Chapter 7. Programming Simulations

7.2 MORPHOLOGICAL ASSIGNMENTS.

The morphological parameters of nerve cells may be entered into NEURON in two ways:

Box2. Morphology.hoc

//CREATE SECTIONS

 create 	soma	hillock		axon	dendrite[ndend]
	      		        myelin[nmyelin], node[nmyelin]
		    // names cell components to be used
		    // and calls for "ndend" dendrites
		    // "nmyelin" myelin-node pairs: "nmyelin" and
		    // "ndend" provide for convenient global changes
		    // create may be used to assign other names such 
		    // as "patch", etc.
	   
 // CONNECT SECTIONS to construct cell

		   // See example for simple cell in fig below
		   // Here we connect sections so that all indices radiate out from the soma
	soma	connect hillock(1), 0
	hillock	connect axon(1), 0
	if (nmylin>0)	{ axon	 connect myelin[0](1), 0
			myelin[0] connect node[0](1), 0
		if (nmyelin>1) {
			for i=1,nmyelin-1 {
				node[i-1]   connect myelin[i](1),0
				myelin[i] connect node[i](1), 0
			}
		}
	}

	   
   // ASSIGN DIMENSIONS and number of segments

	soma	{  L=25	  	diam=25  	nseg=1}
	           // length of 25 microns, & diameter of 25
 		   // single segment

	axon	{   L=alen	  diam=10 	nseg=15 }
		   // length of alen microns, & diameter of 10
 		   // split into 15 segments (compartments)
		/* give soma and axon dimensions before hillock, because  
		hillock is to be tapered between soma and axon diameters */
	
	hillock   {L= hlen	nseg=4	
		dsoma	= soma.diam(0)
		daxon	= axon.diam(1)
		diam(0:1) = daxon:dsoma 	// linear taper of
			//diameter of hillock between that of soma and axon
		}
		
	// myelininated and nodal sections are handled in pairs
	for i=0, nmyelin-1 {
		myelin[i].nseg = 5	// 5 segments per myelin region
		node[i].nseg = 1	// single nodal compartment
		}
	mdiam=10	// myelin diameter in microns
	mlen0 = 275	mlen1 = 500	mlen2 = 1000
		// myelinated axon lengths in microns
		// below the myelin length is increased from mlen0 to mlen2
		// while the nodal dimensions remain constant with
		// diam = 10 microns and length = 3.2
	myelin[0] { L= mlen0   diam= mdiam }
	node[0]   { L= 3.2   diam= 10 }
	myelin[1] { L= mlen1   diam= mdiam }
	node[1]   { L= 3.2   diam= 10 }
	if (nmyelin > 2)  for i=2,nmyelin-1 {
		myelin[i] { L= mlen2  diam= mdiam }
		node[i]   { L= 3.2   diam= 10 }
	}
Simple dendritic structures such as
  • a Rall cylinder or
  • a number of dendrites of uniform diameter, again whose Rall diameters depend on their number and each concatenates its progeny a full dendritic tree requiring more complex treatment
may be handled as in the example below. A full dendritic tree requiring more complex treatment to deal with the branching pattern.

Connecting Sections to Construct Cell

All "created" sections have an origin (or 0 end) and a terminal ( or 1) end as shown in the diagram below. In order to construct a cell in the form shown in this figure: 

	soma connect axon(0), 1
		// connects right end of soma (1) to left end of axon (0)
	for i=0,2 soma connect dendrite[i] (1), 0
		// connects  right end (1) of each dendrite to
		// left end of soma (0)

As soon as the any name has been assigned ("created") to describe a component, it receives "legacy default parameter values for diameter, length, and axial resistivity. The membrane capacitance for almost all membranes is a constant and the default assignment is: Cm = 1 (microfarads/cm2) These default assignments may be seen by selecting (pressing) the "Distributed Mechanisms" on the mainmenu panel. When the "Viewer" is selected, one may choose the "Name Values" button. This brings up the the browser panel. Here one may choose to view the parameter set of the appropriate named component by "double clicking" on it in the browser panel. Note that one may restrict or expand the items viewed by choosing from one to all of the options listed on the right side of the browser by clicking to toggle "parameters", "states", etc on or off before selecting the named component. Alternatively, one can choose global mechanisms which brings up a browser panel containing all of the global parameters.

The squid legacy values for the dimensions of a "patch" or soma are readily reassigned the desired value as shown in the line just under "create soma". This can be verified by selecting ("double click" on) the soma for viewing; the panel below should appear.

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Mechanisms
Synapses
Electrodes