Cell Types

A cell types contains information about cell populations. There are 2 categories: cells, and entities. A cell has a position, while an entity does not. Cells can also have morphologies and orientations associated with them. On top of that, both cells and entities support additional arbitrary properties.

A cell type is an abstract description of the population. During placement, the concrete data is generated in the form of a PlacementSet. These can then be connected together into ConnectivitySets. Furthermore, during simulation, cell types are represented by cell models.

Basic configuration

The radius and density are the 2 most basic placement indicators, they specify how large and dense the cells in the population generally are. The plotting block allows you to specify formatting details.

{
  "cell_types": {
    "my_cell_type": {
      "spatial": {
        "radius": 10.0,
        "density": 3e-9
      },
      "plotting": {
        "display_name": "My Cell Type",
        "color": "pink",
        "opacity": 1.0
      }
    }
  }
}

Specifying spatial density

You can set the spatial distribution for each cell type present in a NrrdVoxels partition.

To do so, you should first attach your nrrd volumetric density file(s) to the partition with either the source or sources blocks. Then, label the file(s) with the keys list block and refer to the keys in the cell_types with density_key:

{
  "partitions": {
    "declive": {
      "type": "nrrd",
      "sources": ["first_cell_type_density.nrrd",
                  "second_cell_type_density.nrrd"],
      "keys": ["first_cell_type_density",
               "second_cell_type_density"]
      "voxel_size": 25,
    }
  }
  "cell_types": {
    "first_cell_type": {
      "spatial": {
        "radius": 10.0,
        "density_key": "first_cell_type_density"
      },
      "plotting": {
        "display_name": "First Cell Type",
        "color": "pink",
        "opacity": 1.0
      }
    },
    "first_cell_type": {
      "spatial": {
        "radius": 5.0,
        "density_key": "second_cell_type_density"
      },
      "plotting": {
        "display_name": "Second Cell Type",
        "color": "#0000FF",
        "opacity": 0.5
      }
    }
  }
}

The nrrd files should contain voxel based volumetric density in unit of cells / voxel volume, where the voxel volume is in cubic unit of voxel_size. i.e., if voxel_size is in µm then the density file is in cells/µm^3.

Specifying morphologies

If the cell type is represented by morphologies, you can list multiple selectors to fetch them from the Morphology repositories.

{
  "cell_types": {
    "my_cell_type": {
      "spatial": {
        "radius": 10.0,
        "density": 3e-9,
        "morphologies": [
          {
            "select": "by_name",
            "names": ["cells_A_*", "cell_B_2"]
          }
        ]
      },
      "plotting": {
        "display_name": "My Cell Type",
        "color": "pink",
        "opacity": 1.0
      }
    }
  }
}