Soma class¶

(Shortest import: from brian2 import Soma)

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

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

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

Details

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.

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)

Tutorials and examples using this¶