Models and neuron groups

The core of every simulation is a NeuronGroup, a group of neurons that share the same equations defining their properties. The minimum NeuronGroup specification contains the number of neurons and the model description in the form of equations:

G = NeuronGroup(10, 'dv/dt = -v/(10*ms) : volt')

This defines a group of 10 leaky integrators. The model description can be directly given as a (possibly multi-line) string as above, or as an Equation object. For more details on the form of equations, see Equations. Note that model descriptions can make reference to physical units, but also to scalar variables declared outside of the model description itself:

tau = 10*ms
G = NeuronGroup(10, 'dv/dt = -v/tau : volt')

If a variable should be taken as a parameter of the neurons, i.e. if it should be possible to vary its value across neurons, it has to be declared as part of the model description:

G = NeuronGroup(10, '''dv/dt = -v/tau : volt
                       tau : second''')

To make complex model descriptions more readable, named subexpressions can be used:

G = NeuronGroup(10, '''dv/dt = I_leak / Cm : volt
                       I_leak = g_L*(E_L - v) : amp''')

Sometimes it can also be useful to introduce scalar variables or subexpressions, i.e. variables that have a common value for all neurons. In contrast to external variables (such as Cm above), such variables can change during a run, e.g. by using a CodeRunner. This can be for example used for an external stimulus that changes in the course of a run:

G = NeuronGroup(10, '''shared_input : volt (scalar)
                       dv/dt = (-v + shared_input)/tau : volt
                       tau : second''')

Note that there are several restrictions around the use of scalar variables: they cannot be written to in contexts where statements apply only to a subset of neurons (e.g. reset statements, see below). If a code block mixes statements writing to scalar and vector variables, then the scalar statements have to come first.

Threshold and reset

To emit spikes, neurons need a threshold. Threshold and reset are given as strings in the NeuronGroup constructor:

tau = 10*ms
G = NeuronGroup(10, 'dv/dt = -v/tau : volt', threshold='v > -50*mV',
                reset='v = -70*mV')

Whenever the threshold condition is fulfilled, the reset statements will be executed. Again, both threshold and reset can refer to physical units, external variables and parameters, in the same way as model descriptions:

v_r = -70*mV  # reset potential
G = NeuronGroup(10, '''dv/dt = -v/tau : volt
                       v_th : volt  # neuron-specific threshold''',
                threshold='v > v_th', reset='v = v_r')

Refractoriness

To make a neuron non-excitable for a certain time period after a spike, the refractory keyword can be used:

G = NeuronGroup(10, 'dv/dt = -v/tau : volt', threshold='v > -50*mV',
                reset='v = -70*mV', refractory=5*ms)

This will not allow any threshold crossing for a neuron for 5ms after a spike. The refractory keyword allows for more flexible refractoriness specifications, see Refractoriness for details.

State variables

Differential equations and parameters in model descriptions are stored as state variables of the NeuronGroup. They can be accessed and set as an attribute of the group:

>>> G = NeuronGroup(10, '''dv/dt = (-v + shared_input)/tau : volt
                           shared_input : volt (scalar)
...                        tau : second''')
>>> G.v = -70*mV
>>> print G.v
<neurongroup.v: array([-70., -70., -70., -70., -70., -70., -70., -70., -70., -70.]) * mvolt>
>>> G.shared_input = 5*mV
>>> print G.shared_input
<neurongroup.shared_input: 5.0 * mvolt>

The value of state variables can also be set using string expressions that can refer to units and external variables, other state variables, mathematical functions, and a special variable i, the index of the neuron:

>>> G.tau = '5*ms + 5*ms*rand() + i*5*ms'
>>> print G.tau
<neurongroup.tau: array([  5.03593449,  10.74914808,  19.01641896,  21.66813281,
        27.16243388,  31.13571924,  36.28173038,  40.04921519,
        47.28797921,  50.18913711]) * msecond>

For scalar variables, such string expressions can only refer to scalar values:

>>> G.shared_input = 'rand()*mV + 4*mV'
>>> print G.shared_input
<neurongroup.shared_input: 4.2579690100000001 * mvolt>