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High-throughput methods for yielding the set of connections in a neural system, the connectome, are now being developed. This tutorial describes ways to analyze the topological and spatial organization of the connectome at the macroscopic level of connectivity between brain regions as well as the microscopic level of connectivity between neurons. We will describe topological features at three different levels: the local scale of individual nodes, the regional scale of sets of nodes, and thedoi:10.1016/j.neuroimage.2011.05.025 pmid:21605688 fatcat:mmtl3dsfyzdtjaisybsawcchju