Connectome Files

The Connectome file is a plain text file that specifies every synapse in the model. With the exception of the first line, each line in the Connectome file corresponds to one neuron, and gives a list of synaptic connections which that neuron receives. Neurons should be listed in this file in the same order that they appear in the Cell List file. The incoming connections for a particular neuron are given as a list of pairs of integers, where the first integer gives the ID of the presynaptic neuron and the second integer gives its type ID. The first column on each line should be an integer that specifies the total number of columns on that line, inclusive of itself. Columns can be separated by tabs or spaces. The first line in the file is special: it should consist of a single integer that gives the maximum column count across all lines in the file.

Note

Gap junctions are not considered synapses by the simulator, and are not specified in this file (see the Simulation Parameters file documentation for how gap junctions are defined).

The following example shows the contents of a Connectome file that defines a network of six neurons. In this example, assume that the odd-numbered neurons are of type 1 and the even-numbered neurons are of type 2. Synaptic connectivity here is random, except that neurons of type 1 never synapse onto other type 1 neurons:

7
5    6    2    4    2
7    4    2    3    1    5    1
3    2    2
5    4    2    5    1
1
7    1    1    5    1    2    2

Hint

A neuron can receive multiple synaptic connections from the same pre-synaptic neuron. In this case, synaptic conductances will sum linearly. A neuron can also receive connections from itself, as shown for neuron 4 in the above example (line 5).