NEURON Tutorial #3

Goals: Set passive properties and measure time constant

Specific aims:

• Set passive properties
• Record voltage
• Save voltage to v.dat
• Measure time constant with FunctionFitter
  Main Menu / Tools / Fitting / Parameterized Function >> FunctionFitter
  Args: A(-1), tau(1), v0(-65), t0(101)
  Y-expr: A*exp(-(t-t0)/tau)+v0

Downloads:

• Main.hoc
• RunControl.hoc
• VGraph.hoc
• ParameterControl.hoc
• 03.zip

External links:

• Chapter 9. Data Analysis and Fitting
• Fitting a function to data

Steps:

• Run Main.doc
• Initiate and run
• Save response to file
• Start FunctionFitter and run fitting (tau = 30 ms)

//======================================
// Title: Tutorial #3
// Author: Payne Y. Chang
// File Name: Main.hoc

//======================================
// Display panels
load_file("nrngui.hoc")		// Display main menu
load_file("RunControl.hoc")	// Display run control
load_file("VGraph.hoc")		// Display v plot

//======================================
// soma
create soma	// Create soma

// Set properties
soma {
	nseg = 1		// Number of segments = 1
	diam = 100		// Diameter [um]
	L = 100			// Length [um]
	Ra = 100		// Axial risistance [ohm-cm]
	cm = 1			// Capacitance of membrane [uF/cm2]
	
	insert pas		// Insert passive properties
	g_pas = 1/30000		// [S/cm2]. Tau = 30 ms
	e_pas = -65		// Reversal potential. [mV]
}

R = 1/soma.g_pas	// Resistance [ohm.cm^2]

print "Surface Area = ", diam*PI*L, " (um^2)"
print "C = ", soma.cm, " (uF/cm^2)"
print "R = ", R, " (ohm cm^2)"
print "C * R = ", soma.cm * R * 1e-3, " (ms)"

//======================================
// Set one current clamp electrode
objectvar electrode
soma electrode = new IClamp(0.5)

electrode.del = 100	// Delay [ms]
electrode.dur = 1	// Duration [ms]
electrode.amp = -0.4	// Amplitude [nA]

//======================================
// Set recording vectors
objref tVector, vVector
tVector = new Vector()	// Time
vVector = new Vector()	// Voltage

tVector.record(&t)		// Record t
vVector.record(&soma.v(0.5))	// Record v at soma

//======================================
// Codes for saving the data to v.dat
objref outputFile		// Output File
outputFile = new File()		// Create file object

objref t2Vector, v2Vector	// Vectors for recording
t2Vector = new Vector()		// Time vector
v2Vector = new Vector()		// Voltage vector

// Procedure to save data to a file(v.dat)
proc save_response() {
	index = tVector.indwhere(">", 101)	// Get the index of the response
	print "index = ", index				// Print index
	t2Vector = tVector.c(index)			// Create time vector
	v2Vector = vVector.c(index)			// Create voltage vector
	
	outputFile.wopen("v.dat")					// Open file
	outputFile.printf("%d\n", t2Vector.size())	// Save number of points
	
	// Save each point
	for i=0, t2Vector.size()-1 {
		outputFile.printf("%g %g\n", t2Vector.x(i), v2Vector.x(i))
	}
	
	outputFile.close()	// Close file
	
	print "Save response to file - Done."	// Display Done information
}

//======================================
// Load Parameter Control panel
load_file("ParameterControl.hoc")

//======================================
// File Name: ParameterControl.hoc
// Create "Parameter Control" panel

// Start of an xpanel 
xpanel("Parameter Control", 0)	// ("Title", 0: vertical lay out)

// Save Response
xbutton("Save Response to File","save_response()")

// Close the xpanel (x, y)
xpanel(1150,10)

FunctionFitter