The Soma

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The Soma is the spherical central part of the neuron It is typically about 20 um in diameter and contains a salty potassium solution inside the cell. It is separated by the neural membrane as described earlier. Contained inside the Soma are a number of very important structures called organells but that can be ignored for this study.

The Soma

Inputs to the Soma arrive from the Dendrites. Its single output is to the Axon

The key feature of the Soma is its ability to initiate an Action Potential in the area labeled the Axon Hillock (shown below). Membranes of dendrites and the Soma body do not generate action potentials because they have very few voltage-gated sodium channels. Only the Axon is capable of generating action potentials, but the process starts in the Hillock. This area is also called the spike-initiation zone.

A Soma simulator that is the equivalent of a Soma Body and the Axon Hillock is available for you to download and run on your Windows machine.

The Action Potential profile begins at the membrane rest potential (about - 60 mV) and rises rapidly in the depolarization phase toward 0 mV. It overshoots the mark and then reverses back down to the resting potential. It then overshoots that and moves to the hyperpolarized region and then recovers to the resting potential.

The various charges moving through the Soma are amazing and worth studying but for this project we need a model that faithfully reproduces all the features of the neuron in a manor simple enough to be coded and run on your home computer. The model is called a Quadratic Integrate-and-fire neuron and can be represented by this Delphi code:

Vout := Vin + tau * (k * (Vin - Vr) * (Vin - Vt) - Uin + i) / CAP;
Uout := Uin + tau * a * (b * (Vout - VRest) - Uin);
if Vout >= vpeak then
  Vout := c;
  Vin := vpeak; // Reset the membrane
  Uout := Uout + d; // Reset the recovery variable 


  • Vout = The current calculated membrane potential
  • Vin = The last membrane potential
  • Uout = The current calculated recovery value
  • Uin = The current calculated recovery value
  • tau = Step time between samples
  • Cap = 100 Membrane capacitance [pF]
  • Vr = -60 Resting membrane potential [mV]
  • Vt = -40 instantaneous threshold potential [mV]
  • k = 0.7 Parameters used for RS type
  • a = 0.03 ; Recovery time constant [ms]
  • b = -2.0 Constant [pA/ohm]
  • c = -50 Membrane voltage reset
  • d = 100 ; For a neocortical pyramidal neuron

The numeric values for k,a,b,c, and d vary by the type of neuron being simulated.

This Soma model contains the Cortex, Thalamus, Hippocampal, Basal Ganglia, Brain Stem, Entorhinal Cortex and Olfactory Bulb simulations. These all come directly from 'Dynamical Systems in Neuroscience. by Eugene Izhikevich

Eugene Izhikevich founder and CEO Brain Corp. San Diego

Download( Windows only)

To Use

  1. Start the application. It will begin spiking as a Cortex RS neuron
  2. From the top menu select a different neuron
  3. Adjust the input current with the slider. Depending on the type of neuron the spiking pattern will change.
  4. Click the 'Status' bar on the right side. A new panel will slide out to give you access to the inter-workings of the neuron.
  5. Adjust the sliders and see the result on the spike pattern
  6. Slide the left and right points on the bottom of the display to set the start/stop point of current injection.
  7. Turn sound of/off through the Help menu.

Next: The Axon