Soma class
(Shortest import: from brian2 import Soma)
- class brian2.spatialneuron.morphology.Soma(**kwds)[source]
Bases:
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
The membrane surface area of this section (as an array of length 1).
The diameter of this section (as an array of length 1).
The total distance between the midpoint of this section and the root of the morphology.
The distance to the root of the morphology at the end of this section.
The x-coordinate of the current section (as an array of length 1).
The y-coordinate of the current section (as an array of length 1).
The z-coordinate of the current section (as an array of length 1).
The "length" (equal to
diameter
) of this section (as an array of length 1).The geometry-dependent term to calculate the conductance between the start and the midpoint of each compartment.
The geometry-dependent term to calculate the conductance between the midpoint and the end of each compartment.
The x-coordinate of the current section (as an array of length 1).
The y-coordinate of the current section (as an array of length 1).
The z-coordinate of the current section (as an array of length 1).
The volume of this section (as an array of length 1).
The x-coordinate of the current section (as an array of length 1).
The y-coordinate of the current section (as an array of length 1).
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
- 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.
- 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.
- 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
Example compartmental/bipolar_cell
Example compartmental/morphotest
Example compartmental/spike_initiation
Example frompapers/Brette_2012/Fig1
Example frompapers/Brette_2012/Fig3AB
Example frompapers/Brette_2012/Fig3CF
Example frompapers/Brette_2012/Fig4
Example frompapers/Brette_2012/Fig5A