Dendritica (Vetter et al 2001)

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Accession:7907
Dendritica is a collection of programs for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in: Vetter, P., Roth, A. & Hausser, M. (2001) For reprint requests and additional information please contact Dr. M. Hausser, email address: m.hausser@ucl.ac.uk
Reference:
1 . Vetter P, Roth A, Häusser M (2001) Propagation of action potentials in dendrites depends on dendritic morphology. J Neurophysiol 85:926-37 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Cerebellum Purkinje GABA cell;
Channel(s): I Na,t; I L high threshold; I p,q; I K; I M; I K,Ca;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Bursting; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Axonal Action Potentials; Action Potentials;
Implementer(s): Hausser, M [M.Hausser at ucl.ac.uk];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Cerebellum Purkinje GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; I Na,t; I L high threshold; I p,q; I K; I M; I K,Ca;
Files displayed below are from the implementation
/* Relating dendritic geometry and signal propagation   */
/* Philipp Vetter, Arnd Roth and Michael Hausser        */
/* gui.hoc Version 1.0                       11.10.1999 */

xopen("init.hoc")

/*********************************************************
 GUI Graphical User Interface
 *********************************************************/

proc Main() { 
/* Calls main panel and allows */
/* - Loading a cell */
/* - Clearing the Screen */
/* - Plotting various Graphs */
/* - Loading other Panels */
/* - Miscellaneous */
/* - Quit */

	xpanel("Main")
		xbutton("Load Neuron","Load_cell()")
		xbutton("Clear Screen","clf()")
		Graph_menu()

		xmenu("Other Panels")
		 xbutton("Electrophysiology","Electrophysiology()")
		 xbutton("Statistics","Statistics()")
		 xbutton("Channels","Conductances()")
		 xbutton("Simulation settings","Simulation()")
		 xbutton("Geometry","Geometry()")
		xmenu()

			/* copied from "graphpanel" */

		xmenu("Miscellaneous")

		 xmenu("Clipboard")
		  xbutton("Save to File","load_proc(\"clipboard_save\") clipboard_save()")
		  xbutton("Retrieve from File","load_proc(\"clipboard_retrieve\") clipboard_retrieve()")
		  xbutton("Gather Values","load_template(\"GatherVec\") makeGatherVec()")
		  xbutton("Vector Play","load_template(\"VectorPlay\") makeVectorPlay()")
		  xbutton("Vector Wrapper","load_template(\"VecWrap\") makeVecWrap()")
		 xmenu()

		 xmenu("Family")
		  xbutton("Family","load_template(\"Family\") makeFamily()")
		  xbutton("Command","load_template(\"ExecCommand\") newcommand()")
		 xmenu()

		xbutton("Parameterized Function","load_template(\"FunctionFitter\") makefitter()")
		xbutton("Run Fitter","load_template(\"RunFitter\") makerunfitter()")

		xmenu("Impedance")
		 xbutton("Frequency","load_template(\"ImpedanceRatio\") makeImpRatio()")
		 xbutton("Path","load_template(\"Impx\") makeImpx()")
		 xbutton("log(A) vs x","load_template(\"LogAvsX\") makelogax()")
		 xbutton("Shape","load_template(\"ImpShape\") makeImpShape()")
		xmenu()

		xmenu("Viewers")
		 xbutton("Shape Name","load_template(\"MenuExplore\") makeMenuExplore()")
		 xbutton("Name Values","nrnallsectionmenu()")
		 xmenu("Mechanisms (Globals)")
		  xbutton("na_ion","nrnglobalmechmenu(\"na_ion\")")
		  xbutton("k_ion","nrnglobalmechmenu(\"k_ion\")")
		  xbutton("hh","nrnglobalmechmenu(\"hh\")")
		  xbutton("ca_ion","nrnglobalmechmenu(\"ca_ion\")")
		  xbutton("ca","nrnglobalmechmenu(\"ca\")")
		  xbutton("cad","nrnglobalmechmenu(\"cad\")")
		  xbutton("kca","nrnglobalmechmenu(\"kca\")")
		  xbutton("km","nrnglobalmechmenu(\"km\")")
		  xbutton("kv","nrnglobalmechmenu(\"kv\")")
		  xbutton("na","nrnglobalmechmenu(\"na\")")
		 xmenu()
		xmenu()

		xmenu("Point Processes")
		 xbutton("IClamp","makePointBrowser(\"IClamp\")")
		 xbutton("SEClamp","makePointBrowser(\"SEClamp\")")
		 xbutton("AlphaSynapse","makePointBrowser(\"AlphaSynapse\")")
		 xbutton("syn2","makePointBrowser(\"syn2\")")
		 xbutton("TrigKSyn","makePointBrowser(\"TrigKSyn\")")
		 xbutton("SEClamp","makePointBrowser(\"SEClamp\")")
		 xbutton("VClamp","makePointBrowser(\"VClamp\")")
		 xbutton("APCount","makePointBrowser(\"APCount\")")
		xmenu()

		xmenu("Distributed Mechanisms")
		 xmenu("Managers")
		  xbutton("Inserter","load_template(\"Inserter\") makeinserter()")
		  xbutton("Homogeneous Spec","load_proc(\"makeshowmechanism\") makeshowmechanism()")
		 xmenu()
		xmenu()

	xmenu()
		xbutton("Quit","quit()")
		xpanel(400,0)

		// Conductances()
		
		}

proc Geometry() { 
/* Calls Geometry panel and allows */
/* - Removing/Adding an Axon to cell */
/* - Calculate Geometric parameters */
/* - Shape Name */

		vbox1 = new VBox()
		vbox1.intercept(1)

	xpanel("1",1)
		xbutton("Remove Axon","remove_axon()")
		xbutton("Connext Axon","clf()")
	xpanel()	
	xpanel("1",1)
		 xbutton("Recalculate Geometry","geometry_calc()")
		 xbutton("Shape Name","load_template(\"MenuExplore\") makeMenuExplore()")


	xpanel(400,0)


		vbox1.intercept(0)
		vbox1.map("Geometry",800,300,300,25)


		}




proc Simulation() {
/* Calls Simulation panel and allows */
/* - Simulation duration,dt,recording delay */
/* - Stimulus electrode amplitude, delay & duration */
/* - Recording (for plotting purposes) duration, delay, dt */

		xpanel("Simulation", 0)
		xpvalue("rec dur",&rec_dur,1,"rec_set(rec_del,rec_dur,rec_dt)")
		xpvalue("rec del",&rec_del,1,"rec_set(rec_del,rec_dur,rec_dt)")
		xpvalue("rec dt",&rec_dt,1,"rec_set(rec_del,rec_dur,rec_dt)")
		xpvalue("stim amp",&st_amp,1,"st_set(st_amp,st_del,st_dur)")
		xpvalue("stim del",&st_del,1,"st_set(st_amp,st_del,st_dur)")
		xpvalue("stim dur",&st_dur,1,"st_set(st_amp,st_del,st_dur)")
		xpvalue("sim dur",&sim_dur,1,"sim_set(sim_dur,sim_dt,sim_durI,sim_dtI)")
		xpvalue("sim dt",&sim_dt,1,"sim_set(sim_dur,sim_dt,sim_durI,sim_dtI)")
		xpvalue("sim durI",&sim_durI,1,"sim_set(sim_dur,sim_dt,sim_durI,sim_dtI)")
		xpvalue("sim dtI",&sim_dtI,1,"sim_set(sim_dur,sim_dt,sim_durI,sim_dtI)")
		xpanel(950,270)
                 }

proc Nonuniform() {
/* Calls Nonuniform panel and allows */
/* - setting of nonuniform passive membrane properties */
		nonuniform_Rm = 1
		xpanel("Nonuniform", 0)
		xlabel("nonuniformity")
		xpvalue("rm",&rm,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpvalue("rm_end",&rm_end,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpvalue("rm_steep",&rm_steep,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpvalue("rm_half",&rm_half,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpanel(1050,270)
                 }



proc Electrophysiology() {
/* Calls Electrophysiology panel and allows */
/* - voltage clamping [press "voltage clamp"] */
/* - resetting location, scaling, and chosing waveform to be played */
/* - current clamping [press "current clamp"] */
/* - resetting location, amplitude of current */
/* - synaptic activation [press "synapse"] */
/* - resetting location, parameters of synapse */



		vbox1 = new VBox()
		vbox1.intercept(1)
		xpanel("yo",1)
			xvarlabel(cellnameact)
			xcheckbox("movie",&movie)
		xpanel()

		xpanel("Voltage Clamp", 1)
			xbutton("Voltage Clamp","gactive_run(1)")
			xbutton("Location","PointLocator(0)")
			xpvalue("scaling",&VClampScale)
			xmenu("Waveform")
			 xbutton("somatic AP (p18)","set_waveform()")
			 xbutton("dendritic AP (p21)","set_waveform(\"dendspike_p21\",1)")
			 xbutton("currently picked waveform","set_waveform(hoc_obj_[0])")
			 xbutton("load waveform...","set_waveform(\"dendspike_p21\",1,1)")
			xmenu()
		xpanel()

		xpanel("Current Clamp",1)
			xbutton("Current Clamp","gactive_run(0)")
			xbutton("Location","PointLocator(1)")
			xpvalue("Amplitude",&st_amp,1,"st_set(st_amp,st_del,st_dur)")
		xpanel()

		xpanel("Synaptic",1)
			xbutton("Synapse","gactive_run(5)")
			xbutton("Location","PointLocator(2)")
			xpvalue("gmax",&synapse_gmax,0.1,"set_synapse(synapse_gmax,synapse_tau0,synapse_tau1,synapse_onset,synapse_e)")
		xpanel()

		xpanel("other",1)
		xbutton("Input Resistance","rinput_calc()")
		xbutton("g_na threshold","threshold_find()")
		xvarlabel(Nathreshold)
		xpanel()

		vbox1.intercept(0)
		vbox1.map("Electrophysiology",500,0,400,180)
		}


proc Statistics() { local i
/* Calls Statistics panel and allows */
/* [get_data] load simulation results for analysis */
/* [legend] plot legend of the different cell-types (see below) */
/* [Average] print cell-type averaged values of the parameter specified under [y] */
/* [Single] correlate parameter specified under [y] with [x1] */
/* [Double] correlate parameter specified under [y] with combination of [x1]&[x2] */ 
/* [Triple] correlate parameter specified under [y] with combination of [x1]&[x2]&[x3] */ 
/* [x powers] specifies whether correlations are optimized w.r.t  power of x1 */ 


		vbox1 = new VBox()
		vbox1.intercept(1)

		xpanel("Ho",1)
		 xbutton("Get Data","Getdata()")
		 xbutton("Legend","clegend()")
		 xvarlabel(actname)
		xpanel()

		xpanel("1",1)
		 xbutton("Average","averages(Yval)")
		xbutton("Single","singlecorrelation(Yval,Xval1)")
		xbutton("Double","doublecorrelation(Yval,Xval1,Xval2)")
		xbutton("Triple","triplecorrelation(Yval,Xval1,Xval2,Xval3)")
		xcheckbox("Powers",&powers)
		xpanel(300,20)
		for i=0,3 { stats_sub(i) }


		vbox1.intercept(0)
		vbox1.map("Statistics",500,0,380,260)		

		}
			


proc Graph_menu() { 
		xmenu("Graphs")
			xmenu("New Graph")
			xbutton("Voltage axis","newPlotV()")
			xbutton("Current axis","newPlotI()")
			xbutton("State axis","newPlotS()")
			xbutton("Shape plot","newshapeplot()")
			xbutton("Vector movie","newvectorplot()")
			xbutton("Phase Plane","newphaseplane()")
			xbutton("Grapher","load_proc(\"makegrapher\") makegrapher()")
			xmenu()

		xbutton("-------------------","n=1")

		xmenu("Which Sections")
			xradiobutton("trunk","sim_plt(1)")
			xradiobutton("all","sim_plt(2)")
			xradiobutton("branchpoints","sim_plt(3)")
			xradiobutton("terminations","sim_plt(4)")
			xradiobutton("branchpoints_noend","sim_plt(5)")
			xradiobutton("all_noend","sim_plt(6)")
		xmenu()
		xmenu("Which Length")
			xradiobutton("electrotonic","L_switch(1) sim_plt()")
			xradiobutton("physical","L_switch(0) sim_plt()")
			xmenu()

		xbutton("-------------------","n=1")

		xbutton("Simulation","sim_plot()")
		xbutton("Geometric values","geom_plot()")
		xbutton("Functional values","impedance_plot()")

		xbutton("-------------------","n=1")

		xmenu("Simulation X against distance")
	xbutton("peak voltage change","APdvdr_plot()")   /* dvpeak/dr(distance soma) */
	xbutton("AP amplitude","APamp_plot()")      /* AP amplitude(distance soma) */
	xbutton("AP max velocity","APvmax_plot()")	/* AP maxvelocity(distance soma) */
	xbutton("AP peak latency","APplat_plot()")     /* AP peak latency(distance soma) */
	xbutton("AP onset latency","APolat_plot()")     /* AP onset latency(distance soma) */
	xbutton("AP halfwidth","APhalf_plot()")     /* AP halfwidth(distance soma) */
	xbutton("AP voltage vs time","APvolt_plot()")      
	xbutton("AP peak","APpeak_plot()")
	xbutton("general info","APtext_plot()")     /* general info on cell */
		xmenu()

		xmenu("Gemeotric individual")
		xradiobutton("attenuation_plot()")   
		xradiobutton("interbranchdist()")  
		xradiobutton("areadist()")  
		xradiobutton("dareadist()") 
		xradiobutton("diamdist()")  
		xradiobutton("ralldistribution()")/* plot rall ration distribution */
		xradiobutton("diam_distance()")   /* plot distance upstream branchpoint v distance soma */
		xradiobutton("branchhist()")      /* histogram of branchpoints and terminations */
		xradiobutton("branchgauss()")     /* Gaussian distribution of branchpoints and terminations */
		xradiobutton("crossarea()")       /* plot crossectional area as fxn of distance */
		xradiobutton("ralldarea()")        /* plot "ralldarea" as a fxn of distance */
		xmenu()
		xmenu("Impedance individual")
		xradiobutton("Rmismatch_plot()")        /* Resistance mismatch */
		xradiobutton("Zmismatch_plot()")        /* Impedance mismatch */
		xradiobutton("APsine()")          /* AP sine frequency */
		xradiobutton("mismatch_bar()")           /* bar chart of R & Z mean values */
		xradiobutton("Rmismatchgauss()")   /* plot distribution of R (distal/distal + proximal) */
		xradiobutton("Zmismatchgauss()")
		xmenu()
		xmenu()
		}















proc runcontrol() {
		xpanel("RunControl", 0)
		xcheckbox("Use CVode",&using_cvode_,"cvode.active(using_cvode_)")
		v_init = -70
		xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
		xbutton("Init & Run","run()")
		xbutton("Stop","stoprun=1")
		runStopAt = 5
		xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
		runStopIn = 1
		xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
		xbutton("Single Step","steprun()")
		t = 0
		xvalue("t","t", 2 )
		tstop = 1000
		xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
		dt = 0.025
		xvalue("dt","dt", 1,"setdt()", 0, 1 )
		steps_per_ms = 40
		xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
		xpanel(970,340)
                 }

proc mainpanel() {
			xpanel("NEURON Main Panel", 0)
			xcheckbox("Quiet",&stdrun_quiet,"")
			realtime = 0
			xvalue("Real Time","realtime", 0,"", 0, 1 )
			celsius = 37
			xvalue("celsius","celsius", 1,"", 0, 1 )
			global_ra = 150
			xvalue("Axial Resistivity","global_ra", 1,"set_ra()", 1, 1 )
			xbutton("RunControl","nrncontrolmenu()")
			xmenu("New Graph")
			xbutton("Voltage axis","newPlotV()")
			xbutton("Current axis","newPlotI()")
			xbutton("State axis","newPlotS()")
			xbutton("Shape plot","newshapeplot()")
			xbutton("Vector movie","newvectorplot()")
			xbutton("Phase Plane","newphaseplane()")
			xbutton("Grapher","load_proc(\"makegrapher\") makegrapher()")
			xmenu()
			xmenu("Point Processes")
			xmenu("Managers")
			xbutton("Point Manager","load_template(\"PointProcessManager\") makeppm()")
			xbutton("Point Group","load_template(\"PointProcessGroupManager\") makeppgm()")
			xbutton("Electrode","load_proc(\"makeelectrode\") makeelectrode()")
			xmenu()
			xmenu("Viewers")
			
			xmenu("PointProcesses")
			xbutton("IClamp","makePointBrowser(\"IClamp\")")
			xbutton("AlphaSynapse","makePointBrowser(\"AlphaSynapse\")")
			xbutton("Synapse","makePointBrowser(\"syn2\")")
			xbutton("TrigKSyn","makePointBrowser(\"TrigKSyn\")")
			xbutton("SEClamp","makePointBrowser(\"SEClamp\")")
			xbutton("VClamp","makePointBrowser(\"VClamp\")")
			xbutton("APCount","makePointBrowser(\"APCount\")")
			xmenu()
			xmenu()
			xmenu()
			xmenu("Distributed Mechanisms")
			xmenu("Managers")
			xbutton("Inserter","load_template(\"Inserter\") makeinserter()")
			xbutton("Homogeneous Spec","load_proc(\"makeshowmechanism\") makeshowmechanism()")
			xmenu()
			xmenu("Viewers")
			xbutton("Shape Name","load_template(\"MenuExplore\") makeMenuExplore()")
			xbutton("Name Values","nrnallsectionmenu()")
			xmenu("Mechanisms (Globals)")
			xbutton("na_ion","nrnglobalmechmenu(\"na_ion\")")
			xbutton("k_ion","nrnglobalmechmenu(\"k_ion\")")
			xbutton("hh","nrnglobalmechmenu(\"hh\")")
			xbutton("ca_ion","nrnglobalmechmenu(\"ca_ion\")")
			xbutton("ca","nrnglobalmechmenu(\"ca\")")
			xbutton("cad","nrnglobalmechmenu(\"cad\")")
			xbutton("kca","nrnglobalmechmenu(\"kca\")")
			xbutton("km","nrnglobalmechmenu(\"km\")")
			xbutton("kv","nrnglobalmechmenu(\"kv\")")
			xbutton("na","nrnglobalmechmenu(\"na\")")
			xmenu()
			xmenu()
			xmenu()

			xmenu("Miscellaneous")
			xmenu("Clipboard")
			xbutton("Save to File","load_proc(\"clipboard_save\") clipboard_save()")
			xbutton("Retrieve from File","load_proc(\"clipboard_retrieve\") clipboard_retrieve()")
			xbutton("Gather Values","load_template(\"GatherVec\") makeGatherVec()")
			xbutton("Vector Play","load_template(\"VectorPlay\") makeVectorPlay()")
			xbutton("Vector Wrapper","load_template(\"VecWrap\") makeVecWrap()")
			xmenu()
			xmenu("Family")
			xbutton("Family","load_template(\"Family\") makeFamily()")
			xbutton("Command","load_template(\"ExecCommand\") newcommand()")
			xmenu()
			xbutton("Parameterized Function","load_template(\"FunctionFitter\") makefitter()")
			xbutton("Run Fitter","load_template(\"RunFitter\") makerunfitter()")
			xmenu("Impedance")
			xbutton("Frequency","load_template(\"ImpedanceRatio\") makeImpRatio()")
			xbutton("Path","load_template(\"Impx\") makeImpx()")
			xbutton("log(A) vs x","load_template(\"LogAvsX\") makelogax()")
			xbutton("Shape","load_template(\"ImpShape\") makeImpShape()")
			xmenu()
			xmenu()
			xpanel(910,70)
		}



proc PointLocator() { 
		if ($1==0) ppl = new PointProcessLocator(vclamp)
		if ($1==1) ppl = new PointProcessLocator(st)
		if ($1==2) ppl = new PointProcessLocator(synapse)

		}


proc select_ref() { ref2.loc(hoc_ac_)
			ref.point_mark_remove()
			ref.point_mark(ref2,3)
		     }


proc gactive_run() { 	local n
			/* simupanel run for GUI */
			n = numarg()
			rinput_calc()
			if (n>0) { simMode = $1	 }
		     	if (n>0) sim(VClampScale) else sim()
			sim_calc()
			sim_plot()
		   }	

equiv=0


proc neuron_set() {     local dummy,dummy2,ct,i

		dummy=equiv
		equiv=0
		forward = 0
		printcellnameact = 0

		dcell = cell	
		dcore = core	
		dsuffix = suffix	
		dcellname = cellname
		dcelladdress = celladdress


	xmenu("Neuron")
	for i=0,7 {
	if (i==0) xmenu("Pyramidal")
	if (i==1) xmenu("Nigral")
	if (i==2) xmenu("Purkinje")
	if (i==3) xmenu("DG granule cells")
	if (i==4) xmenu("DG interneurons")
	if (i==5) xmenu("CA1 Pyramidal")
	if (i==6) xmenu("CA3 Pyramidal")
	if (i==7) xmenu("CA3 interneurons")


	for ct=0,CellList.count-1 {  if (CellList.object(ct).type==i) {
	  cell_name(CellList.object(ct).loc)
	  sprint(str1,"xradiobutton(cellname,\"cell_name(CellList.object(%d).loc,1)\")",ct)
	  execute(str1)
				}}
	xmenu()   }
	xmenu()

	equiv=dummy 
	printcellnameact = 1
		cell = dcell	
		core = dcore	
		suffix = dsuffix	
		cellname = dcellname
		celladdress = dcelladdress
} 








proc stats_sub() { local ct

		n = $1

		if (n==0) str1 = "y"
		if (n==1) str1 = "x1"
		if (n==2) str1 = "x2"
		if (n==3) str1 = "x3"
		
		xpanel(str1)
		xmenu(str1)
		if (n==1) xbutton("functional","geometric=0 Xval1=-2 Xval1str = \"functional\"")
		if (n==1) xbutton("geometric","geometric=1 Xval1=-1  Xval1str = \"geometric\"")

		ct = 0
		for i=0,parameters.count()-1 {
			if ((mod(i,25)==0)) { 
						if (ct>0) xmenu() 
						sprint(str1,"%d",ct+1)
						xmenu(str1)
						ct += 1 }

			str2 = parameters.object(i).str
			N    = parameters.object(i).n       
			sprint(str2,"xbutton(\"%s\",\"pick(%d,%d)\")",str2,n,N)
			execute(str2) // makes button entry
					   }
		xmenu() 
		
		if (n==0) xvarlabel(Yvalstr)
		if (n==1) xvarlabel(Xval1str)
		if (n==2) xvarlabel(Xval2str)
		if (n==3) xvarlabel(Xval3str)
		xmenu()

		xpanel(300,0)
	}
 

proc pick() {
		dissect($2)

		if ($1==0) { Yvalstr = Data[ci][cj][ck].str 
			     Yval = $2 }
		if ($1==1) { Xval1str = Data[ci][cj][ck].str 
			     Xval1 = $2 }
		if ($1==2) { Xval2str = Data[ci][cj][ck].str 
			     Xval2 = $2 }
		if ($1==3) { Xval3str = Data[ci][cj][ck].str 
			     Xval3 = $2 }

		}		



proc singlecorrelation() { local i

		if ($2==-2) { if (powers) single_corrf(Yval,1) else single_corrf(Yval) }
		if ($2==-1) { if (powers) single_corr(Yval,1)  else single_corr(Yval) }

		if (($2<0)&&(powers==0)) { for i=0,5 cplot(Yval,goodcorr[1].x[i]) }
		if (($2<0)&&(powers==1)) { for i=0,5 powerplot(Yval,goodcorr[1].x[i]) }

		if ($2>-1) {if (powers) powerplot($1,$2) else cplot($1,$2)}		
		}

proc doublecorrelation() {

	if ($2==-1) {if (powers) double_corr(Yval) else double_corr(Yval,1)}
	if ($2==-2) continue_dialog("This is not implemented at present")
	if ($2>-1) { if (powers) powerplot(Yval,Xval1,Xval2) else { c3(Yval,Xval1,Xval2) cplot()} }

			 }

proc triplecorrelation() { 
			if (($2>-1)&&(powers==1)) powerplot(Yval,Xval1,Xval2,Xval3) else {
				continue_dialog("This is not implemented at present") }
			}

proc sim_plot() {	/* plot simulation results of trunk segments */
			
			clf()	
			APvolt_plot()
			APamp_plot()
		//	APvmax_plot()
		//	APplat_plot()
		//	APolat_plot()
		//	APhalf_plot()

			if (cells >3) APvolt_plot(3)
			// APpeak_plot()			
			APtext_plot()
			APdvdr_plot()
		}


proc geom_plot() { 	/* plot geometric measures */

			if (!numarg())	{ geometry_calc(1) }

			// interbranchdist()
			/* branchgauss() */
			branchhist()
			areadist()
			dareadist()
			if (electrotonicL) crossarea()
			/* rallarea() */
			ralldistribution()
			/* diam_distance() */
			diamdist()
         	       }					


proc geom_pt()      { 	local i, max /* print some geometric values */

			i = max = 0 

			forsec branchpoints {
				if (max < ralldiam.x[i]) { max = ralldiam.x[i]
							       this_section() sref = new SectionRef()
								}
				print ralldiam.x[i] , " ", secname()
				i+=1
					    }
			sref.sec print "section ", secname(), " has the highest rall ratio (",max,")"
			sref.sec get_children()
			totaldiam = 0
			forsec children { print 1 
					  print (diam(0)^(1.5))
					  totaldiam += (diam(0)^(1.5))
					}
			sref.sec print totaldiam/(diam(1)^(1.5))
		      }



proc impedance_plot() { /* plot impedance values (all points) */
			clf()
		//	mismatch_bar()
			Rmismatch_plot()
			Zmismatch_plot()
		//	APsine()
		//	Rmismatchgauss()
		//	Zmismatchgauss()
		}


proc sim_plt2()	{ electrotonicL = $1
		  dist_switch()
		sim_plt()
		}

proc sim_plt() { /* plot simulation values */
		if (numarg() == 1) dist_switch($1) else dist_switch()
		sim_calc()
		sim_plot()
		}




/*****************************************************************
  Single Plots
 *****************************************************************/


proc APamp_plot() 	{ local i  /* AP amplitude(distance soma) */

		  fig(dist,amp,1,0,2,3)

			ref  	= dist.c
			ref.div(-amp_lmd).apply("exp").mul(amp_max).add(amp_bas)
			sort(dist,ref)
			if (!electrotonicL)	fig(v1,v2,0,1,1)

			figlab("AP amplitude",0.3,0.9)

			}

proc APvmax_plot() 	{ local i /* AP maxvelocity(distance soma) */

		  fig(dist,vmax,1,0,2,3)

			ref = dist.c
			ref.div(-vmax_lmd).apply("exp").mul(vmax_amp)
			sort(dist,ref)
			if (!electrotonicL) fig(v1,v2,0,1,1)
			figlab("AP max velocity",0.3,0.9)

			}


proc APplat_plot() 	{ local i  /* AP peak latency(distance soma) */


		  fig(dist,plat,1,0,2,3)


			ref 	= dist.c
			ref.div(plat_s)
			sort(dist,ref)
			if (!electrotonicL) fig(v1,v2,0,1,1)

			figlab("AP peak latency",0.3,0.9)

			}


proc APolat_plot() 	{ local i  /* AP onset latency(distance soma) */


		  fig(dist,olat,1,0,2,3)

			ref  	= dist.c
			ref.div(olat_s)
			sort(dist,ref)
			if (!electrotonicL) fig(v1,v2,0,1,1)

			figlab("AP onset latency",0.3,0.9)

			}



proc APhalf_plot() 	{ local i,a  /* AP halfwidth(distance soma) */

			  fig(dist,half,1,0,2,3)

			ref = dist.c
			ref.mul(half_s).add(half_b)
			sort(dist,ref)
			if (!electrotonicL) fig(v1,v2,0,1,1)

			figlab("AP halfwidth",0.3,0.9)

			}



proc APvolt_plot()	{ local n

			fig(time,vsoma)
			fig(time,vnode,0,1,3)
			fig(time,vdend,0,1,2)
			if (simMode==1 || simMode==3) fig(time,voltrec,0,1,4)
			if (simMode==5 ) fig(time,synapserec,0,1,5)

			if (n==0)	figlab(activecell,0.7,0.9)\

					figlab("soma")
					figlab("node",3)
					figlab("dendrite",2)
			if (simMode==1 || simMode==3) figlab("vclamp site",4)
			if (simMode==5) figlab("synaptic site",5)

			}


proc APpeak_plot()	{
			sort(dist,vpk)
			fig(v1,v2)
			figlab("Vpeak",0.7,0.9)
			}



proc APdvdr_plot() 	{ local i /* AP maxvelocity(distance soma) */

		    fig(dist,dvdr,1,0,2,3)

			figlab("dvpeak/dr",0.3,0.9)

			}



proc APtext_plot()	{ /* general info on cell */

			fig(dist,dist,0,0,0)

			fsize = 1.2
		        figlab(activecell,0.02,0.9)
			fsize = 0.9

			figlab("active",0.02,0.7)
			sprint(str1,"gna\t\t%g",g_na)
			figlab(str1)
			sprint(str1,"gkv\t\t%g",g_kv)
			figlab(str1)
			sprint(str1,"gna (node)\t%g",g_nanode)
			figlab(str1)
			sprint(str1,"gkv (node)\t%g",g_kvnode)
			figlab(str1)

			sprint(str1,"%1.2f nA",st.amp)
			figlab(str1)

			figlab("passive",0.4,0.7)
			sprint(str1,"Rm %g",rm)
			figlab(str1)
			sprint(str1,"Ra %g",rax)
			figlab(str1)
			sprint(str1,"cm %1.2f",c_m)
			figlab(str1)
			sprint(str1,"err %3.1f",err)
			figlab(str1,0.7,0.7)
			sprint(str1,"tau %3.1f",(c_m*rm/1000))
			figlab(str1)
			if (cells>3)	sprint(str1,"rin %3.1f+-%1.1f",rin.mean, rin.stdev)
			if (cells<=3)	sprint(str1,"rin %3.1f",rin.x[0])
			figlab(str1)
			figlab(date)
			sprint(str1,"equiv_diam %2.2f",equiv_diam)
			figlab(str1)
			figure[figcurrent].yaxis(3)
//			figure[figcurrent].unmap
//			figure[figcurrent].view(0,0,1,1,650,300,250,125)
			}



proc attenuation_plot() {  


				Soma.sec { impR = new Impedance()
					    impR.loc(0.5)
					    impR.compute($1)
					  }
			rest()        			
			ref.resize(0)
			forsec distlist for k = 0,nseg-1 {ref.append(impR.transfer(0.5))}
			ref.scale(ref.min/ref.max,1)
			
			fig(dist,ref,1,add.x[i],colour.x[i])
			ref = dist.c
			ref.sort()
	 		if (i==0) fig(ref,ref.mul(Slope).add(Offset),0,1)


			figlab("passive attenuation",0.3,0.9)
			figlab(activecell)
			sprint(str1,"Input frequency %g Hz",$1)
			figlab(str1)
			}
	
proc interbranchdist() { 
				marksize = 4
				fig(somadist,updst,1,0)
				figlab("Distance to upstream branchpoint",0.2,0.9)
			}

proc areadist() 	{	
				fig(gdist,Ar,0,0)
				figlab("Area",0.3,0.9)
				figure[figcurrent].color(2)
				figlab(activecell)
			}				


proc dareadist()	{

				fig(gdist,dAr,0,0)
				figlab("dArea/dr",0.3,0.9)
			}

proc diamdist()		{

				fig(gdist,mdiam,0,0)
				fig(gdist,sections,0,1,2)
				fig(somadist,branchpointdiam,1,1,1,4,"o")
				figlab("# sections",0.2,0.9,2)
				figlab("average diam",0.42,0.9,1)
				figlab("parent diam",0.7,0.9)
			}
			

proc ralldistribution() {	/* plot rall ration distribution */

			gauss(ralldiam,0.01,0.01)
			fig(gaussx,gaussy)

			onex = new Vector(2,1)
			oney = new Vector(2,0)
			oney.x[1] = gaussy.max
			fig(onex,oney,0,1,2)
			figlab("d3/2 ratio distribution",0.3,0.9)
			}


proc diam_distance()	{ /* plot distance upstream branchpoint v distance soma */

			fig(somadist,ralldiam,1,0,1,4)

			onex = new Vector(2,0)
			onex.x[1] = gdist.max
			oney      =  new Vector(2,1)

			fig(onex,oney,0,1,2)
			figlab("d3/2 ratio",0.3,0.9)

			}


proc branchhist()    {  /* histogram of branchpoints and terminations */

			hist(somadist,14,terminationdist.max,0)
			fig(histx,histy,0,0,2,2)
			hist(terminationdist,14,terminationdist.max,0)
			fig(histx,histy,0,1,1)
			figlab("Terminations",0.5,0.9)
			figlab("Branchpoints",0.2,0.9,2)

		     }


proc branchgauss()     { /* Gaussian distribution of branchpoints and terminations */

			gauss(somadist,gstep(),somadist.max/2)
			fig(gaussx,gaussy,0,0,2)
			gauss(terminationdist,gstep(),terminationdist.max/2)
			fig(gaussx,gaussy,0,1,1)
			figlab("Branchpoints",0.2,0.9,2)
			figlab("Terminations",0.5,0.9)
		      }


proc crossarea() {	/* plot equivalent crosssectional" diameter as fxn of distance */

			fig(gdist,mdiam)
			figlab("membranearea diam",0.3,0.9)

			fig(gdist,rdiam,0,1,2)
			figlab("ralldiam",2)

			fig(gdist,cdiam,0,1,3)
			figlab("relcrossareadiam",3)

		}


proc ralldarea() {	/* plot "ralldarea" as a fxn of distance */

			fig(gdist,rdiam.c.mul(PI))
			figlab("ralldarea/dr",0.3,0.9)
		}			
						
			
proc Rmismatch_plot()	{ local i,x
			/* Resistance mismatch */

			Rmismatch.resize(0)
			aRmismatch.resize(0)

			forsec distlist {for i = 0,nseg-1  { 	x = (i+.5)/nseg
								Rmismatch.append(Rmismatch_pk(x))
						 		aRmismatch.append(aRmismatch_pk(x)) }}

			fig(dist,Rmismatch, 1,0,1,3)
			fig(dist,aRmismatch,1,1,2,3)

			onex = new Vector(2,0)
			onex.x[1] = dist.max
			oney = new Vector(2,1)
			fig(onex,oney,0,1,2)

			figlab("Resistance mismatch",0.3,0.9)
		}


proc Zmismatch_plot()	{ local i, x /* Impedance mismatch */

			Zmismatch.resize(0)
			aZmismatch.resize(0)

			forsec distlist { for i = 0,nseg-1  { 	x = (i+.5)/nseg
								Zmismatch.append(Zmismatch_pk(x))
						 		aZmismatch.append(aZmismatch_pk(x)) }}
			fig(dist,Zmismatch, 1,0,1,3)
			fig(dist,aZmismatch,1,1,2,3)

			onex = new Vector(2,0)
			onex.x[1] = dist.max
			oney = new Vector(2,1)
			fig(onex,oney,0,1,2)

			figlab("Impedance mismatch",0.3,0.9)
		}

proc APsine()	{ 	/* AP sine frequency */

			Zfrequency.resize(0)
			ref.resize(0)
			forsec distlist { Zfrequency.append(f_pk)
 					  ref.append(fdistance(0.5)) }
			fig(ref,Zfrequency,1)
			figlab("AP sine frequency")
		}


			
			

proc mismatch_bar()	{	/* bar chart of R & Z mean values */

			ref.resize(0)
			ref.append(Rmismatch_mean)
			ref.append(aRmismatch_mean)
			ref.append(Zmismatch_mean)
			ref.append(aZmismatch_mean)
			bar(ref,2,0.2)
			fig(barx,bary)

			figlab("Rp",0.27,0.2)
			figlab("Ra",0.45,0.2,2)
			figlab("Zp",0.62,0.2)
			figlab("Za",0.82,0.2,2)
			figlab(activecell,0.45,0.06)
			figure[figcurrent].xaxis(1)
		}



proc Rmismatchgauss() {	/* plot distribution of R (distal/distal + proximal) */

			gauss(Rmismatch,0.01,0.02)
			fig(gaussx,gaussy)
			gauss(aRmismatch,0.01,0.02)
			fig(gaussx,gaussy,0,1,2)

			gauss(Zmismatch,0.01,0.02)	/* to scale with Z */
			fig(gaussx,gaussy,0,1,0)

			figlab("Resistance (distal/distal+proximal)",0.25,0.9)
			figlab("passive")
			figlab("active",2)

			}


proc Zmismatchgauss() {	/* plot distribution of R (distal/distal + proximal) */

			gauss(Zmismatch,0.01,0.02)
			fig(gaussx,gaussy)
			gauss(aZmismatch,0.01,0.02)
			fig(gaussx,gaussy,0,1,2)

			gauss(Rmismatch,0.01,0.02)	/* to scale with R */
			fig(gaussx,gaussy,0,1,0)

			figlab("Impedance (distal/distal+proximal)",0.25,0.9)
			figlab("passive")
			figlab("active",2)

			}
			
			
			
			

proc branchinfo() { 	/* plot distance to upstream branchpoint against distance from soma */

			histx.resize(0)		/* distance to upstream branchpoint */
			histy.resize(0)		/* distance of branchpoint from soma */
			
			forsec branchpoints { 	histy.append(upstreamdst())
						histx.append(fdistance(0))
					   }				    
			fig(histx,histy,1)
         	       }				


proc rall()         {	/* print rall ratio for given section */
 
			p = diam(1)^1.5
			get_children()						
			d = 0
	       	        forsec children  d += diam(0)^1.5
			print p,d, d/p, secname()

		    }



proc Getdata() {

dlog = new VBox()
dlog.intercept(1)
	xpanel("signal propagation toolbox")
			xvarlabel(actname)
			activemodel_set()
			xcheckbox("equivalent",&equiv)
			xradiobutton("backpropagation","{forward=0 hdecay=0}")
			xradiobutton("forward200","{forward=1 hdecay=0}")
			xradiobutton("forwardhdecay","{forward=0 hdecay=1}")
	xpanel()
dlog.intercept(0)

printcellnameact = 0
cell_name(n2.loc,1)
printcellnameact = 1
actname_set(0)

if (dlog.dialog("Select dataset to analyse","Load","Cancel")==1) {
		get_data(ActiveModel)
		}
		}




proc Load_cell() {

dlog = new VBox()
dlog.intercept(1)
	xpanel("signal propagation toolbox",1)
			xvarlabel(cellnameact)
	xpanel()
	xpanel("",1)
			neuron_set()
			activemodel_set()
	xpanel()
dlog.intercept(0)

printcellnameact = 0
cell_name(n2.loc,1)
printcellnameact = 1
actname_set(0)

if (dlog.dialog("Please pick a neuron and an active model")==1) {


		get(cell,ActiveModel)
		Electrophysiology()
//		show()
	}



		}




/*********************************************************************/
/*********************************************************************/
/*********************************************************************/



if (boolean_dialog("Welcome to ProgagationGeometry","Load Cell","Statistics")==1) {
 Main() Load_cell() } else { Getdata() Statistics() Main()}




proc Kap() {
/* Calls Nonuniform panel and allows */
/* - setting of nonuniform passive membrane properties */
	xpanel("Kap", 0)
	xlabel("nonuniformity")
	xcheckbox("Kap",&Kap_current ,"insert_channels()")
	xpvalue("gbar_kap",&gbar_kap,1,"kap_set(gbar_kap,kap_end,kap_steep,kap_half,kap_rel)")
	xpvalue("kap_end",&kap_end,1,"kap_set(gbar_kap,kap_end,kap_steep,kap_half,kap_rel)")
	xpvalue("kap_steep",&kap_steep,1,"kap_set(gbar_kap,kap_end,kap_steep,kap_half,kap_rel)")
	xpvalue("kap_half",&kap_half,1,"kap_set(gbar_kap,kap_end,kap_steep,kap_half,kap_rel)")
	xpvalue("kap_rel",&kap_rel,1,"kap_set(gbar_kap,kap_end,kap_steep,kap_half,kap_rel)")
	xpanel(1050,270)
                 }




proc Kad() {
/* Calls Nonuniform panel and allows */
/* - setting of nonuniform passive membrane properties */
	xpanel("Kad", 0)
	xlabel("nonuniformity")
	xcheckbox("Kad",&Kad_current ,"insert_channels()")
	xpvalue("gbar_kad",&gbar_kad,1,"kad_set(gbar_kad,kad_end,kad_steep,kad_half,kad_rel)")
	xpvalue("kad_end",&kad_end,1,"kad_set(gbar_kad,kad_end,kad_steep,kad_half,kad_rel)")
	xpvalue("kad_steep",&kad_steep,1,"kad_set(gbar_kad,kad_end,kad_steep,kad_half,kad_rel)")
	xpvalue("kad_half",&kad_half,1,"kad_set(gbar_kad,kad_end,kad_steep,kad_half,kad_rel)")
	xpvalue("kad_rel",&kad_rel,1,"kad_set(gbar_kad,kad_end,kad_steep,kad_half,kad_rel)")
	xpanel(1050,270)
                 }





proc Conductances() {
/* Calls Conductances panel and allows */
/* - setting of passive membrane properties */
/* - setting of channel parameters */
/* - setting of nonuniform passive membrane parameters */

		xpanel("Conductances", 0)
		xpvalue("Ra",&rax,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpvalue("Rm",&rm,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpvalue("cm",&c_m,1,"passive_set(rm,rax,c_m,cm_myelin,rm_node,rm_end,rm_steep,rm_half)")
		xpvalue("gkv",&g_kv,1,"active_set(g_na,g_kv,g_nanode,g_kvnode)")
		xpvalue("gna",&g_na,1,"active_set(g_na,g_kv,g_nanode,g_kvnode)")
		xpvalue("gkv (node)",&g_kvnode,1,"active_set(g_na,g_kv,g_nanode,g_kvnode)")
		xpvalue("gna (node)",&g_nanode,1,"active_set(g_na,g_kv,g_nanode,g_kvnode)")
		if (Ca_current)  xpvalue("gca",&g_ca,1,"ca_set(g_ca)")
		if (KCa_current) xpvalue("gkca",&g_kca,1,"kca_set(g_kca)")
		if (Km_current)  xpvalue("gkm",&g_km,1,"km_set(g_km)")

		if (Kad_current) {	
		xcheckbox("Kad",&Kad_current ,"insert_channels()")	
		xpvalue("gbar_kad",&gbar_kad,0.001,"lkad_set(gbar_kad,kad_slope,kad_rel)")
		xpvalue("kad_slope",&kad_slope,0.1,"lkad_set(gbar_kad,kad_slope,kad_rel)")
		xcheckbox("kad_rel",&kad_rel,"lkad_set(gbar_kad,kad_slope,kad_rel)")

		xcheckbox("Kap",&Kap_current ,"insert_channels()")
		xpvalue("gbar_kap",&gbar_kap,0.001,"lkap_set(gbar_kap,kap_slope,kap_rel)")
		xpvalue("kap_slope",&kap_slope,0.1,"lkap_set(gbar_kap,kap_slope,kap_rel)")
		xcheckbox("kap_rel",&kap_rel,"lkap_set(gbar_kap,kap_slope,kap_rel)")
		}
		
		xbutton("Nonuniform","Nonuniform()")
		xpanel(950,0) 
                 }





















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