EphysProperties

class dendrify.ephysproperties.EphysProperties(name=None, 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)

Bases: object

A class for calculating various important electrophysiological properties for a single compartment.

Note

An EphysProperties object is automatically created and linked to a single compartment during the initialization of the latter.

Parameters:

• name (str, optional) – A compartment’s name.

• 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.

Attributes:

area	Returns compartment's surface area (open cylinder) based on its length and diameter.
capacitance	Returns a compartment's capacitance based on its specific capacitance (cm) and surface area.
g_cylinder	The conductance (of coupling currents) passing through a cylindrical compartment based on its dimensions and its axial resistance.
g_leakage	Returns a compartment's absolute leakage conductance based on its specific leakage conductance (gl) and surface area.
parameters	Returns a dictionary of all the major electrophysiological parameters that describe a single compartment.

Methods:

g_couple

The conductance (of coupling currents) between the centers of two adjacent cylindrical compartments, based on their dimensions and the axial resistance.

property area

Returns compartment’s surface area (open cylinder) based on its length and diameter.

Returns:

A compartment’s surface area

Return type:

Quantity

property capacitance

Returns a compartment’s capacitance based on its specific capacitance (cm) and surface area. If an absolute capacitance (cm_abs) has been provided by the user, it returns this value instead.

Return type:

Quantity

static g_couple(comp1, comp2)

The conductance (of coupling currents) between the centers of two adjacent cylindrical compartments, based on their dimensions and the axial resistance.

Parameters:

• comp1 (EphysProperties) – An EphysProperties object

• comp2 (EphysProperties) – An EphysProperties object

Return type:

Quantity

property g_cylinder

The conductance (of coupling currents) passing through a cylindrical compartment based on its dimensions and its axial resistance. To be used when then the total number of compartments is low and the adjacent-to-soma compartments are highly coupled with the soma.

Return type:

Quantity

property g_leakage

Returns a compartment’s absolute leakage conductance based on its specific leakage conductance (gl) and surface area. If an absolute leakage conductance (gl_abs) has been provided by the user, it returns this value instead.

Return type:

Quantity

property parameters

Returns a dictionary of all the major electrophysiological parameters that describe a single compartment.

Return type:

dict