Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016)

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Accession:190140
LFPsim - Simulation scripts to compute Local Field Potentials (LFP) from cable compartmental models of neurons and networks implemented in the NEURON simulation environment.
References:
1 . Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational Modeling of Single Neuron Extracellular Electric Potentials and Network Local Field Potentials using LFPsim. Front Comput Neurosci 10:65 [PubMed]
2 . Diwakar S, Medini C, Nair M, Parasuram H, Vijayan A, Nair B (2017) Computational Neuroscience of Timing, Plasticity and Function in Cerebellum Microcircuits (Chapter 12) Computational Neurology and Psychiatry, Springer Series in Bio-/Neuroinformatics, √Črdi P:et al, ed. pp.343
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Cerebellum interneuron granule GLU cell; Hippocampus CA1 pyramidal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Extracellular Fields; Methods;
Implementer(s): Parasuram, Harilal [harilalp@am.amrita.edu]; Diwakar, Shyam [shyam at amrita.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Cerebellum interneuron granule GLU cell;
/*LFPsim - Simulation scripts to compute Local Field Potentials (LFP) from cable compartmental models of neurons and networks implemented in NEURON simulation environment.

LFPsim works reliably on biophysically detailed multi-compartmental neurons with ion channels in some or all compartments.

Last updated 12-March-2016
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro 
*/


// GUI for the tool is scripted in this file

// Initializing variables
objref h00,h11,h22,h33,v1,v2,v3,v4,v11,v22,v33,v44
objref MoveElec,MoveElec_plot, g1, g2, g3  

objref h44,h55,h66
objref sl

// Script for interface partition
h00=new VBox()
h11=new HBox()
h22=new HBox()
h33=new HBox()
h44=new VBox()
h55=new VBox()
h66=new VBox()

proc run_run(){
	//run_control()
	init()
	run()
	file_write()
	g1.exec_menu("View = plot")
	g2.exec_menu("View = plot")
	g3.exec_menu("View = plot")
}


h00.intercept(1)
		xpanel("Control Panel")
		xlabel("                                                  ===== LFPsim ===== ")
		xlabel("LFPsim allows reconstructing LFP of multi-compartmental models of neurons and microcircuits with active ion channels")
		xlabel("Developed at Computational Neuroscience Lab, Amrita University, India.")
		xpanel()

h11.intercept(1)
	
	v1=new VBox()
	v22=new VBox()
	v33=new VBox()
	v44=new VBox()
	
	//Defining Morphology view window
	v1.intercept(1)
		xpanel("")
		xlabel("Morphology view window")
		xpanel()

		MoveElec = new Shape(0)
		MoveElec.view(571.097, 572.916, 54.0667, 53.8575, 463, 88, 201.6, 200.82)
		MoveElec.exec_menu("View = plot")

		xpanel("")
		xlabel("Voltage changes view window")
		xpanel()

		MoveElec_plot = new PlotShape(0)
		MoveElec_plot.view(571.097, 572.916, 54.0667, 53.8575, 463, 88, 201.6, 200.82)		
		MoveElec_plot.exec_menu("View = plot")
		MoveElec_plot.exec_menu("Space Plot")
		MoveElec_plot.exec_menu("Shape Plot")

	v1.intercept(0)
	v1.map("Shape plots", 1, 1, 500, 600)

	//Defining LFP trace view window
	v2=new VBox()
	v2.intercept(1)
		
		h44.intercept(1)

			xpanel("Reconstructed LFP", 0)
			xlabel("                  Simulated LFP")
			xlabel("                 ------------------")
		
			//xbutton("Save traces","file_write()") 
			xlabel("Point Source Approximation")
			
			
		
			xpanel()

		h44.intercept(0)
		h44.map()
		
		g1 = new Graph()	
		g1.addvar("Point_source", 1, 1, 0.8, 0.9, 2)
		graphList[0].append(g1)
		


		h55.intercept(1)
			xpanel("", 0)
			xlabel("Line Source Approximation")

			xpanel()
		h55.intercept(0)
		h55.map()



		g2 = new Graph()	
		g2.addvar("Line_source", 1, 1, 0.8, 0.9, 2)
		graphList[0].append(g2)

		h66.intercept(1)
			xpanel("", 0)
			xlabel("Simple Low-pass Filter")
			
			
			xpanel()
		h66.intercept(0)
		h66.map()

		g3 = new Graph()	
		g3.addvar("Simple_RC_filter", 1, 1, 0.8, 0.9, 2)
		graphList[0].append(g3)
		
				
		
	v2.intercept(0)
	v2.map("Shape plots", 1, 1, 400, 500)

	//Defining electrode parameter setting pannel and simulation control
	v3=new VBox()
	v3.intercept(1)
	
		xpanel("Extracellular Electrode Location", 0)
		xlabel("Set Extracellular Single Electrode Location")
		xlabel("============================================")
		xlabel("Move the electrode by changing X,Y,Z")
		xlabel("X,Y,Z coordinates are in um")
		xvalue("X", "elec_x", 1, "setelec(elec_x,elec_y,elec_z)", 0, 1)
		xvalue("Y", "elec_y", 1, "setelec(elec_x,elec_y,elec_z)", 0, 1)
		xvalue("Z", "elec_z", 1, "setelec(elec_x,elec_y,elec_z)", 0, 1)
		xlabel("")
		xlabel("To interactively move the electrode, move the mouse pointer on ")
		xlabel("\"Morphology view\" window and right click on the plot then")
		xlabel("select \"LFP_electrode\" and move the mouse pointer")
		xlabel("to change electrode position and click the location on the plot")
		xlabel("to record extracellular potential.")

		xbutton("Run single electrode simulation and Save tarces","run_control()")


		xlabel("")
		xlabel("Simulating Multi Electrode Array (MEA)")
		xlabel("===============================================")

	
		xlabel("MEA reconstruction of extracellular potential allows to study extracellular")
		xlabel("current dynamics at variouse location in the extracellular medium.")
		xlabel("")
		xbutton("Set Multiple_Electrode","multi_electrode_panel()")
		xbutton("Run MEA simulation","run_multi_button()")
		xlabel("")
		xlabel("")

		xbutton("Definitions","extra_definition()")
		xlabel("Set Extracellular Medium Properties")
		xlabel("===================================")
		xlabel("Any changes to these parameters will reflect in all compartments")
		xlabel("in the model.")	
		xlabel("Extracellular Capacitance (in uF / cm2)")
		xvalue("xc[0] (Layer 1)", "local_xc_0", 1, "change_local_xc_0(local_xc_0)", 0, 1)
		xvalue("xc[1] (Layer 2)", "local_xc_1", 1, "change_local_xc_1(local_xc_1)", 0, 1)

		xlabel("")
		xlabel("Extracellular Conductance (in mhn/cm2)")
		xvalue("xg[0] (Layer 1)", "local_xg_0", 1, "change_local_xg_0(local_xc_0)", 0, 1)
		xvalue("xg[1] (Layer 2)", "local_xg_1", 1, "change_local_xg_1(local_xc_1)", 0, 1)
		xlabel("")

		xlabel("Extracellular axial resistance (in uF / cm2)")
		xvalue("xraxial[0] (Layer 1)", "local_xraxial_0", 1, "change_local_xraxial_0(local_xraxial_0)", 0, 1)
		xvalue("xraxial[1] (Layer 2)", "local_xraxial_1", 1, "change_local_xraxial_1(local_xraxial_1)", 0, 1)
		xpanel()
		
		

		setelec(elec_x,elec_y,elec_z)	
			

		//h22.intercept(0)
		//h22.map()

		
	v3.intercept(0)
	v3.map()


h11.intercept(0)
h11.map()

h00.intercept(0)
h00.map("LFP Simulation tool", 1, 1, 1200, 800)



// multi electrode panel
proc multi_electrode_panel(){

		place_mea_electrode = 1

		xopen("multiple_electrode1.hoc")
		xpanel("Multi Electrode Panel")
		xlabel("                  Multi Electrode Panel")
		xlabel("                  ==================")
		xlabel("")

		//xlabel("Enter starting X,Y,Z coordinates of 4x4 electrode array")
		//xvalue("X", "mul_start_point_x", 1, "set_multi_electrode(mul_start_point_x,mul_start_point_y,mul_start_point_z,mul_elec_distance)", 0, 1)
		//xvalue("Y", "mul_start_point_y", 1, "set_multi_electrode(mul_start_point_x,mul_start_point_y,mul_start_point_z,mul_elec_distance)", 0, 1)
		//xvalue("Z", "mul_start_point_z", 1, "set_multi_electrode(mul_start_point_x,mul_start_point_y,mul_start_point_z,mul_elec_distance)", 0, 1)

		xlabel("By default the electrodes will be placed on z plane")
		xlabel("For electrodes on z plane, plane=3")
		xlabel("For electrodes on y plane, plane=2")
		xlabel("For electrodes on x plane, plane=1")
		xvalue("plane", "plane", 1,"", 0, 1)
		xlabel("")

		xvalue("Distance between electrodes", "mul_elec_distance", 1, "set_multi_electrode(mul_start_point_x,mul_start_point_y,mul_start_point_z,mul_elec_distance)", 0, 1)
		xbutton("Place the electrodes","multi_electrode()")

		xpanel(500,300)

}


// Defining NEURON's extracellular mechanism
proc extra_definition(){

	xpanel("NEURON's Extracellular mechanism")
	xlabel("NEURON's extracellular mechanism adds two layers of extracellular field to the section. Vext is solved simultaneously with the v.")
	xlabel("When the extracellular mechanism is present, v refers to the membrane potential and vext (i.e. vext[0])")
	xlabel("refers to the extracellular potential just next to the membrane. ")
	xlabel("")
	xlabel("")
	xlabel("")
	xlabel("          Ra")
	xlabel("o/`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\o vext + v")
	xlabel("     |          |          |          |")
	xlabel("    ---        ---        ---        ---")
	xlabel("   |   |      |   |      |   |      |   |")
	xlabel("    ---        ---        ---        ---")
	xlabel("     |          |          |          | ")
	xlabel("     |          |          |          |     i_membrane")
	xlabel("     |  xraxial |          |          |")
	xlabel(" /`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\ vext")
	xlabel("     |          |          |          |")
	xlabel("    ---        ---        ---        ---     xc and xg")
	xlabel("   |   |      |   |      |   |      |   |    in  parallel")
	xlabel("    ---        ---        ---        ---")
	xlabel("     |          |          |          | ")
	xlabel("     |          |          |          |")
	xlabel("     |xraxial[1]|          |          | ")
	xlabel(" /`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\ vext[1]")
	xlabel("     |          |          |          |")
	xlabel("    ---        ---        ---        ---     the series xg[1], e_extracellular")
	xlabel("   |   |      |   |      |   |      |   |    combination is in parallel with")
	xlabel("   |  ---     |  ---     |  ---     |  ---   the xc[1] capacitance. This is")
	xlabel("   |   -      |   -      |   -      |   -    identical to a membrane with")
	xlabel("    ---        ---        ---        ---     cm, g_pas, e_pas")
	xlabel("     |          |          |          |")
	xlabel("-------------------------------------------- ground")

	xpanel(500,300)

}

// Run pannel for LFP simulation
proc run_control(){

		xpanel("Simulation Control")
		xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
		xbutton("Run","run_run()")
		xbutton("Stop","stoprun=1")
		xvalue("t","t", 2 )
		xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
		xvalue("dt","dt", 1,"setdt()", 0, 1 )
		xvalue("Real Time","realtime", 0,"", 0, 1 )
		xpanel(900,300)

}

// Run pannel for MEA simulation
proc mea_run_control(){

		xpanel("Simulation Control")
		xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
		xbutton("Run","xopen(\"mea_run_then_plot.hoc\")")
		xbutton("Stop","stoprun=1")
		xvalue("t","t", 2 )
		xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
		xvalue("dt","dt", 1,"setdt()", 0, 1 )
		xvalue("Real Time","realtime", 0,"", 0, 1 )
		xpanel(900,300)

}

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