Soma class

(Shortest import: from brian2 import Soma)

class brian2.spatialneuron.morphology.Soma(**kwds)[source]

Bases: brian2.spatialneuron.morphology.Morphology

A spherical, iso-potential soma.

Parameters:

diameter : Quantity

Diameter of the sphere.

x : Quantity, optional

The x coordinate of the position of the soma.

y : Quantity, optional

The y coordinate of the position of the soma.

z : Quantity, optional

The z coordinate of the position of the soma.

type : str, optional

The type of this section, defaults to 'soma'.

Attributes

area The membrane surface area of this section (as an array of length 1).
diameter The diameter of this section (as an array of length 1).
distance The total distance between the midpoint of this section and the root of the morphology.
end_distance The distance to the root of the morphology at the end of this section.
end_x_ The x-coordinate of the current section (as an array of length 1).
end_y_ The y-coordinate of the current section (as an array of length 1).
end_z_ The z-coordinate of the current section (as an array of length 1).
length The “length” (equal to diameter) of this section (as an array of length 1).
r_length_1 The geometry-dependent term to calculate the conductance between the start and the midpoint of each compartment.
r_length_2 The geometry-dependent term to calculate the conductance between the midpoint and the end of each compartment.
start_x_ The x-coordinate of the current section (as an array of length 1).
start_y_ The y-coordinate of the current section (as an array of length 1).
start_z_ The z-coordinate of the current section (as an array of length 1).
volume The volume of this section (as an array of length 1).
x_ The x-coordinate of the current section (as an array of length 1).
y_ The y-coordinate of the current section (as an array of length 1).
z_ The z-coordinate of the current section (as an array of length 1).

Methods

copy_section() Create a copy of the current section (attributes of this section only, not re-creating the parent/children relation)

Details

area

The membrane surface area of this section (as an array of length 1).

diameter

The diameter of this section (as an array of length 1).

distance

The total distance between the midpoint of this section and the root of the morphology. The Soma is most likely the root of the morphology, and therefore the distance is 0.

end_distance

The distance to the root of the morphology at the end of this section. Note that since a Soma is modeled as a point (see docs of x, etc.), it does not add anything to the total distance, e.g. a section connecting to a Soma has a distance of 0 um at its start.

end_x_

The x-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

end_y_

The y-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

end_z_

The z-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

length

The “length” (equal to diameter) of this section (as an array of length 1).

r_length_1

The geometry-dependent term to calculate the conductance between the start and the midpoint of each compartment. Returns a fixed (high) value for a Soma, corresponding to a section with very low intracellular resistance.

r_length_2

The geometry-dependent term to calculate the conductance between the midpoint and the end of each compartment. Returns a fixed (high) value for a Soma, corresponding to a section with very low intracellular resistance.

start_x_

The x-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

start_y_

The y-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

start_z_

The z-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

volume

The volume of this section (as an array of length 1).

x_

The x-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

y_

The y-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

z_

The z-coordinate of the current section (as an array of length 1). Note that a Soma is modelled as a “point” with finite surface/volume, equivalent to that of a sphere with the given diameter. It’s start-, midpoint-, and end-coordinates are therefore identical.

copy_section()[source]

Create a copy of the current section (attributes of this section only, not re-creating the parent/children relation)

Returns:

copy : Morphology

A copy of this section (without the links to the parent/children)