SpatialNeuron class

(Shortest import: from brian2 import SpatialNeuron)

class brian2.spatialneuron.spatialneuron.SpatialNeuron(morphology=None, model=None, threshold=None, refractory=False, reset=None, events=None, threshold_location=None, dt=None, clock=None, order=0, Cm=0.009 * metre ** -4 * kilogram ** -1 * second ** 4 * amp ** 2, Ri=1.5 * metre ** 3 * kilogram * second ** -3 * amp ** -2, name='spatialneuron*', dtype=None, namespace=None, method=('linear', 'exponential_euler', 'rk2', 'heun'))[source]

Bases: brian2.groups.neurongroup.NeuronGroup

A single neuron with a morphology and possibly many compartments.

Parameters:

morphology : Morphology

The morphology of the neuron.

model : (str, Equations)

The equations defining the group.

method : (str, function), optional

The numerical integration method. Either a string with the name of a registered method (e.g. “euler”) or a function that receives an Equations object and returns the corresponding abstract code. If no method is specified, a suitable method will be chosen automatically.

threshold : str, optional

The condition which produces spikes. Should be a single line boolean expression.

threshold_location : (int, Morphology), optional

Compartment where the threshold condition applies, specified as an integer (compartment index) or a Morphology object corresponding to the compartment (e.g. morpho.axon[10*um]). If unspecified, the threshold condition applies at all compartments.

Cm : Quantity, optional

Specific capacitance in uF/cm**2 (default 0.9). It can be accessed and modified later as a state variable. In particular, its value can differ in different compartments.

Ri : Quantity, optional

Intracellular resistivity in ohm.cm (default 150). It can be accessed as a shared state variable, but modified only before the first run. It is uniform across the neuron.

reset : str, optional

The (possibly multi-line) string with the code to execute on reset.

events : dict, optional

User-defined events in addition to the “spike” event defined by the threshold. Has to be a mapping of strings (the event name) to strings (the condition) that will be checked.

refractory : {str, Quantity}, optional

Either the length of the refractory period (e.g. 2*ms), a string expression that evaluates to the length of the refractory period after each spike (e.g. '(1 + rand())*ms'), or a string expression evaluating to a boolean value, given the condition under which the neuron stays refractory after a spike (e.g. 'v > -20*mV')

namespace : dict, optional

A dictionary mapping identifier names to objects. If not given, the namespace will be filled in at the time of the call of Network.run(), with either the values from the namespace argument of the Network.run() method or from the local context, if no such argument is given.

dtype : (dtype, dict), optional

The numpy.dtype that will be used to store the values, or a dictionary specifying the type for variable names. If a value is not provided for a variable (or no value is provided at all), the preference setting core.default_float_dtype is used.

dt : Quantity, optional

The time step to be used for the simulation. Cannot be combined with the clock argument.

clock : Clock, optional

The update clock to be used. If neither a clock, nor the dt argument is specified, the defaultclock will be used.

order : int, optional

The priority of of this group for operations occurring at the same time step and in the same scheduling slot. Defaults to 0.

name : str, optional

A unique name for the group, otherwise use spatialneuron_0, etc.

Attributes

user_equations The original equations as specified by the user (i.e.

Methods

spatialneuron_attribute(neuron, name) Selects a subtree from SpatialNeuron neuron and returns a SpatialSubgroup.
spatialneuron_segment(neuron, item) Selects a segment from SpatialNeuron neuron, where item is a slice of either compartment indexes or distances.

Details

user_equations

The original equations as specified by the user (i.e. before inserting point-currents into the membrane equation, before adding all the internally used variables and constants, etc.).

static spatialneuron_attribute(neuron, name)[source]

Selects a subtree from SpatialNeuron neuron and returns a SpatialSubgroup. If it does not exist, returns the Group attribute.

static spatialneuron_segment(neuron, item)[source]

Selects a segment from SpatialNeuron neuron, where item is a slice of either compartment indexes or distances. Note a: segment is not a SpatialNeuron, only a Group.