Placement¶

This block in the configuration is responsible for placing cells into partitions. All placement strategies derive from the PlacementStrategy class, and should provide functions to define the positions of each CellType within a Partition volume.

BSB offers several built-in strategies (here is a list), or you can implement your own. The placement data is stored in PlacementSets for each cell type.

Add a placement strategy¶

In the placement block, all placement strategies are defined. For each strategy, it is necessary to specify the references to their related partitions and cell_types with the corresponding attributes.

JSON

"placement": {
    "place_A_in_my_layer": {
        "strategy": "bsb.placement.RandomPlacement",
        "partitions": [
            "my_layer"
        ],
        "cell_types": [
            "A_type"
        ]
    }
}

PYTHON

config.placement.add(
  "place_A_in_my_layer",
  strategy="bsb.placement.RandomPlacement",
  partitions=["my_layer"],
  cell_types=["A_type"],
)

Use indications¶

When a cell type is created, it is possible to define spatial attributes called placement indications. These attributes are used by the placement strategy to determine the distribution of cells within the volume.

JSON

"cell_types": {
    "A_type": {
        "spatial": {
            "density": 0.005,
            "radius": 2.5
        }
    },
    "B_type": {
        "spatial": {
            "count": 50,
            "radius": 5
        }
    }
}

"placement": {
    "place_A_and_B_in_my_layer": {
        "strategy": "bsb.placement.RandomPlacement",
        "partitions": [
            "my_layer"
        ],
        "cell_types": [
            "A_type","B_type"
        ]
    }
}

PYTHON

config.cell_types.add(
  "A_type",
  spatial=dict(radius=2.5, density=0.005)
)
config.cell_types.add(
  "B_type",
  spatial=dict(radius=5, count=50)
)

config.placement.add(
  "place_A_and_B_in_my_layer",
  strategy="bsb.placement.RandomPlacement",
  partitions=["my_layer"],
  cell_types=["A_type","B_type"],
)

In this example, type A cells are placed with a density of 0.005 cells/µm^3, while we place 50 type B cells with a radius of 5 µm.

Add dependencies to Placement Strategies¶

It may be necessary to place a set of cells 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_placement that is executed only after the place_A_and_B_in_my_layer placement has been completed.

JSON

"placement": {
    "secondary_placement": {
        "strategy": "bsb.placement.RandomPlacement",
        "partitions": [
            "my_layer"
        ],
        "cell_types": [
            "C_type"
        ],
        "depends_on": ["place_A_and_B_in_my_layer"]
    }
}

PYTHON

config.placement.add(
  "secondary_placement",
  strategy="bsb.placement.RandomPlacement",
  partitions=["my_layer"],
  cell_types=["C_type"],
  depends_on=["place_A_and_B_in_my_layer"],
)