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

class
brian2.spatialneuron.morphology.
Cylinder
(**kwds)[source]¶ Bases:
brian2.spatialneuron.morphology.Section
A cylindrical section. For sections with more complex geometry (varying length and/or diameter of each compartment), use the
Section
class.Parameters: diameter :
Quantity
The diameter of the cylinder.
n : int, optional
The number of compartments in this section. Defaults to 1.
length :
Quantity
, optionalThe length of the cylinder. Cannot be combined with the specification of coordinates.
x :
Quantity
, optionalA sequence of two values, the start and the end point of the cylinder. 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 aSoma
, 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 ofx
,y
, orz
to specify a morphology in 3D, or only one or two out of them to specify a morphology in 1D or 2D.y :
Quantity
, optionalSee
x
z :
Quantity
, optionalSee
x
type : str, optional
The type (e.g.
"axon"
) of thisCylinder
.Attributes
area
The membrane surface area of each compartment in this section. diameter
The diameter at the middle of each compartment in this section. end_diameter
The diameter at the end of each compartment in this section. 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_diameter
The diameter at the start of each compartment in this section. volume
The volume of each compartment in this section. 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 each compartment in this section. The surface area of each compartment is calculated as \(\pi d l\), where \(l\) is the length of the compartment, and \(d\) is its diameter. Note that this surface area does not contain the area of the two disks at the two sides of the cylinder.

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

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

r_length_1
¶ The geometrydependent 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 geometrydependent 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.

volume
¶ The volume of each compartment in this section. The volume of each compartment is calculated as \(\pi \frac{d}{2}^2 l\) , where \(l\) is the length of the compartment, and \(d\) is its diameter.

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/lfp
 Example compartmental/hodgkin_huxley_1952
 Example compartmental/infinite_cable
 Example compartmental/bipolar_cell
 Example compartmental/bipolar_with_inputs
 Example compartmental/hh_with_spikes
 Example compartmental/morphotest
 Example compartmental/spike_initiation
 Example compartmental/bipolar_with_inputs2
 Example compartmental/cylinder
 Example compartmental/rall
 Example frompapers/Destexhe_et_al_1998
 Example frompapers/Brette_2012/Fig1
 Example frompapers/Brette_2012/Fig3CF
 Example frompapers/Brette_2012/Fig5A
 Example frompapers/Brette_2012/Fig3AB