# 2.4. Spiking neurons¶

Contrary to rate-coded neurons, the use of spiking neurons requires the additional definition of a spike condition (the criteria defining the emission of a spike, typically when the membrane potential exceeds a threshold) and reset equations, governing the evolution of all variables after a spike is emitted.

## 2.4.1. Built-in neurons¶

ANNarchy provides standard spiking neuron models, similar to the ones defined in PyNN (http://neuralensemble.org/docs/PyNN/reference/neuronmodels.html).

Their definition (parameters, equations) are described in Built-in neuron types. The classes can be used directly when creating the populations (no need to instantiate them). Ex:

```
pop = Population(geometry = 1000, neuron = Izhikevich)
```

## 2.4.2. User-defined neurons¶

Let’s consider a simple leaky integrate-and-fire spiking neuron model (LIF) using a voltage-gated excitatory conductance:

where \(v(t)\) is the membrane potential, \(\tau\) is the membrane time constant (in milliseconds), \(E_r\) the resting potential, \(E_e\) the target potential for excitatory synapses and \(g_\text{exc}(t)\) the total current induced by excitatory synapses.

This neural model can be defined in ANNarchy by:

```
LIF = Neuron(
parameters="""
tau = 10.0 : population
Er = -60.0 : population
Ee = 0.0 : population
T = -45.0 : population
""",
equations="""
tau * dv/dt = (Er - v) + g_exc *(Ee- v) : init = 0.0
""",
spike = "v > T",
reset = "v = Er",
refractory = 5.0
)
```

As for rate-coded neurons, the parameters are defined in the `parameters`

description, here globally for the population. `equations`

contains the description of the ODE followed by the membrane potential. The additional information to provide is:

`spike`

: a boolean condition on a single variable (typically the membrane potential) deciding when a spike is emitted.`reset`

: the modifications to the neuron’s variables after a spike is emitted (typically, clamping the membrane potential to its reset potential).`refractory`

: optionally a refractory period in ms.

### 2.4.2.1. Spike condition¶

The spike condition is a single constraint definition. You may use the different available comparison operators (>, <, ==, etc) on a **single** neuron variable, using as many parameters as you want.

The use of assignment statements or ODEs will lead to an error. Conditional statements can be used. Example:

```
parameters="""
...
T = -45.0
""",
equations="""
prev_v = v
noise = Uniform (-5.0, 5.0)
tau*dv/dt = E - v + g_exc
""",
spike = """
(v > T + noise) and (prev_v < T + noise)
"""
```

### 2.4.2.2. Reset¶

Here you define the variables which should be set to certain values after a spike occured. Any assignment statements is allowed (`=`

, `+=`

, etc), but the use of ODEs is not possible, as the reset is performed only once at the end of the time step.

Example:

```
reset = """
v = Er
u += 0.1
"""
```

### 2.4.2.3. Conductances¶

Contrary to rate-coded neurons, spiking neurons use conductance variables to encode the received inputs, not weighted sums. In ANNarchy, the conductances are defined by `g_`

followed by the target name. For example, if a population receives excitatory input (target `exc`

) from another one, you can access the total conductance provoked by `exc`

spikes with:

```
tau * dv/dt + v = g_exc
```

The dynamics of the conductance can be specified after its usage in the membrane potential equation.

- The default behaviour for conductances is an
**instantaneous reset**(or infinitely fast exponential decay). In practice, this means that all incoming spikes are summed up (weighted by the synaptic efficiency) at the beginning of a simulation step, and the resulting conductance is reset to 0.0 at the end of the step. This default behaviour is equivalent to :

```
LIF = Neuron(
parameters=""" ... """,
equations="""
tau * dv/dt = (Er - v) + g_exc *(Ee- v) : init = 0.0
g_exc = 0.0
""",
spike = " ... ",
reset = " ... "
)
```

Incoming spikes increase `g_exc`

and can provoke a post-synaptic spike at the next step, but leave no trace beyond that point.

- Most models however use
**exponentially decaying synapses**, where the conductance decays with a short time constant after a spike is received. This behavior should be explicitely specified in the neuron’s equations:

```
LIF = Neuron(
parameters=""" ... """,
equations="""
tau * dv/dt = (Er - v) + g_exc *(Ee- v) : init = 0.0
tau_exc * dg_exc/dt = - g_exc
""",
spike = " ... ",
reset = " ... "
)
```

`g_exc`

is increased by incoming spikes, and slowly decays back to 0.0 until the next spikes arrive.

### 2.4.2.4. Refractory period¶

The refractory period in milliseconds is specified by the `refractory`

parameter of `Neuron`

.

```
LIF = Neuron (
parameters = """ ... """,
equations = """ ... """,
spike = """ ... """,
reset = """
v = c
u += d
""",
refractory = 5.0
)
```

The `refractory`

argument can be a floating value or the name of a parameter/variable (string).

If `dt = 0.1`

, this means that the `equations`

will not be evaluated for 50 consecutive steps after a spike is emitted, except for the conductances (starting with `g_`

) which are evaluated normally during the refractory period (the neuron is not “deaf”, it only is frozen in a refractory state).

`refractory`

becomes an attribute of a spiking `Population`

object, so it can be set specifically for a population even when omitted in the neuron definition:

```
LIF = Neuron (
parameters = " ... ",
equations = " ... ",
spike = " ... ",
reset = """
v = c
u += d
"""
)
pop = Population(geometry = 1000, neuron = LIF)
pop.refractory = Uniform(1.0, 10.0)
```

It can be either a single value, a `RandomDistribution`

object or a Numpy array of the same size/geometry as the population.

### 2.4.2.5. Instantaneous firing rate¶

**Method 1: ISI**

Spiking neurons define an additional variable `t_last`

which represents the timestamp (in ms) of the last emitted spike (updated at the end of the `reset`

statement). The time elapsed since the last spike is then `t - t_last`

.

This can be used to update the instantaneous firing rate of a neuron, by inverting the inter-spike interval (ISI) during the `reset`

statement following the emission of a spike:

```
neuron = Neuron(
parameters = "tau = 20.0; tauf = 1000.",
equations = """
tau * dv/dt + v = ...
tauf * df/dt = -f
""",
spike = "v > 1.0",
reset = """
v = 0.0
f = 1000./(t - t_last)
"""
)
```

Here, a leaky integrator on f is needed to 1) smooth the firing rate and 2) slowly decay to 0 when the neuron stops firing. This method reflects very fast changes in the firing rate, but is also very sensible to noise.

**Method 2: Window**

A more stable way to compute the firing rate of a neuron is to count at each time step the number of spikes emitted during a sliding temporal window (of 100 ms or 1s for example). By default, spiking neurons only record the time of the last spike they emitted (`t_last`

), so this mechanism has to be explicitely enabled by calling the `compute_firing_rate()`

method of the desired population:

```
pop = Population(100, Izhikevich)
pop.compute_firing_rate(window=1000.0)
```

The `window`

argument represents the period in milliseconds over which the spikes will be counted. The resulting firing rate (in Hz) will be stored in the local variable `r`

(as for rate-coded neurons), which can be accessed by the neuron itself or by incoming and outgoing synapse (`pre.r`

and `post.r`

).

If the method has not been called, the variable `r`

of a spiking neuron will be constantly 0.0.

Warning

The window method is not available on CUDA yet.