methods for characterizing ’microcircuits’—that is, the connectome on the synaptic level.
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