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"# Analyzing Connectomics Data\n",
"---\n",
"The `netsci` package comes with an out-of-box dataset describing the [neuronal network](https://en.wikipedia.org/wiki/Neural_network) among ~2,000 neurons from a rat brain. In this notebook, we shortly explain the nature of this data and demonstrate a basic network analysis applied upon it.\n",
"\n",
"Essentially, after completing this tutorial, you will know:\n",
"1. What are the brain's neural networks and what is the connectome.\n",
"2. How to load the (toy) connectomics data and convert it to a network.\n",
"3. How to identify and count three-node motifs in a network.\n",
"4. That, in neuronal networks, a motif connectivity is highly related to the spatial embedding of its composing neurons.\n",
"\n",
"A deeper description of this network study, together with its neuroscientific context and implication, can be found in [this recent paper](https://doi.org/10.1101/656058).\n",
"\n",
"\n",
"Let’s get started.\n",
"\n",
"\n",
"## Connectomics\n",
"> *You are more than your genes. You are your connectome.* --Sebastian Seung\n",
"\n",
"The human brain is composed of about 100 billion specialized nerve cells, [**neurons**](https://en.wikipedia.org/wiki/Neuron). Neurons can connect to up to 10,000 other target neurons each, altogether forming the vast and complex [biological neural networks](https://en.wikipedia.org/wiki/Neural_circuit). The inter-connections between neurons are formed by [**synapses**](https://en.wikipedia.org/wiki/Synapse) - structural \"junctions\" that allow transferring electric impulses, [**action potentials**](https://en.wikipedia.org/wiki/Action_potential), from one neuron the another. The precise wiring diagram of all neuronal connections, or [**the connectome**](https://en.wikipedia.org/wiki/Connectome), shapes the network-wide electric activity and underlies the different brain functions like information processing, memory, and, ultimately, behavior. However, how exactly does the network structure affect brain activity and function, is a long-standing and still open question in neuroscience for more than a century. \n",
"\n",
"
\n",
" from www.khanacademy.org\n",
"