Dendrite#

class dendrify.compartment.Dendrite(name, model='passive', length=None, diameter=None, cm=None, gl=None, cm_abs=None, gl_abs=None, r_axial=None, v_rest=None, scale_factor=1.0, spine_factor=1.0)[source]#

Bases: Compartment

A class that automatically generates and handles all differential equations and parameters needed to describe a dendritic compartment, its active mechanisms, and any currents (synaptic, dendritic, ionic, noise) passing through it.

See also

Dendrite inherits all the methods and attributes of its parent class Compartment. For a complete list, please refer to the documentation of the latter.

Parameters:

  • name (str) – A unique name used to tag compartment-specific equations and parameters. It is also used to distinguish the various compartments belonging to the same NeuronModel.

  • model (str, optional) – A keyword for accessing Dendrify’s library models. Dendritic compartments are by default set to 'passive'.

  • length (Quantity, optional) – A compartment’s length.

  • diameter (Quantity, optional) – A compartment’s diameter.

  • cm (Quantity, optional) – Specific capacitance (usually μF / cm^2).

  • gl (Quantity, optional) – Specific leakage conductance (usually μS / cm^2).

  • cm_abs (Quantity, optional) – Absolute capacitance (usually pF).

  • gl_abs (Quantity, optional) – Absolute leakage conductance (usually nS).

  • r_axial (Quantity, optional) – Axial resistance (usually Ohm * cm).

  • v_rest (Quantity, optional) – Resting membrane voltage.

  • scale_factor (float, optional) – A global area scale factor, by default 1.0.

  • spine_factor (float, optional) – A dendritic area scale factor to account for spines, by default 1.0.

Examples

>>> # specifying equations only:
>>> compX = Dendrite('nameX')
>>> # specifying equations and ephys properties:
>>> compY = Dendrite('nameY', length=100*um, diameter=1*um,
>>>                     cm=1*uF/(cm**2), gl=50*uS/(cm**2))
>>> # specifying equations and absolute ephys properties:
>>> compY = Dendrite('nameZ', cm_abs=100*pF, gl_abs=20*nS)

Methods:

dspikes

Adds the ionic mechanisms and parameters needed for dendritic spiking.

Attributes:

event_names

Returns a list of all dSpike event names created for a single dendrite.

events

Returns a dictionary of all dSpike events created for a single dendrite.

parameters

Returns a dictionary of all parameters that have been generated for a single compartment.
dspikes(name, threshold=None, g_rise=None, g_fall=None, duration_rise=None, duration_fall=None, reversal_rise=None, reversal_fall=None, offset_fall=None, refractory=None)[source]#

Adds the ionic mechanisms and parameters needed for dendritic spiking. Under the hood, this method creates the equations, conditions and actions to take advantage of Brian’s custom events. dSpikes are generated through the sequential activation of a positive (sodium or calcium-like) and a negative current (potassium-like current) when a specified dSpike threshold is crossed.

Hint

The dendritic spiking mechanism as implemented here has three distinct phases.

INACTIVE PHASE:

When the dendritic voltage is subthreshold OR the simulation step is within the refractory period. dSpikes cannot be generated during this phase.

RISE PHASE:

When the dendritic voltage crosses the dSpike threshold AND the refractory period has elapsed. This triggers the instant activation of a positive current that is deactivated after a specified amount of time (duration_rise). Also a new refractory period begins.

FALL PHASE:

This phase starts automatically with a delay (offset_fall) after the dSpike threshold is crossed. A negative current is activated instantly and then is deactivated after a specified amount of time (duration_fall).

Parameters:

  • name (str) – A unique name to describe a single dSpike type.

  • threshold (Quantity, optional) – The membrane voltage threshold for dendritic spiking.

  • g_rise (Quantity, optional) – The max conductance of the channel that is activated during the rise (depolarization phase).

  • g_fall (Quantity, optional) – The max conductance of the channel that is activated during the fall (repolarization phase).

  • duration_rise (Quantity, optional) – The duration of g_rise staying open.

  • duration_fall (Quantity, optional) – The duration of g_fall staying open.

  • reversal_rise ((Quantity, str), optional) – The reversal potential of the channel that is activated during the rise (depolarization) phase.

  • reversal_fall ((Quantity, str), optional) – The reversal potential of the channel that is activated during the fall (repolarization) phase.

  • offset_fall (Quantity, optional) – The delay for the activation of g_rise.

  • refractory (Quantity, optional) – The time interval required before dSpike can be activated again.

property event_names#

Returns a list of all dSpike event names created for a single dendrite.

Return type:

list

property events#

Returns a dictionary of all dSpike events created for a single dendrite.

Returns:

Keys: event names, values: events conditions.

Return type:

dict

property parameters#

Returns a dictionary of all parameters that have been generated for a single compartment.

Return type:

dict