This section describes some of the core concepts of Arbor.
The basic unit of abstraction in an Arbor model is a cell. A cell represents the smallest model that can be simulated. Cells interact with each other via spike exchange and gap junctions. Cells can be of various types, admitting different representations and implementations. Arbor currently supports specialized leaky integrate and fire cells and cells representing artificial spike sources in addition to multi-compartment neurons.
||integral||The unique global identifier of a cell.|
||integral||The index of an item in a cell-local collection. For example the 7th synapse on a cell.|
||The global identification of a cell-local item with index into a cell-local collection on the cell identified by gid. For example, the 7th synapse on cell 42.|
- Gap Junction Sites
A cell can have multiple sources, targets and gap junction site objects. Each object has a local
relative to other objects of the same type on that cell.
A unique (
index) pair defned by a
cell_member can be used to uniquely identify
objects on a cell in a global model.
|cable||Cell with morphology described by branching 1D cable segments.|
|lif||Leaky-integrate and fire neuron.|
|spiking||Proxy cell that generates spikes from a user-supplied time sequence.|
|benchmark||Proxy cell used for benchmarking (developer use only).|
Cable cells are morphologically-detailed cells represented as branching linear 1D segments. They can be coupled to other cell types via the following mechanisms:
- Spike exchange over a connection with fixed latency. Cable cells can receive spikes from any kind of cell, and can be a source of spikes cells that have target sites (i.e. cable and lif cells).
- Direct electrical coupling between two cable cells via gap junctions.
- Morphology: The morphology of a cable cell is composed of a branching tree of one-dimensional line segments. Strictly speaking, Arbor represents a morphology is an acyclic directed graph, with the soma at the root.
- Detectors: Spike detectors generate spikes when the voltage at location on the cell passes a threshold. Dectectors act as sources of connections.
- Synapses: Synapases act as targets of connections. A synapse is described by a synapse type (with associated parameters) and location on a cell.
- Gap Junction Sites: These refer to the sites of gap junctions. They are declared by specifying a location on a branch of the cell.
A single compartment leaky integrate and fire neuron with one source and one target. LIF cells does not support adding additional sources or targets or gap junctions.
Spike source from values inserted via a schedule description. It is a point neuron with one built-in source and no targets. It does not support adding additional sources or targets. It does not support gap junctions.
Proxy cell used for benchmarking, and used by developers to benchmark the spike exchange and event delivery infrastructure.
Connections implement chemical synapses between source and target cells and are characterized by having a transmission delay.
Connections in Arbor are defined in two steps:
Gap junctions represent electrical synapses where transmission between cells is bidirectional and direct. They are modeled as a conductance between two gap junction sites on two cells.
Similarly to Connections, Gap Junctions in Arbor are defined in two steps:
A gap junction site is created on each of the two cells. These locations need to be declared on the cell.
Gap Junction instantiation in the recipe: The gap junction sites are indexed using
cell_memberbecause a single cell may have more than one gap junction site. A gap junction is instantiated by providing two gap junction sites’ and a conductance in μS.
Only cable cells support gap junctions as of now.