Defining connections#

Adding a connection type#

Connections are defined in the configuration under the connectivity block:

{
  "connectivity": {
    "type_A_to_type_B": {
      "strategy": "bsb.connectivity.VoxelIntersection",
      "presynaptic": {
        "cell_types": ["type_A"]
      },
      "postsynaptic": {
          "cell_types": ["type_B"]
      }
    }
  }
}

  • strategy: Which ConnectionStrategy to load.

  • pre/post: The pre/post-synaptic hemitypes:

    • cell_types: A list of cell types.

    • labels: (optional) a list of labels to filter the cells by

    • morphology_labels: (optional) a list of labels that filter which pieces of the morphology to consider when forming connections (such as axon, dendrites, or any other label you’ve created)

What each connection type does depends entirely on the selec

The framework will load the specified strategy, and will ask the strategy to determine the regions of interest, and will queue up one parallel job per region of interest. In each parallel job, the data generated during the placement step is used to determine presynaptic to postsynaptic connection locations.

Targetting subpopulations using cell labels#

Each hemitype (presynaptic and postsynaptic) accepts an additional list of labels to filter the cell populations by. This can be used to connect subpopulations of cells that are labelled with any of the given labels:

{
  "components": ["my_module.py"],
  "connectivity": {
    "type_A_to_type_B": {
      "class": "my_module.ConnectBetween",
      "min": 10,
      "max": 15.5,
      "presynaptic": {
        "cell_types": ["type_A"],
        "labels": ["subgroup1", "example2"]
      },
      "postsynaptic": {
        "cell_types": ["type_B"]
      }
    }
  }
}

This snippet would connect only the cells of type_A that are labelled with either subgroup1 or example2, to all of the cells of type_B, within 10 to 15.5 micrometer distance of each other.

Specifying subcellular regions using morphology labels#

You can also specify which regions on a morphology you’re interested in connecting. By default axodendritic contacts are enabled, but by specifying different morphology_labels you can alter this behavior. This example lets you form dendrodendritic contacts:

{
  "components": ["my_module.py"],
  "connectivity": {
    "type_A_to_type_B": {
      "class": "my_module.ConnectBetween",
      "min": 10,
      "max": 15.5,
      "presynaptic": {
        "cell_types": ["type_A"],
        "morphology_labels": ["dendrites"]
      },
      "postsynaptic": {
        "cell_types": ["type_B"],
        "morphology_labels": ["dendrites"]
      }
    }
  }
}

In general this works with any label that is present on the morphology. You could process your morphologies to add as many labels as you want, and then create different connectivity targets.