Tutorial 8: Multi-Compartment Models

Table of Contents

• 8.1 Introduction
• 8.2 Setting-Up Multi-Compartment Neurons

Author

Stanislav Listopad

8.1 Introduction

In this tutorial we introduce generating multi-compartment models in CARLsim. We set-up a group of four compartment (four layer) neurons. We then proceed to inject current into one of the compartments (soma) and then observe the effects of this current injection on all of the connected compartments.

The multi-compartment tutorial can be found at doc/source/tutorial/8_compartments/src/ directory.

8.2 Setting-Up Multi-Compartment Neurons

We first set-up several CARLsim groups. These groups must have the same number of neurons and cannot be synaptically connected to each other.

int grpSoma = sim->createGroup("excit", N, EXCITATORY_NEURON);    // grpSoma 
int grpD_one = sim->createGroup("excit", N, EXCITATORY_NEURON);   // grpD_one
int grpD_two = sim->createGroup("excit", N, EXCITATORY_NEURON);   // grpD_two 
int grpD_three = sim->createGroup("excit", N, EXCITATORY_NEURON); // grpD_three 

We then set-up neuron parameters as we would normally with CARLsim groups. Afterwards, we set-up coupling constants for the compartments via the setCompartmentParameters method.

sim->setCompartmentParameters(grpD_one, 28.396f, 5.526f); // grpD_one 28 and 5
sim->setCompartmentParameters(grpD_two, 50.474f, 0.0f);   // grpD_two 50 and 0
sim->setCompartmentParameters(grpD_three, 0.0f, 49.14f);  // grpD_three 0 and 49
sim->setCompartmentParameters(grpSoma, 116.861f, 4.60f);  // grpSoma (somatic) 116 and 4

Now, each of the above defined groups is a compartment.

The following formula is used to calculate the current going into each compartment: Idendr = Gdown*(V - Vdown) + Sum(up)(Gup*(V - Vup))

We then proceed to connect the compartment groups together.

sim->connectCompartments(grpD_two, grpD_one);
sim->connectCompartments(grpD_one, grpSoma);
sim->connectCompartments(grpSoma, grpD_three);

These four compartmentally connected CARLsim groups now represent N neurons with four compartments each (1 soma compartment & 3 dendrite compartments).

Note: Any given compartment group can only be directly connected to at most 4 other compartment groups.

Finally, we proceed to run the CARLsim network as we would normally. We inject current into the soma using the setExternalCurrent function:

sim->setExternalCurrent(grpSoma, 600);

The soma compartment and one neighbouring dendrite compartment will spike as a result. Changing the coupling constants, injection current, or neuron parameters will affect the results.