Scaffold

Scaffold is the main object of the BSB infrastructure (see the Top Level Guide for an introduction to this class).

Properties

The Scaffold object tights together the network description of the Configuration with the data stored in the Storage. You can access the latter classes with respectively the scaffold.configuration and the scaffold.storage attributes. Scaffold also provides a direct access to all of its main configuration components as class attributes:

• scaffold.network -> NetworkNode

• scaffold.regions -> Region

• scaffold.partitions -> Partition

• scaffold.cell_types -> CellType

• scaffold.morphologies -> Morphology

• scaffold.morphologies -> CellType

• scaffold.placement -> PlacementStrategy

• scaffold.connectivity -> ConnectionStrategy

• scaffold.simulations -> Simulation

• scaffold.after_placement -> AfterPlacementHook

• scaffold.after_connectivity -> AfterConnectivityHook

There are also a list of methods starting with get_ that allows you to retrieve these components with some additional filtering parameters (get_cell_types, get_placement, get_placement_of, get_connectivity)

Workflow methods

Scaffold contains also all the functions required to run the reconstruction pipeline, and to simulate the resulting networks. You can run the full reconstruction with the compile method or any of its sub-step:

• Topology creation / update: resize

• Cell placement: run_placement

• After placement hook: run_after_placement

• Cell connectivity: run_connectivity

• After placement hook: run_after_connectivity

• Run a simulation: run_simulation

Similarly, you can clear the results of the reconstruction stored so far with the clear or any of its sub-step:

• Cell placement: clear_placement

• Cell connectivity: clear_connectivity

Get Stored data

You can also inspect the data produced during the reconstruction from the storage:

• PlacementSet from get_placement_set, get_placement_sets

• ConnectivitySet from get_connectivity_set, get_connectivity_sets