Three-dimensional reengineering of neuronal microcircuits : The cortical column in silico

The presented thesis will describe a pipeline to reengineer three-dimensional, anatomically realistic, functional neuronal networks with subcellular resolution. The pipeline consists of five methods: 1. "NeuroCount" provides the number and three-dimensional distribution of all neuron somata in large brain regions. 2. "NeuroMorph" provides authentic neuron tracings, comprising dendrite and axon morphology. 3. "daVinci" registers the neuron morphologies to a standardized reference framework. 4. "NeuroCluster" objectively groups the standardized tracings into anatomical neuron types. 5. "NeuroNet" combines the number and distribution of neurons and neuron-types with the standardized tracings and determines the neuron-type- and position-specific number of synaptic connections for any two types of neuron. The developed methods are demonstrated by reengineering the thalamocortical lemniscal microcircuit in the somatosensory system of rats. There exists an one-to-one correspondence between the sensory information obtained by a single facial whisker and segregated areas in the thalamus and cortex. The reengineering of this pathway results in a column-shaped network model of ~15200 excitatory full-compartmental cortical neurons. This network is synaptically connected to ~285 pre-synaptic thalamic neurons. Animation of this "cortical column in silico" with measured physiological input will help to gain a mechanistic understanding of neuronal sensory information processing in the mammalian brain