Ex_03_simple_axon.m

create('axon');                                 %create a variable named axon with default parameters.
%-------------------------------------------------------------------------------------------
global axon                                     %required for all variable created
%-------------------------------------------------------------------------------------------
axon.nseg	=55;                                %change the number of segments
axon.L		=10*axon.dia*(axon.nseg);           %(um) change the length of axon
insert(axon,'hh')                               %insert HH channel into AXON    [variable model]  
%the stimulator can be set as a square pulse
Iinstim(axon,0.5,0.01,500,0)                    %intracellular stimulation     [variable positon(0-1) amp(uA) pw(us)  delay(us)]
%Multiple stimulators supported
if 0
Iinstim(axon,0.1,'Isin')                        %Stimulation as a function of time       [variable positon(0-1) Function_Name]
Iinstim(axon,0.9,'SquarePulse')                 %Stimulation as a function of time       [variable positon(0-1) Function_Name]
end
%-------------------------------------------------------------------------------------------

%The parameters that are used in Neurocal are
%.name			%  	    internal use.
%.varnum        %  	    internal use.
%.nseg			% 	    number of segments for the variable.
%.dia       	%(um)	the outer diameter of the variable.
%.da_D  		%		axon/Fiber diameter ratio for calculating the axonal resistance 
                %         - for myelinated axon. if this value is empty(default), 
%                         - .dia will be used instead.
%.dn_D      	%	    node/Fiber diameter ratio for node of Ranvior for calculating the membrane resistance
                %         - and membrane capacitance for myelinated axon. If this value is empty(default), 
                %         - .dia will be used instead.
%.Linter_D      %       Internodal distance / Diameter                
%.L  		    %(um)	the total length of the variable.
%.Lmode         %       1=fix=L, 2 = Linter_D x D x nseg
%.lnodal      	%(um)	Lengh of node of Ranvior for calculating the membrane resistance
                %         - and membrane capacitance for myelinated axon. If this value is empty(default), 
                %         - L/nseg will be used instead.
%.cm	       	%(uf/cm2)for calculating membrane capacitance
%.ra           	%(ohm-cm)for calculating axonal resistance
%.rm           	%(kohm-cm2)for calculating membrane resistance.
%.vini	    	%(mV)
%.model         %
%.vestim		%(mV)   Extracellular voltage (when Ve is not calculated,
%                         - but assigned manually
%.xyz			%(um)   Coordinate of the nodes used for calculating the Ve
%.xyzi    	    % unitless: Vector of the variable (axon) for calculating the coordinate for all nodes
%.xyzc          % um:       The coordinate of the node at the center