Generator Definitions¶

CellCompositionGenerator¶

The CellCompositionGenerator is responsible for manipulating an input CellComposition in terms of density.

The final resource generated by the generator is a new CellComposition incorporating the changes listed in overrides.

CellPositionGenerator¶

The CellPositionGenerator consumes the upstream CellComposition registered by :ref`CellCompositionGenerator <cell_composition_generator>` and places cell somata, along with properties such as mtypes, and etype.

The final resource generated by the generator is a partial DetailedCircuit with a circuit config as follows:

{
   "version": 2,
   "manifest": {
     "$BASE_DIR": "."
   },
   "node_sets_file": "path/to/nodesets/json",
   "networks": {
     "nodes": [
       {
         "nodes_file": "path/to/nodes/h5",
         "populations": {
           "root__neurons": {
             "type": "biophysical",
           }
         }
       }
     ],
     "edges": []
   },
   "metadata": {
     "status": "partial"
   }
 }

where the node population has the following properties:

etype
hemisphere
morph_class
mtype
region
subregion
synapse_class
x
y
z

See SONATA documentation for column definitions.

MorphologyAssignmentGenerator¶

Config: MorphologyAssignmentConfig

The MorphologyAssignmentGenerator takes the DetailedCircuit from CellPositionGenerator and depending on the configuration assigns or/and synthesizes morphologies for each cell in the node population.

The final resource generated by the generator is a partial DetailedCircuit with a circuit config as follows:

{
  "version": 2,
  "manifest": {
    "$BASE_DIR": "."
  },
  "metadata": {
    "status": "partial"
  },
  "node_sets_file": "path/to/nodests/json",
  "networks": {
    "nodes": [
      {
        "nodes_file": "path/to/nodes/h5",
        "populations": {
          "root__neurons": {
            "type": "biophysical",
            "alternate_morphologies": {
               "h5v1": "$BASE_DIR/morphologies",
               "neurolucida-asc": "$BASE_DIR/morphologies"
            }
          }
        }
      }
    ],
    "edges": []
  }
}

where the node population has the following properties:

etype
hemisphere
morph_class
morphology
morphology_producer
mtype
orientation_w
orientation_x
orientation_y
orientation_z
region
subregion
synapse_class
x
y
z

See SONATA documentation for column definitions.

MEModelGenerator¶

Config: MEModelConfig

The MEModelGenerator takes the DetailedCircuit from MorphologyAssignmentGenerator and assigns emodels and emodel properties.

The final resource generated by the generator is a partial DetailedCircuit with a circuit config as follows:

{
   "version": 2,
   "manifest": {
     "$BASE_DIR": "."
   },
   "node_sets_file": "path/to/nodesets/json",
   "networks": {
     "nodes": [
       {
         "nodes_file": "path/to/nodes/h5",
         "populations": {
           "root__neurons": {
             "type": "biophysical",
             "partial": [
               "cell-properties",
               "morphologies"
             ],
             "alternate_morphologies": {
               "h5v1": "path/to/morphologies/dir",
               "neurolucida-asc": "path/to/morphologies/dir"
             },
             "biophysical_neuron_models_dir": "path/to/hoc/dir"
           }
         }
       }
     ],
     "edges": []
   },
   "metadata": {
     "status": "partial"
   }
 }

where the node population has the following properties:

dynamics_params/AIS_scaler
dynamics_params/holding_current
dynamics_params/input_resistance
dynamics_params/resting_potential
dynamics_params/soma_scaler
dynamics_params/threshold_current
etype
hemisphere
model_template
morph_class
morphology
morphology_producer
mtype
orientation_w
orientation_x
orientation_y
orientation_z
region
subregion
synapse_class
x
y
z

See SONATA documentation for column definitions.

MacroConnectomeGenerator¶

Config: MacroConnectomeConfig

The MacroConnectomeGenerator is a relay generator that propagates its config downstream to MicroConnectomeGenerator.

The final resource of MacroConnectomeGenerator is a clone of its input config.

MicroConnectomeGenerator¶

Config: MicroConnectomeConfig

The MicroConnectomeGenerator takes as an input the MacroConnectomeConfig from MacroConnectomeGenerator and the DetailedCircuit from MEModelGenerator and establishes the connectivity of the node population.

The final resource generated by the generator is a partial DetailedCircuit with a circuit config as follows:

{
  "version": 2,
  "manifest": {
    "$BASE_DIR": "."
  },
  "node_sets_file": "path/to/nodesets/json",
  "networks": {
    "nodes": [
      {
        "nodes_file": "path/to/nodes/h5",
        "populations": {
          "root__neurons": {
            "type": "biophysical",
            "alternate_morphologies": {
              "h5v1": "path/to/morphologies/dir",
              "neurolucida-asc": "path/to/morphologies/dir"
            },
            "biophysical_neuron_models_dir": "path/to/hoc/dir"
          }
        }
      }
    ],
    "edges": [
      {
        "edges_file": "path/to/edges/h5",
        "populations": {
          "root__neurons__root__neurons__chemical": {
            "type": "chemical"
          }
        }
      }
    ]
  },
  "metadata": {
    "status": "partial"
  }
}

where the nodes file has the same properties as in the MEModelGenerator ones and the edges file has the following properties:

afferent_center_x
afferent_center_y
afferent_center_z
afferent_section_id
afferent_section_pos
afferent_section_type
delay
syn_type_id

See SONATA documentation for column definitions.

ConnectomeFilteringGenerator¶

Config: SynapseConfig

The ConnectomeFilteringGenerator takes the DetailedCircuit from MicroConnectomeGenerator and filters the according to the configuration.

The final resource is a simulation-ready DetailedCircuit where the where the nodes file has the same properties as in the MEModelGenerator ones and the edges file has the following properties:

afferent_center_x
afferent_center_y
afferent_center_z
afferent_section_id
afferent_section_pos
afferent_section_type
conductance
conductance_scale_factor
decay_time
delay
depression_time
facilitation_time
n_rrp_vesicles
syn_property_rule
syn_type_id
u_hill_coefficient
u_syn

See SONATA documentation for column definitions.