# Section class¶

(Shortest import: from brian2 import Section)

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

A section (unbranched structure), described as a sequence of truncated cones with potentially varying diameters and lengths per compartment.

Parameters

diameter : Quantity

Either a single value (the constant diameter along the whole section), or a value of length n+1. When n+1 values are given, they will be interpreted as the diameters at the start of the first compartment and the diameters at the end of each compartment (which is equivalent to: the diameter at the start of each compartment and the diameter at the end of the last compartment.

n : int, optional

The number of compartments in this section. Defaults to 1.

length : Quantity, optional

Either a single value (the total length of the section), or a value of length n, the length of each individual compartment. Cannot be combined with the specification of coordinates.

x : Quantity, optional

n+1 values, specifying the x coordinates of the start point of the first compartment and the end-points of all compartments (which is equivalent to: the start point of all compartments and the end point of the last compartment). The coordinates are interpreted as relative to the end point of the parent compartment (if any), so in most cases the start point should be 0*um. The common exception is a cylinder connecting to a Soma, here the start point can be used to make the cylinder start at the surface of the sphere instead of at its center. You can specify all of x, y, or z to specify a morphology in 3D, or only one or two out of them to specify a morphology in 1D or 2D.

y : Quantity, optional

See x

z : Quantity, optional

See x

type : str, optional

The type (e.g. "axon") of this Section.

Attributes

 area The membrane surface area of each compartment in this section. diameter The diameter at the middle of each compartment in this section. distance The total distance between the midpoint of each compartment and the root of the morphology. end_diameter The diameter at the end of each compartment in this section. end_distance The distance to the root of the morphology at the end of this section. end_x_ The x coordinate (as a unitless floating point number) at the end of each compartment. end_y_ The y coordinate (as a unitless floating point number) at the end of each compartment. end_z_ The z coordinate (as a unitless floating point number) at the end of each compartment. length The length of each compartment in this section. 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_diameter The diameter at the start of each compartment in this section. start_x_ The x coordinate (as a unitless floating point number) at the beginning of each compartment. start_y_ The y coordinate (as a unitless floating point number) at the beginning of each compartment. start_z_ The z coordinate (as a unitless floating point number) at the beginning of each compartment. volume The volume of each compartment in this section. x_ The x coordinate (as a unitless floating point number) at the midpoint of each compartment. y_ The y coordinate (as a unitless floating point number) at the midpoint of each compartment. z_ The z coordinate (as a unitless floating point number) at the midpoint of each compartment.

Methods

 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 each compartment in this section. The surface area of each compartment is calculated as $$\frac{\pi}{2}(d_1 + d_2)\sqrt{\frac{(d_1 - d_2)^2}{4} + l^2)}$$, where $$l$$ is the length of the compartment, and $$d_1$$ and $$d_2$$ are the diameter at the start and end of the compartment, respectively. Note that this surface area does not contain the area of the two disks at the two sides of the truncated cone.

diameter

The diameter at the middle of each compartment in this section.

distance

The total distance between the midpoint of each compartment and the root of the morphology.

end_diameter

The diameter at the end of each compartment in this section.

end_distance

The distance to the root of the morphology at the end of this section.

end_x_

The x coordinate (as a unitless floating point number) at the end of each compartment. Returns None for morphologies without coordinates.

end_y_

The y coordinate (as a unitless floating point number) at the end of each compartment. Returns None for morphologies without coordinates.

end_z_

The z coordinate (as a unitless floating point number) at the end of each compartment. Returns None for morphologies without coordinates.

length

The length of each compartment in this section.

r_length_1

The geometry-dependent term to calculate the conductance between the start and the midpoint of each compartment. Dividing this value by the Intracellular resistivity gives the conductance.

r_length_2

The geometry-dependent term to calculate the conductance between the midpoint and the end of each compartment. Dividing this value by the Intracellular resistivity gives the conductance.

start_diameter

The diameter at the start of each compartment in this section.

start_x_

The x coordinate (as a unitless floating point number) at the beginning of each compartment. Returns None for morphologies without coordinates.

start_y_

The y coordinate (as a unitless floating point number) at the beginning of each compartment. Returns None for morphologies without coordinates.

start_z_

The z coordinate (as a unitless floating point number) at the beginning of each compartment. Returns None for morphologies without coordinates.

volume

The volume of each compartment in this section. The volume of each compartment is calculated as $$\frac{\pi}{12} l (d_1^2 + d_1 d_2 + d_2^2)$$, where $$l$$ is the length of the compartment, and $$d_1$$ and $$d_2$$ are the diameter at the start and end of the compartment, respectively.

x_

The x coordinate (as a unitless floating point number) at the midpoint of each compartment. Returns None for morphologies without coordinates.

y_

The y coordinate (as a unitless floating point number) at the midpoint of each compartment. Returns None for morphologies without coordinates.

z_

The z coordinate (as a unitless floating point number) at the midpoint of each compartment. Returns None for morphologies without coordinates.

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)