.. py:class:: SymCompartment
SymCompartment object, for branching neuron models. In symmetric
compartments the axial resistance is equally divided on two sides of
the node. The equivalent circuit of the passive compartment becomes:
(NOTE: you must use a fixed-width font like Courier for correct rendition of the diagrams below)::
Ra/2 B Ra/2
A-/\/\/\\_\_\_\_\_/\/\/\-- C
|
\_\_\_\_|\_\_\_\_
| |
| \
| / Rm
---- Cm \
---- /
| |
| \_\_\_\_\_
| --- Em
|\_\_\_\_\_\_\_\_\_|
|
\_\_|\_\_
/////
In case of branching, the B-C part of the parent's axial resistance
forms a Y with the A-B part of the children::
B'
|
/
\
/
\
/
|A'
B |
A-----/\/\/\-----/\/\/\------|C
|
|A"
/
\
/
\
/
|
B"
As per basic circuit analysis techniques, the C node is replaced using
star-mesh transform. This requires all sibling compartments at a
branch point to be connected via 'sibling' messages by the user (or
by the cell reader in case of prototypes). For the same reason, the
child compartment must be connected to the parent by
distal-proximal message pair. The calculation of the
coefficient for computing equivalent resistances in the mesh is done
at reinit.
.. py:attribute:: proximal
void (*shared message field*) This is a shared message between symmetric compartments.
It goes from the proximal end of the current compartment to
distal end of the compartment closer to the soma.
.. py:attribute:: distal
void (*shared message field*) This is a shared message between symmetric compartments.
It goes from the distal end of the current compartment to the
proximal end of one further from the soma.
The Ra values collected from children and
sibling nodes are used for computing the equivalent resistance
between each pair of nodes using star-mesh transformation.
Mathematically this is the same as the proximal message, but
the distinction is important for traversal and clarity.
.. py:attribute:: sibling
void (*shared message field*) This is a shared message between symmetric compartments.
Conceptually, this goes from the proximal end of the current
compartment to the proximal end of a sibling compartment
on a branch in a dendrite. However,
this works out to the same as a 'distal' message in terms of
equivalent circuit. The Ra values collected from siblings
and parent node are used for
computing the equivalent resistance between each pair of
nodes using star-mesh transformation.
.. py:attribute:: sphere
void (*shared message field*) This is a shared message between a spherical compartment
(typically soma) and a number of evenly spaced cylindrical
compartments, typically primary dendrites.
The sphere contributes the usual Ra/2 to the resistance
between itself and children. The child compartments
do not connect across to each other
through sibling messages. Instead they just connect to the soma
through the 'proximalOnly' message
.. py:attribute:: cylinder
void (*shared message field*) This is a shared message between a cylindrical compartment
(typically a dendrite) and a number of evenly spaced child
compartments, typically dendritic spines, protruding from the
curved surface of the cylinder. We assume that the resistance
from the cylinder curved surface to its axis is negligible.
The child compartments do not need to connect across to each
other through sibling messages. Instead they just connect to the
parent dendrite through the 'proximalOnly' message
.. py:attribute:: proximalOnly
void (*shared message field*) This is a shared message between a dendrite and a parent
compartment whose offspring are spatially separated from each
other. For example, evenly spaced dendrites emerging from a soma
or spines emerging from a common parent dendrite. In these cases
the sibling dendrites do not need to connect to each other
through 'sibling' messages. Instead they just connect to the
parent compartment (soma or dendrite) through this message
.. py:method:: raxialSym
(*destination message field*) Expects Ra and Vm from other compartment.
.. py:method:: sumRaxial
(*destination message field*) Expects Ra from other compartment.
.. py:method:: raxialSym
(*destination message field*) Expects Ra and Vm from other compartment.
.. py:method:: sumRaxial
(*destination message field*) Expects Ra from other compartment.
.. py:method:: raxialSym
(*destination message field*) Expects Ra and Vm from other compartment.
.. py:method:: sumRaxial
(*destination message field*) Expects Ra from other compartment.
.. py:method:: raxialSphere
(*destination message field*) Expects Ra and Vm from other compartment. This is a special case when other compartments are evenly distributed on a spherical compartment.
.. py:method:: raxialCylinder
(*destination message field*) Expects Ra and Vm from other compartment. This is a special case when other compartments are evenly distributed on the curved surface of the cylindrical compartment, so we assume that the cylinder does not add any further resistance.
.. py:method:: raxialSphere
(*destination message field*) Expects Ra and Vm from other compartment. This is a special case when other compartments are evenly distributed on a spherical compartment.
.. py:attribute:: proximalOut
double,double (*source message field*) Sends out Ra and Vm on each timestep, on the proximal end of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOut but provides a logical orientation of the dendrite. One can traverse proximalOut messages to get to the soma.
.. py:attribute:: sumRaxialOut
double (*source message field*) Sends out Ra
.. py:attribute:: distalOut
double,double (*source message field*) Sends out Ra and Vm on each timestep, on the distal end of a compartment. This end should be pointed away from the soma. Mathematically the same as proximalOut, but gives an orientation to the dendrite and helps traversal.
.. py:attribute:: sumRaxialOut
double (*source message field*) Sends out Ra
.. py:attribute:: distalOut
double,double (*source message field*) Sends out Ra and Vm on each timestep, on the distal end of a compartment. This end should be pointed away from the soma. Mathematically the same as proximalOut, but gives an orientation to the dendrite and helps traversal.
.. py:attribute:: sumRaxialOut
double (*source message field*) Sends out Ra
.. py:attribute:: distalOut
double,double (*source message field*) Sends out Ra and Vm on each timestep, on the distal end of a compartment. This end should be pointed away from the soma. Mathematically the same as proximalOut, but gives an orientation to the dendrite and helps traversal.
.. py:attribute:: cylinderOut
double,double (*source message field*) Sends out Ra and Vm to compartments (typically spines) on the curved surface of a cylinder. Ra is set to nearly zero, since we assume that the resistance from axis to surface is negligible.
.. py:attribute:: proximalOut
double,double (*source message field*) Sends out Ra and Vm on each timestep, on the proximal end of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOut but provides a logical orientation of the dendrite. One can traverse proximalOut messages to get to the soma.