Cell types

Cell types are the main component of the scaffold. They will be placed into the simulation volume and connected to eachother.

Configuration

In the root node of the configuration file the cell_types dictionary configures all the cell types. The key in the dictionary will become the cell type name. Each entry should contain a correct configuration for a placement.PlacementStrategy and morphologies.Morphology under the placement and morphology attributes respectively.

Optionally a plotting dictionary can be provided when the scaffold’s plotting functions are used.

Basic usage

1. Configure the following attributes in placement:

• class: the importable name of the placement strategy class. 3 built-in implementations of the placement strategy are available: ParticlePlacement, ParallelArrayPlacement and Satellite

• layer: The topological layer in which this cell type appears.

• soma_radius: Radius of the cell soma in µm.

• density: Cell density, see Cell count for more possibilities.

2. Select one of the morphologies that suits your cell type and configure its required attributes. Inside of the morphology attribute, a detailed_morphologies attribute can be specified to select detailed morphologies from the morphology repository.

3. The cell type will now be placed whenever the scaffold is compiled, but you’ll need to configure connection types to connect it to other cells.

Example

{
  "name": "My Test configuration",
  "output": {
    "format": "bsb.output.HDF5Formatter"
  },
  "network_architecture": {
    "simulation_volume_x": 400.0,
    "simulation_volume_z": 400.0
  },
  "layers": {
    "granular_layer": {
      "origin": [0.0, 0.0, 0.0],
      "thickness": 150
    }
  },
  "cell_types": {
    "granule_cell": {
      "placement": {
        "class": "bsb.placement.ParticlePlacement",
        "layer": "granular_layer",
        "soma_radius": 2.5,
        "density": 3.9e-3
      },
      "morphology": {
        "class": "bsb.morphologies.GranuleCellGeometry",
        "pf_height": 180,
        "pf_height_sd": 20,
        "pf_length": 3000,
        "pf_radius": 0.5,
        "dendrite_length": 40,
        "detailed_morphologies": ["GranuleCell"]
      },
      "plotting": {
        "display_name": "granule cell",
        "color": "#E62214"
      }
    }
  },
  "connection_types": {},
  "simulations": {}
}

Use bsb -c=my-config.json compile to test your configuration file.