Soma class¶
(Shortest import: from brian2 import Soma)

class
brian2.spatialneuron.morphology.
Soma
(**kwds)[source]¶ Bases:
brian2.spatialneuron.morphology.Morphology
A spherical, isopotential soma.
Parameters: diameter :
Quantity
Diameter of the sphere.
x :
Quantity
, optionalThe x coordinate of the position of the soma.
y :
Quantity
, optionalThe y coordinate of the position of the soma.
z :
Quantity
, optionalThe 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 xcoordinate of the current section (as an array of length 1). end_y_
The ycoordinate of the current section (as an array of length 1). end_z_
The zcoordinate 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 geometrydependent term to calculate the conductance between the start and the midpoint of each compartment. r_length_2
The geometrydependent term to calculate the conductance between the midpoint and the end of each compartment. start_x_
The xcoordinate of the current section (as an array of length 1). start_y_
The ycoordinate of the current section (as an array of length 1). start_z_
The zcoordinate of the current section (as an array of length 1). volume
The volume of this section (as an array of length 1). x_
The xcoordinate of the current section (as an array of length 1). y_
The ycoordinate of the current section (as an array of length 1). z_
The zcoordinate 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 recreating 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 thedistance
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 ofx
, etc.), it does not add anything to the total distance, e.g. a section connecting to aSoma
has adistance
of 0 um at its start.

end_x_
¶ The xcoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

end_y_
¶ The ycoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

end_z_
¶ The zcoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

r_length_1
¶ The geometrydependent 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 geometrydependent 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 xcoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

start_y_
¶ The ycoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

start_z_
¶ The zcoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

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

x_
¶ The xcoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

y_
¶ The ycoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

z_
¶ The zcoordinate 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 givendiameter
. It’s start, midpoint, and endcoordinates are therefore identical.

copy_section
()[source]¶ Create a copy of the current section (attributes of this section only, not recreating the parent/children relation)
Returns: copy :
Morphology
A copy of this section (without the links to the parent/children)

Tutorials and examples using this¶
 Example compartmental/spike_initiation
 Example compartmental/morphotest
 Example compartmental/bipolar_with_inputs
 Example compartmental/bipolar_with_inputs2
 Example compartmental/bipolar_cell
 Example frompapers/Brette_2012/Fig3CF
 Example frompapers/Brette_2012/Fig3AB
 Example frompapers/Brette_2012/Fig5A
 Example frompapers/Brette_2012/Fig1
 Example frompapers/Brette_2012/Fig4