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
The membrane surface area of each compartment in this section.
The diameter at the middle of each compartment in this section.
The diameter at the end of each compartment in this section.
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 diameter at the start of each compartment in this section.
The volume of each compartment in this section.
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 \(\pi d l\), 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 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.
- 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 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/cylinder
Example compartmental/hh_with_spikes
Example compartmental/infinite_cable
Example compartmental/lfp
Example compartmental/morphotest
Example compartmental/rall
Example compartmental/spike_initiation
Example frompapers/Brette_2012/Fig1
Example frompapers/Brette_2012/Fig3AB
Example frompapers/Brette_2012/Fig3CF
Example frompapers/Brette_2012/Fig5A
Example frompapers/Destexhe_et_al_1998