Soma class¶
(Shortest import: from brian2 import Soma)
-
class
brian2.spatialneuron.morphology.
Soma
(*args, **kwds)[source]¶ Bases:
brian2.spatialneuron.morphology.Morphology
A spherical, iso-potential 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 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
()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 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 givendiameter
. 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 givendiameter
. 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 givendiameter
. It’s start-, midpoint-, and end-coordinates are therefore identical.
-
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 givendiameter
. 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 givendiameter
. 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 givendiameter
. 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 givendiameter
. 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 givendiameter
. It’s start-, midpoint-, and end-coordinates are therefore identical.
-
Tutorials and examples using this¶
- Example frompapers/Brette_2012/Fig1
- Example frompapers/Brette_2012/Fig5A
- Example frompapers/Brette_2012/Fig4
- Example frompapers/Brette_2012/Fig3CF
- Example frompapers/Brette_2012/Fig3AB
- Example compartmental/spike_initiation
- Example compartmental/bipolar_with_inputs
- Example compartmental/bipolar_cell
- Example compartmental/morphotest
- Example compartmental/bipolar_with_inputs2