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.
Identifier |
Type |
Description |
|---|---|---|
|
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. |
Cell interactions via connections and gap junctions occur between source, target and gap junction site locations on a cell. Connections are formed from sources to targets. Gap junctions are formed between two gap junction sites. An example of a source on a cable cell is a threshold detector (spike detector); an example of a target on a cable cell is a synapse.
Each cell has a global identifier gid, and each source, target and gap junction site has a
global identifier cell_member. These are used to refer to them in recipes.
A cell can have multiple sources, targets and gap junction site objects. Each object is ordered relative to other
objects of the same type on that cell. The unique cell_member (gid, index) identifies an object
according to the gid of the cell it is placed on, and its index on the cell enumerated according to the
order of insertion on the cell relative to other objects of the same type.
The gid of a cell is used to determine its cell kind and
description in the recipe. The cell_member of a source,
target or gap junction site is used to form connections and
gap junctions in the recipe.
Cell kind¶
Cell Kind |
Description |
|---|---|
Cable cell |
Cell with morphology and user configurable dynamics. |
LIF cell |
Leaky integrate-and-fire neuron. |
Spiking cell |
Proxy cell that generates spikes. |
Benchmark cell |
Proxy cell used for benchmarking (developer use only). |
Cable Cells
Cable cells are morphologically-detailed cells. They can be coupled to other cells 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 to cells that have target sites (i.e. cable and lif cells).
Direct electrical coupling between two cable cells via gap junctions.
LIF Cells
LIF cells are single-compartment leaky integrate and fire neurons. They are typically used to simulate point-neuron networks.
LIF cells can only interact with other cells via spike exchange over a connection where they can receive spikes from any kind of cell, and can be a source of spikes to cells that have target sites (i.e. cable and lif cells).
Spiking Cells
Spiking cells act as spike sources from user-specified values inserted via a schedule description. They are typically used as stimuli in a network of more complex cells.
Spiking Cells can only interact with other cells via spike exchange over a connection where they be a source of spikes to cells that have target sites (i.e. cable and lif cells), but they can not receive spikes.
Benchmark Cells
Benchmark cells are proxy cells used for benchmarking, and used by developers to benchmark the spike exchange and event delivery infrastructure.
Cell description¶
The description of a cell is referred to in the recipe, and elsewhere in the docs. It details everything needed to build a cell. The degree of detail differs according to the cell kind.
Cable Cells
The description of a cable cell can include all the following:
Morphology: composed of a branching tree of one-dimensional line segments. Strictly speaking, Arbor represents a morphology as an acyclic directed graph, with the soma at the root.
Discretisation: specifies how to split the morphology into discrete components for the simulation.
Initial membrane voltage.
Initial axial resistivity.
Intial membrane capacitance.
Initial temperature.
Initial ion internal and external concentrations.
Initial ion reversal potential.
Stimuli: such as current clamps; placed on specific locations on the cell.
Density mechanisms: commonly used to describe ion-channel dynamics across regions of the cell.
Ion reversal potential mechanisms: used to control the reversal potentials of ions across regions of the cell.
Synapses: implemented using point mechanisms on specific locations of the cell; typically act as targets of connections in the recipe.
Detectors: used to generate spiking events on specific locations on the cell when the voltage increases above a certain threshold; typically act as sources of connections.
Gap junction sites: placed on a specific location on a cell and used to electrically couple the cell to another gap junction site on another cell by forming a gap junction.
Most Arbor users will want to use the cable cell because it is the only cell kind that supports complex morphologies and user-defined mechanisms. See the cable cell’s dedicated page for more info. And visit the C++ and Python APIs to learn how to programmatically provide the cable cell description in Arbor.
LIF Cells
The description of a LIF cell is used to control the leaky integrate-and-fire dynamics:
Resting potential.
Reset potential.
Initial value of membrane potential.
Membrane potential decaying constant.
Membrane capacitance.
Firing threshold.
Refractory period.
The morphology of a LIF cell is automatically modeled as a single compartment; each cell has one built-in source and one built-in target which do not need to be explicitly added in the cell description. LIF cells do not support adding additional sources or targets to the description. They do not support gap junctions. They do not support adding density or point mechanisms.
Spiking cells
The description of a spiking cell controls the spiking schedule of the cell. Its morphology is automatically modeled as a single compartment; each cell has one built-in source which does not need to be explicitly added in the cell description, and no targets. Spiking cells do not support adding additional sources or targets. They do not support gap junctions. They do not support adding density or point mechanisms.
Benchmark Cells
The description of a benchmark cell is used to determine the spiking schedule of the cell and manipulate its performance efficiency. This cell is mainly used by developers.