Concepts

This section describes some of the core concepts of Arbor.

Cells

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.

Identifiers used to uniquely refer to cells and objects like synapses on cells.
Identifier Type Description
gid
integral The unique global identifier of a cell.
index
integral The index of an item in a cell-local collection. For example the 7th synapse on a cell.
cell_member
tuple (gid, index) 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.

Each cell has a global identifier gid, which is used to refer to cells in recipes. To describe or refer to cell-to-cell interactions, the following object types need to be enumerated:

  1. Sources
  2. Targets
  3. Gap Junction Sites

Cells interact with other cells via connections or gap junctions. Connections are formed from sources to targets. Gap junctions are formed between two gap junction sites.

A cell can have multiple sources, targets and gap junction site objects. Each object has a local index relative to other objects of the same type on that cell. A unique (gid, index) pair defned by a cell_member can be used to uniquely identify objects on a cell in a global model.

Cell Kinds

The types of cell supported by Arbor
Cell Kind Description
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).
  1. Cable Cells

    Cable cells are morphologically-detailed cells represented as branching linear 1D segments. They can be coupled to other cell types via the following mechanisms:

    1. 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).
    2. Direct electrical coupling between two cable cells via gap junctions.

    Key concepts:

    • 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.
  2. LIF Cells

    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.

  3. Spiking Cells

    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.

  4. Benchmark Cells

    Proxy cell used for benchmarking, and used by developers to benchmark the spike exchange and event delivery infrastructure.

Connections

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:

  1. Create Source and Target on two cells: a source defined on one cell, and a target defined on another.
  2. Declare the connection in the recipe: with a source and target idenfied using cell_member, a connection delay and a connection weight.

Gap Junctions

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:

  1. A gap junction site is created on each of the two cells. These locations need to be declared on the cell.

  2. Gap Junction instantiation in the recipe: The gap junction sites are indexed using cell_member because 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.

    Note

    Only cable cells support gap junctions as of now.