SymCompartment

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.

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.

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.

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.

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

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

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

raxialSym()

(destination message field) Expects Ra and Vm from other compartment.

sumRaxial()

(destination message field) Expects Ra from other compartment.

raxialSym()

(destination message field) Expects Ra and Vm from other compartment.

sumRaxial()

(destination message field) Expects Ra from other compartment.

raxialSym()

(destination message field) Expects Ra and Vm from other compartment.

sumRaxial()

(destination message field) Expects Ra from other compartment.

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.

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.

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.

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.

sumRaxialOut

double (source message field) Sends out Ra

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.

sumRaxialOut

double (source message field) Sends out Ra

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.

sumRaxialOut

double (source message field) Sends out Ra

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.

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.

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.