SpatialNeuron class
(Shortest import: from brian2 import SpatialNeuron)
- class brian2.spatialneuron.spatialneuron.SpatialNeuron(*args, **kw)[source]
Bases:
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
), optionalCompartment 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
, optionalSpecific 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
, optionalIntracellular 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
}, optionalEither 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 thenamespace
argument of theNetwork.run
method or from the local context, if no such argument is given.dtype : (
dtype
,dict
), optionalThe
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
, optionalThe time step to be used for the simulation. Cannot be combined with the
clock
argument.clock :
Clock
, optionalThe update clock to be used. If neither a clock, nor the
dt
argument is specified, thedefaultclock
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
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.).
Methods
spatialneuron_attribute
(neuron, name)Selects a subtree from
SpatialNeuron
neuron and returns aSpatialSubgroup
.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 aSpatialSubgroup
. If it does not exist, returns theGroup
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 aSpatialNeuron
, only aGroup
.
Tutorials and examples using this
Example compartmental/bipolar_cell
Example compartmental/cylinder
Example compartmental/hh_with_spikes
Example compartmental/infinite_cable
Example compartmental/lfp
Example compartmental/morphotest
Example compartmental/rall
Example compartmental/spike_initiation
Example frompapers/Brette_2012/Fig1
Example frompapers/Brette_2012/Fig3AB
Example frompapers/Brette_2012/Fig3CF
Example frompapers/Brette_2012/Fig4
Example frompapers/Brette_2012/Fig5A
Example frompapers/Destexhe_et_al_1998