Cell Connectivity

Cell connections are made as the second step of compilation. Each connection type configures one connectivity.ConnectionStrategy and can override the connect method to connect cells to eachother. Use the scaffold instance’s :func:.core.Scaffold.connect_cells` to connect cells to eachother.

See the List of connection strategies.

Configuration

Each ConnectionStrategy is a ConfigurableClass, meaning that the attributes from the configuration files will be copied and validated onto the connection object.

Connecting cells

The connection matrices use a 2 column, 2 dimensional ndarray where the columns are the from and to id respectively. For morphologically detailed connections additional identifiers can be passed into the function to denote the specific compartments and morphologies that were used.