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

Many thousands of Inputs to the Soma arrive from the Dendrites. Its single output is 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 and 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 (below).

Video of a running Soma simulation. It shows:

  • Typical Soma spiking with audio for each spike
  • Adjustment of current input to the Soma
  • Adjustment of the time scale for close up views
  • Different types of Soma parameters
  • Recovery varable
  • Phase chart of the operation and
  • Individual adjustment of Soma parameters.

 

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 hyperpolerized region and then recovers to the resting potential.

The model used here is of a neuron described in the book, Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting by Izhikevich, is not based upon biophysical parameters but is a simple model that faithfully reproduces all the neurocomputational dynamical features of the neuron. The model is a two-dimensional systems having a fast voltage variable and a slower “recovery” variable u, which may describe activation of the K+ current or inactivation of the Na+ current or their combination. The simple model to reproduce spiking and bursting behavior of many known types of neurons is described by a pair of differential equations

C dv dt =k(v v r )(v v t )u+S and du dt =a{b(v v r )u} if V V peak vc,uu+d


Those two equations make up a model called a Quadratic Integrate-and-fire neuron. The downloadable simulater is implemented in this Delph with this code:

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

Where:

  • 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 Neuron Simulator