Connectivity

The connection between cells is managed with ConnectivityStrategy objects. A strategy present all the rules to apply for the definition of connection among cells. In BSB is implemented a set of strategies ready to use (here is a list), but it also possible to build a customised strategy. Once created the connectivity are stored in ConnectivitySets.

Adding a connection type

Connections are defined in the configuration under the connectivity block:

JSON

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

PYTHON

config.connectivity.add(
  "type_A_to_type_B",
  strategy="bsb.connectivity.VoxelIntersection",
  presynaptic=dict(cell_types=["type_A"]),
  postsynaptic=dict(cell_types=["type_B"]),
)

• strategy: Which bsb.connectivity.strategy.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:

JSON

{
  "connectivity": {
    "type_A_to_type_B": {
      "strategy": "bsb.connectivity.AllToAll",
      "presynaptic": {
      "cell_types": ["type_A"],
      "labels": ["subgroup1", "subgroup2"]
    },
    "postsynaptic": {
      "cell_types": ["type_B"]
    }
  }
}

PYTHON

config.connectivity.add(
  "type_A_to_type_B",
  strategy="bsb.connectivity.AllToAll",
  presynaptic=dict(cell_types=["type_A"],labels=["subgroup1","subgroup2"]),
  postsynaptic=dict(cell_types=["type_B"]),
)

This snippet would connect only the cells of type_A that are labelled with either subgroup1 or subgroup2, to all of the cells of type_B.

Specifying subcellular regions using morphology labels

You can also specify which regions on a morphology you are 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:

JSON

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

PYTHON

config.connectivity.add(
  "type_A_to_type_B",
  strategy="bsb.connectivity.VoxelIntersection",
  presynaptic=dict(cell_types=["type_A"],morphology_labels= ["dendrites"]),
  postsynaptic=dict(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.

Define an order for the execution of your Connectivity Strategies

It may be necessary to establish certain connections only after specific strategies have been executed. In such cases, you can define a list of strategies as dependencies. For example, you can create a secondary_connection that is established only after the type_A_to_type_B connectivity has been completed.

JSON

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

PYTHON

config.connectivity.add(
  "secondary_connection",
  strategy="bsb.connectivity.VoxelIntersection",
  presynaptic=dict(cell_types=["type_B"]),
  postsynaptic=dict(cell_types=["type_C"]),
  depends_on= ["type_A_to_type_B"]
)