Figure 1.

Generating dense statistical connectomes. (A) Generating a dense statistical connectome of a brain or brain region requires a standardized 3D reference frame of this brain region. The reference frame is used to register all anatomical data obtained from different experiments to a common coordinate system. Anatomical data to be collected from the brain region of interest: Number and 3D distribution of excitatory and inhibitory neuron somata; 3D reconstructions of representative samples of dendrites and axons of excitatory and inhibitory neuron cell types; determination of postsynaptic target densities, e.g., spine densities and dendrite surfaces, and presynaptic bouton densities for excitatory and inhibitory neuron cell types. (B) Anatomical data are assembled into a complete 3D network model. First, based on their 3D location, excitatory and inhibitory neuron somata are assigned to different anatomical substructures of the brain regions and to cell types. Next, somata of all cell types are replaced with dendrite and axon morphologies of the respective cell types. (C) Innervation from neuron i to neuron j is computed in 3D at a resolution determined by the anatomical variability of the 3D reference frame. This computation takes all possible postsynaptic targets of neuron i in addition to neuron j into account.