Cell Placement

Cell placement is handled by the placement module. This module will place the cell types in the layers based on a certain Placement Strategy.

Placement occurs as the first step during network architecture compilation.

The placement order starts from cell type with the lowest cell count first unless specified otherwise in the cell type’s placement configuration.

See the List of placement strategies

Contents

• Cell Placement

  • Configuration

    • Cell count

    • Placement order

  • Placement Strategy

    • Placing cells

  • Labels

Configuration

Cell count

Specifying cell count can be done with count, density (µm^-3), planar_density (µm^-2) or a ratio to another cell with placement_relative_to (other cell type) and either density_ratio to place with their density multiplied by the given ratio or placement_count_ratio to place with their count multiplied by the given ratio

Placement order

By default the cell types are placed sorted from least to most cells per type. This default order can be influenced by specifying an after attribute in the cell type’s placement configuration. This is an array of cell type names which need to be placed before this cell type:

{
  "cell_types": {
    "later_cell_type": {
      "...": "...",
      "after": ["first_cell_type"]
    },
    "first_cell_type": { "...": "..." },
  }
}

Placement Strategy

Each cell type has to specify a placement strategy that determines the algorithm used to place cells. The placement strategy is an interface whose place method is called when placement occurs.

Placing cells

Call the scaffold instance’s core.Scaffold.place_cells() function to place cells in the simulation volume.

Labels