Biophysically realistic neuron models for simulation of cortical stimulation (Aberra et al. 2018)

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Accession:241165
This archive instantiates the single-cell cortical models used in (Aberra et al. 2018) and sets up extracellular stimulation with either a point-current source, to simulate intracortical microstimulation (ICMS), or a uniform E-field distribution, with a monophasic, rectangular pulse waveform in both cases.
Reference:
1 . Aberra AS, Peterchev AV, Grill WM (2018) Biophysically realistic neuron models for simulation of cortical stimulation. J Neural Eng 15:066023 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon;
Brain Region(s)/Organism: Neocortex; Barrel cortex;
Cell Type(s): Myelinated neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Detailed Neuronal Models;
Implementer(s): Aberra, Aman [aman.aberra at duke.edu];
/* 
* Procedures for generating myelinated axon from original, unmyelinated morphology
* Preserves original geometry, replaces axon with new sections named Myelin, Node, and Unmyelin 
* AUTHOR: Aman Aberra, Duke University
* CONTACT: aman.aberra@duke.edu
*/
// input scale factor and section list, scales pt3d diam info
proc scale_diam2() { local f,i,ii localobj diams, diams2, diams_sec,scale_seclist
	f = $1 // scale factor
	scale_seclist = $o2
	diams = new Vector()
	forsec scale_seclist {
		diams_sec = getpt3d(5)
		diams.append(diams_sec) // append this sections diam vector
	}
	diams2 = diams.mul(f)
	i = 0
	forsec scale_seclist {
		for ii = 0, n3d() - 1{
			pt3dchange(ii,diams2.x[i])
			i += 1
		}
	}
}
// input myelin section list, scales based on diameter dependent g_ratio taken from (Micheva 2016)
proc scale_diam3() { local f, i, ii, nn, p1,p2,p3,p4 localobj diams, diams2, diams_sec, scale_seclist, g_ratios,g_ratios_sec, ones
	scale_seclist = $o1
	diams = new Vector()	
	g_ratios_sec = new Vector()	
	p1 = 0.6425 // polynomial curve fit of d vs. g_ratio from Micheva 2016 data
	p2 = -1.778
	p3 = 1.749
	p4 = 0.1518
	g_ratios = new Vector()
	forsec scale_seclist {
		diams_sec = getpt3d(5)
		diams.append(diams_sec) // append this sections diam vector		
		g_ratios_sec = diams_sec.c.pow(3).mul(p1) 
		g_ratios_sec = g_ratios_sec.c.add(diams_sec.c.pow(2).mul(p2))
		g_ratios_sec = g_ratios_sec.c.add(diams_sec.c.mul(p3))
		g_ratios_sec = g_ratios_sec.c.add(p4)
		for nn = 0, g_ratios_sec.size()-1 {
			if (g_ratios_sec.x[nn] > 0.8) g_ratios_sec.x[nn] = 0.8 // set max g-ratio 
			if (g_ratios_sec.x[nn] < 0.40) g_ratios_sec.x[nn] = 0.40 // set min g-ratio
		}
		g_ratios.append(g_ratios_sec)		
	}
	ones = new Vector(g_ratios.size())
	ones = ones.c.fill(1)	
	diams2 = diams.c.mul(ones.c.div(g_ratios)) // scale each compartment diameter by its specific g_ratio
	i = 0
	forsec scale_seclist {
		for ii = 0, n3d() - 1{
			pt3dchange(ii,diams2.x[i])			
			i += 1
		}
	}
	printf("Scaled diameter of myelin sections using variable g-ratio\n")	
}
// Skip axon[0] convert every section to myelin + node
INL_ratio = 100
INL_ratio_term = 70 // INL ratio for terminations
nodeL = 1
min_myelinL = 20 // 20 minimum myelinated section length (Waxman 1970)
min_myelinD = 0.2 // 0.2 µm (Hildebrand 1993) 
min_PMAS = 50 // minimum premyelin axon segment (PMAS), i.e. axon hillock + initial segment length
myelinL_error = 0.1 // allowed error in myelin length
nodeL_error = 0.1 // allowed error in node length
max_myelin_order = 0 // max_order - max_myelin_order is max branch order to myelinate. 0 myelinates all branches (same convention as prune_ax)
create Myelin[2], Node[2],Unmyelin[2]
objref iseg_secList, Node_secList,Myelin_secList,Unmyelin_secList, axonal
objref myelinCnts

load_file("myelinBiophysics.hoc") // load after section list objects instantiated
proc myelinate_axon() { localobj axon_secList	
	axon_secList = $o1	
	add_myelin(axon_secList)
	//scale_diam2(1/g_ratio,Myelin_secList) // use constant g_ratio
	scale_diam3(Myelin_secList) // use diam dependent g ratio using 3° polynomial fit to Micheva 2016 data
	//scale_diam4(Node_secList) // use diam dependent g ratio to scale down node diameters
	geom_nseg(40,axonal) // assign nseg to each section (2 per 40 um)	
	myelin_biophys()
	forsec axonal cell.all.append() // add to cell sectionlist
	forsec iseg_secList cell.axonal.append() // add initial segment to cell.axonal()
	forsec axonal cell.axonal.append() // add rest of new myelinated axon to cell.axonal()	
	//forsec iseg_secList axonal.append() // add here to avoid re-adding to cell.all
}

// input axon section list, e.g. cell.axonal
proc add_myelin() { local cnt, myelinL, nn, include_PMAS_myelin, myelinL_sec, max_order localobj secx, secy, secz, length, diamvec, \
                axon_secList, parent_SecList, children_SecList, child_SecRef
	//pt3dconst(1)
	axon_secList = $o1
	iseg_secList = new SectionList()
	Myelin_secList = new SectionList()
	Node_secList = new SectionList()	
	Unmyelin_secList = new SectionList()
	axonal = new SectionList()
	forsec "axon[0]" iseg_secList.append()
	axon_secList.remove(iseg_secList) // remove axon[0] from list
	forsec iseg_secList {
		if (L >= (min_PMAS + min_myelinL) ) { // add myelin/node before 1st bifurcation
			numMyelin=1 // account for first myelin and nodal sections
			numNode=1
			include_PMAS_myelin = 1
		} else { // don't add myelin/node before 1st bifurcation
			numMyelin=0 // start count at 0 for rest of arbor			
			numNode=0
			include_PMAS_myelin = 0
		}
		//axonal.append() // don't add iseg to axonal seclist until adding axonal to all
	}	
	numAxonal = 0	
	numUnmyelin = 0
	objref myelinCnts
	myelinCnts = new Vector() // number of internodal sections to replace each existing axonal section
	// calculate number of new myelin, nodal, and unmyelinated sections to create
	max_order = get_max_order(axon_secList) // get maximum branch order of original axon
	forsec axon_secList {
		numAxonal += 1
		if (type_xtra(1)==2||type_xtra(1)==5){
			myelinL=diam(0)*INL_ratio_term			
		} else {
			myelinL = diam(0)*INL_ratio
		}			
		// 3 conditions for myelination: 1) above min diam 2) above min length 3) below max branch order
		// must be larger than minimum diameter for myelinated fibers 		 
		if (diam(0) >= min_myelinD) {
			// must be below maximum branch order, e.g. if max_order = 10, max_myelin_order = 1 => myelinate up to order = 9
			// unless section is in main axon, which is always myelinated (if diam is below min_myelinD)
			if (check_in_secList(main_ax_list) || order_xtra < max_order + 1 - max_myelin_order) {
				numMyelin_sec = int(L/(myelinL + nodeL))			
				if (numMyelin_sec == 0){ // int rounds down to 0 if < 1, no myelin if L < min_myelinL + nodeL
					numMyelin_sec = int(L/(min_myelinL + nodeL)) // if section is shorter than internodal length calculated by INL_ratio*diam, use minimum myelin length
					//numMyelin_sec = 1 // if section is shorter than INL from INL_ratio*diam, make full section myelinated
				}
			} else { // section is above max order and not part of main axon
				numMyelin_sec = 0
			}			
		} else {
			numMyelin_sec = 0
		}
		numMyelin += numMyelin_sec		
		numNode += numMyelin_sec
		if (numMyelin_sec==0) numUnmyelin+=1 // if section still too thin/short for minimum myelin L, leave unmyelinated
		myelinCnts.append(numMyelin_sec) // keeps number of myelin sections per existing section
	}	
	// create new axonal sections and add to SectionLists
	create Myelin[numMyelin], Node[numNode]
	if (numUnmyelin >= 1) {
		create Unmyelin[numUnmyelin]			
		//printf("Number of unmyelinated sections = %g\n",numUnmyelin)
	}
	forsec "Myelin" {
		Myelin_secList.append() 
		axonal.append()		
	}
	forsec "Node" {
		Node_secList.append()	
		axonal.append()	
	}
	forsec "Unmyelin" {
		Unmyelin_secList.append()	
		axonal.append()	
	}
	printf("Myelinating axon: Replacing %g Axonal sections w/ %g Myelin, %g Node, %g Unmyelin sections\n",numAxonal,numMyelin,numNode,numUnmyelin)
	// connect Myelin[0] to iseg if exists before 1st bifurcation
	if (include_PMAS_myelin==1) { 
		print "Adding myelin before the 1st bifurcation"		
		forsec iseg_secList {			
			children_SecList = getchildren() // get existing children sections
			forsec children_SecList	{disconnect()} // disconnect children from cell.axon[0]				
			connect Myelin[0](0), 1 // connect 1st myelin section to iseg					
			//printf("Iseg: connected Myelin[0] to %s\n",secname())
			// get coordinates of original iseg
			secx = getpt3d(1)
			secy = getpt3d(2)
			secz = getpt3d(3)
			length = getpt3d(4)
			diamvec = getpt3d(5)
			last_pt3d_i = length.indwhere(">",min_PMAS)-1  // until 1st point that's farther than the PMAS length							
			// remove points after last_pt3d_i, assign them to 1st myelin/node
			while (arc3d(n3d()-1) > min_PMAS) {
				pt3dremove(n3d()-1)				
			}				
			// get myelinL
			myelinL = length.x[length.size()-1] - (min_PMAS + nodeL) // get new myelin length to fit all myelin/node sections in old section						
		}			
		Myelin[0] {
			first_pt3d_i = last_pt3d_i
			last_pt3d_i = length.indwhere(">",min_PMAS+myelinL)  // until 1st point that's farther than myelinL	
			if (last_pt3d_i > first_pt3d_i) last_pt3d_i -= 1 // point before point that's farther than myelinL
			//printf("Iseg: Myelin[%g], 1st pt = %g. Last point = %g\n",mye_cnt,first_pt3d_i,last_pt3d_i)
			last_pt3d_i = add_new_points(first_pt3d_i,last_pt3d_i,secx,secy,secz,length,diamvec,myelinL,myelinL_error,1)
		}
		connect Node[0](0), Myelin[0](1) // connect 1st node to 1st myelin		
		Node[0] {
			first_pt3d_i = last_pt3d_i			
			//length = get_arc3d(secx,secy,secz)
			//last_pt3d_i = length.indwhere(">",myelinL + nodeL)
			last_pt3d_i = length.size()-1 // set to last coordinate						
			if (last_pt3d_i > first_pt3d_i) {
				last_pt3d_i -= 1 
			} else { // if less than or equal to 1st pt, use same point
				last_pt3d_i = first_pt3d_i 	
			}			
			//printf("Iseg: Node[0], 1st pt = %g. Last point = %g\n",first_pt3d_i,last_pt3d_i)
			/*
			if (first_pt3d_i == last_pt3d_i){
				//printf("	Adding 1st interpolated point\n")
				add_interp_pt(last_pt3d_i,secx,secy,secz,diamvec,nodeL,-1) // add additional point along same direction as pt3d with distance nodeL							
			}	
			*/				
			//assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz,diamvec)	 // add 2nd point using original coordinates
		
			last_pt3d_i = add_new_points(first_pt3d_i,last_pt3d_i,secx,secy,secz,length,diamvec,nodeL,nodeL_error,1)
			//printf("Iseg: Node[0].L = %.2f\n",L)
		}			
		forsec children_SecList { // reattach children of iseg
			//printf("Disconnecting %s from parent\n",secname())
			child_SecRef = new SectionRef()
			disconnect() // disconnect from original parent (current section)				
			connect child_SecRef.sec(0), Node[0](1)
			//printf("Reconnecting to Node[%g]\n",0)
		}
		mye_cnt = 1 // myelin counter starts at 1, because 0 already added 
		//print "Added myelin before 1st bifurcation"
	} else {
		// otherwise, first myelinated sections will be attached to Node[0], start at 0
		mye_cnt = 0 		
		print "No myelin before 1st bifurcation"		
	} 	
	// Assign parameters for Myelin[0] if necessary		
	// Deal with rest of axon 	
	sec_cnt = 0 // section counter, myelin section counter above (mye_cnt)
	unmye_cnt = 0 // unmyelinated section counter	
	forsec axon_secList { // replace each section with (myelin+node) units
		// get coordinates of current section		
		secx = getpt3d(1) 
		secy = getpt3d(2)
		secz = getpt3d(3)	
		length = getpt3d(4) // outputs lengths of 3d points (not normalized)
		diamvec = getpt3d(5) // outputs diameter of 3d points
		// get children and parent sections in SectionLists
		children_SecList = getchildren()
		parent_SecList = getparent() 		
		numMyelin_sec = myelinCnts.x[sec_cnt] // get number of myelin sections to create 				
		//node_diam = diam(0)  // same node diameter for all nodes in this section
		//myelin_diam = node_diam/g_ratio // same myelin diameter for all myelin in this section				

		// Now that we've gotten all info we need, delete current section		
		delete_section()
		myelinL_sec = 0 // start at 0 for every axonal section being myelinated	
		// Start connecting new sections replacing original axonal section
		if (numMyelin_sec >=1 ) {			
			//printf("First pt sec (%f,%f,%f) \n",secx.x[0],secy.x[0],secz.x[0])
			forsec parent_SecList {
				connect Myelin[mye_cnt](0), 1 // connect first myelin to end of original parent
				// start coordinates at end of parent (in case original parent has already been replaced)
				secx.x[0] = x3d(n3d()-1)
				secy.x[0] = y3d(n3d()-1)
				secz.x[0] = z3d(n3d()-1)
				diamvec.x[0] = diam3d(n3d()-1)
				length = get_arc3d(secx,secy,secz) // get new length vector with updated x,y,z vectors
				//printf("New first pt sec (%f,%f,%f) \n",secx.x[0],secy.x[0],secz.x[0])
				myelinL = (length.x[length.size()-1] - numMyelin_sec*nodeL)/numMyelin_sec // get new myelin length to fit all myelin/node sections in old section
				// connect first myelin and nodal section to original parent			
				//printf("Creating %g myelin (L=%.3f um) and nodes. n3d() = %g\n",numMyelin_sec,myelinL,length.size())
				//printf("Connecting 1st Myelin[%g] to its parent: %s\n",mye_cnt,secname())
			}
			Myelin[mye_cnt] connect Node[mye_cnt](0), 1 // connect first node to end of first myelin
			// assign coordinates and diameters for 1st myelinated section
			Myelin[mye_cnt] {				
				first_pt3d_i = 0 // start from 1st pt3d				
				last_pt3d_i = length.indwhere(">",myelinL)  // until 1st point that's farther than myelinL								
				if (last_pt3d_i > first_pt3d_i) {
					last_pt3d_i -= 1 // point before point that's farther than myelinL
				} 
				//printf("Myelin[%g], 1st pt = %g. Last point = %g\n",mye_cnt,first_pt3d_i,last_pt3d_i)
				//***** Add new point (before or after last_pt3d_i) or use existing ones to trace out myelin path
				last_pt3d_i = add_new_points(first_pt3d_i,last_pt3d_i,secx,secy,secz,length,diamvec,myelinL,myelinL_error,1)								
				//*****
				myelinL_sec = L // add length of 1st myelin section to section's running total
				//printf("L = %.3f. myelinL_sec = %.2f\n",L,myelinL_sec)
			}			
			// loop through remaining nodal/myelin sections, connect and give pt3d coordinates
			if (numMyelin_sec >= 2) {
				for nn = 0, numMyelin_sec-1 { 
					//printf("Adding myelin+node section #%g\n",nn)
					Node[mye_cnt+nn] { // start with 1st node - already connected to 1st myelin						
						first_pt3d_i = last_pt3d_i // start at last point of previous section
						//first_pt3d_i = length.indwhere(">",myelinL_sec)
						last_pt3d_i = length.indwhere(">",myelinL_sec + nodeL)
						if (last_pt3d_i > first_pt3d_i) {
							last_pt3d_i -= 1 
						} else { // if less than or equal to 1st pt, use same point
							last_pt3d_i = first_pt3d_i 	
						}
						//last_pt3d_i = first_pt3d_i + 1 // use next point for interpolation
						//last_pt3d_i = length.indwhere(">",(myelinL + nodeL)*(nn+1))						
						//printf("Node[%g],1st pt = %g. Last point = %g\n",mye_cnt+nn,first_pt3d_i,last_pt3d_i)
						//assign_pts(first_pt3d_i,first_pt3d_i,secx,secy,secz,diamvec) // add first point from original coordinates
						// Add new point 1 µm in the direction of original axon, modify coordinate vectors												
						last_pt3d_i = add_new_points(first_pt3d_i,last_pt3d_i,secx,secy,secz,length,diamvec,nodeL,nodeL_error,-1)																
						//assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz,diamvec)																	
						// If adding another myelinated section, connect it to end of node
						if (nn < numMyelin_sec-1)	connect Myelin[mye_cnt+nn+1](0), 1 // connect 1 end of current node (parent) to 0 end of next myelin (child)										
						myelinL_sec += L
						//printf("Node L=%.2f. myelinL_sec = %f\n",L,myelinL_sec)
					}						
					if (nn < numMyelin_sec-1) { // end section on node
						Myelin[mye_cnt+nn+1] {																							
							first_pt3d_i = last_pt3d_i
							//first_pt3d_i = length.indwhere(">",myelinL_sec + nodeL*(nn+1)) // start at length after current total myelin length  
							//first_pt3d_i = length.indwhere(">",myelinL_sec) // start at length after current total myelin length (incl node) 
							//last_pt3d_i = length.indwhere(">",myelinL+myelinL_sec + nodeL*(nn+1))							
							last_pt3d_i = length.indwhere(">",myelinL_sec+myelinL) // running total incl node							
							//printf("last_i = %g. (%f,%f,%f). length(last_i) = %f. myelinL_sec = %.3f + myelinL = %.3f\n",last_pt3d_i,secx.x[last_pt3d_i],secy.x[last_pt3d_i],secz.x[last_pt3d_i],length.x[last_pt3d_i],myelinL_sec,myelinL)
							//last_pt3d_i = length.indwhere(">",myelinL*(nn+2) + nodeL*(nn+1))														
							if (last_pt3d_i > first_pt3d_i) {
								last_pt3d_i -= 1 // point before point that's farther than myelinL
							} else if (last_pt3d_i < 0) {
								myelinL = length.x[length.size()-1] - length.x[first_pt3d_i] - nodeL // readjust myelinL for remaining part of section
								last_pt3d_i = length.size() - 2 // use second to last point
							}
							//printf("Myelin[%g],1st pt = %g. Last point = %g\n",mye_cnt+nn+1,first_pt3d_i,last_pt3d_i)																					

							last_pt3d_i = add_new_points(first_pt3d_i,last_pt3d_i,secx,secy,secz,length,diamvec,myelinL,myelinL_error,1)																
							/*
							if (first_pt3d_i == last_pt3d_i){
								printf("	Adding interpolated point\n")
								// add additional point along same direction as pt3d with distance myelinL
								add_interp_pt(last_pt3d_i,secx,secy,secz,diamvec,myelinL,1) // use negative to interpolate forward 				 		
							}										
							assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz,diamvec)							
							*/							
							myelinL_sec += L // add to running total
							//printf("L = %.2f. myelinL_sec = %.2f\n",L, myelinL_sec)
							connect Node[mye_cnt+nn+1](0), 1 // connect 0 end of next node (child) to 1 end of current myelin				
						}
					}												
				} 
			} else {
				Node[mye_cnt] {
					//first_pt3d_i = last_pt3d_i+1
					//last_pt3d_i = length.indwhere(">",(myelinL + nodeL)*(nn+1))
					first_pt3d_i = last_pt3d_i
					last_pt3d_i = length.size()-1 // use last coordinate
					/*
					if (last_pt3d_i > first_pt3d_i) {
						last_pt3d_i -= 1 
					} else { // if less than or equal to 1st pt, use same point
						last_pt3d_i = first_pt3d_i 	
					}

					if (first_pt3d_i == last_pt3d_i){
						printf("	Adding 1st interpolated point\n")
						add_interp_pt(last_pt3d_i,secx,secy,secz,diamvec,nodeL,-1) // add additional point along same direction as pt3d with distance nodeL							
					}					
					assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz,diamvec)																	
					*/
					last_pt3d_i = add_new_points(first_pt3d_i,last_pt3d_i,secx,secy,secz,length,diamvec,nodeL,nodeL_error,1)
				}
			}		
			// connect existing children to last node	
			forsec children_SecList {
				//printf("Disconnecting %s from parent\n",secname())
				child_SecRef = new SectionRef()
				disconnect() // disconnect from original parent (current section)								
				connect child_SecRef.sec(0), Node[mye_cnt+numMyelin_sec-1](1)
				//printf("Reconnecting to Node[%g]\n",mye_cnt+numMyelin_sec-1)
			}
			mye_cnt += numMyelin_sec
		} else { // leave section unmyelinated
			//printf("Leaving section unmyelinated\n")
			// connect to parent
			forsec parent_SecList connect Unmyelin[unmye_cnt](0), 1 
			// assign coordinates
			Unmyelin[unmye_cnt] {
				assign_pts(0,secx.size()-1,secx,secy,secz,diamvec)
			}
			// connect to children
			forsec children_SecList {
				//printf("Disconnecting %s from parent\n",secname())
				child_SecRef = new SectionRef()
				disconnect() // disconnect from original parent (current section)
				connect child_SecRef.sec(0), Unmyelin[unmye_cnt](1) // connect end of unmyelianted section to original children
				//printf("Reconnecting to Unmyelin[%g]\n",unmye_cnt)
			}
			unmye_cnt += 1
		}											
		sec_cnt += 1 // increment section counter 1		
	}
	
}

obfunc getpt3d() { local dim, nn, ii localobj vec
	// argument is 1, 2, 3, or 4, for x, y, z, or arc3d
	dim = $1
	nn = n3d()
	vec = new Vector(nn)
	if (dim == 1){
		for ii = 0, nn-1 vec.x[ii] = x3d(ii)		
	} else if (dim == 2){
		for ii = 0, nn-1 vec.x[ii] = y3d(ii)		
	} else if (dim == 3){
		for ii = 0, nn-1 vec.x[ii] = z3d(ii)		
	} else if (dim == 4){
		for ii = 0, nn-1 vec.x[ii] = arc3d(ii)	
		//vec.div(vec.x[nn-1]) // normalize length	
	} else if (dim == 5){
		for ii = 0, nn-1 vec.x[ii] = diam3d(ii)
	}
	return vec
}

// Returns section list with single entry for currently accessed section's parent
obfunc getparent() { localobj current_sec, parent
	current_sec = new SectionRef()
	parent = new SectionList()
	current_sec.parent() {
		parent.append()
	//	print "Parent: ", secname()
	}
	return parent
}
// Returns section list with entries for currently accessed section's parent
obfunc getchildren() { local i localobj current_sec, children	
	children = new SectionList()
	children.children() // append children
	//forsec children print "Child: ", secname()
	return children 
}

//  assign pt3d points from original section to current new section
// input first, last indices and coordinate vectors
// assign_pts(i1,i2,x,y,z)
proc assign_pts() { local i, i1, i2 localobj x, y, z, diamvec
	i1 = $1
	i2 = $2
	x = $o3
	y = $o4
	z = $o5
	diamvec = $o6	
	for i = i1,i2 {
		pt3dadd(x.x[i], y.x[i],z.x[i], diamvec.x[i]) // add selected points from vectors to current section
	}
	//printf("Added points from %g to %g. (%.3f,%.3f,%.3f) to (%.3f,%.3f,%.3f)\n",i1, i2, x.x[i1],y.x[i1],z.x[i1],x.x[i2],y.x[i2],z.x[i2])
}
// adds additional pt3d point using direction of current point and either next or previous point 
// at interpolated distance using input length
// dir is -1 or 1
// add_interp_pt(last_pt3d_i,secx,secy,secz,diamvec,len,dir) 
obfunc add_interp_pt() { local i1, len, xu, yu, zu,xn,yn,zn,dir localobj x,y,z,diams, inds, interp_pt
	i1 = $1 // current coordinate
	x = $o2
	y = $o3
	z = $o4
	diams = $o5
	len = $6
	dir = $7	
	inds = new Vector()
	if (dir == 1){
		inds.append(i1,i1+1) // extract i1 and next index to interpolate forward
		x = x.ind(inds) // extract current coordinate and previous one
		y = y.ind(inds)
		z = z.ind(inds)	
		xu = x.x[1] - x.x[0] // x displacement (forward)
		yu = y.x[1] - y.x[0] 
		zu = z.x[1] - z.x[0]
		r = sqrt(xu^2 + yu^2 + zu^2) // total displacement
		// add point at distance len and direction -<xu,yu,zu> from i2th coordinate (should be within section)
		xn = x.x[0] + len*xu/r // new x point
		yn = y.x[0] + len*yu/r 
		zn = z.x[0] + len*zu/r

	} else if (dir == -1) {
		inds.append(i1-1,i1) // extract previous index and i2 to interpolate from last point
		x = x.ind(inds) // extract current coordinate and previous one
		y = y.ind(inds)
		z = z.ind(inds)	
		xu = x.x[1] - x.x[0] // x displacement (using previous point)
		yu = y.x[1] - y.x[0] 
		zu = z.x[1] - z.x[0]
		r = sqrt(xu^2 + yu^2 + zu^2) // total displacement
		// add point at distance len and direction -<xu,yu,zu> from i2th coordinate (should be within section)
		xn = x.x[1] + len*xu/r // new x point
		yn = y.x[1] + len*yu/r 
		zn = z.x[1] + len*zu/r
	}			
	pt3dadd(xn, yn, zn, diams.x[i1]) 	
	if (dir==1){
		dist = sqrt( (xn - x.x[0] )^2 + (yn - y.x[0] )^2 + (zn - z.x[0] )^2  )
		//printf("+1 Added point to %s (total %g): Start (%.5f,%.5f,%.5f). New (%.5f,%.5f,%.5f). Dist = %.3f\n",secname(),n3d(), x.x[0],y.x[0],z.x[0],xn,yn,zn,dist)
	} else{
		dist = sqrt( (xn - x.x[1])^2 + (yn - y.x[1])^2 + (zn - z.x[1])^2  )
		//printf("-1 Added point to %s (total %g): Start (%.5f,%.5f,%.5f). New (%.5f,%.5f,%.5f). Dist = %.3f\n",secname(),n3d(), x.x[1],y.x[1],z.x[1],xn,yn,zn,dist)
	}	
	interp_pt = new Vector()
	interp_pt.append(xn,yn,zn) // output coordinates of new point
	return interp_pt
}
// add_new_points(secx,secy,secz,length,diamvec,interp_pt)				
func add_new_points() { local first_pt3d_i, last_pt3d_i, secL, secerr, secL_add, dir localobj secx, secy, secz, length, diamvec, interp_pt
	first_pt3d_i = $1
	last_pt3d_i = $2
	secx = $o3
	secy = $o4
	secz = $o5
	length = $o6
	diamvec = $o7
	secL = $8
	secerr = $9	
	dir = $10
	if (length.x[last_pt3d_i] - length.x[first_pt3d_i] >= secL + secerr ) { 		
	// pt3d coordinates would make section too long					
		//printf("dist: %f - %f = %f. secL = %f. secerr = %f\n",length.x[last_pt3d_i],length.x[first_pt3d_i],length.x[last_pt3d_i] - length.x[first_pt3d_i],secL,secerr)	
		last_pt3d_i -= 1 // use 2nd to last coordinate		
		assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz, diamvec) // add existing points (shortened)
		secL_add = secL - (length.x[last_pt3d_i] - length.x[first_pt3d_i]) // distance of interpolated point from last existing point			
		//printf("Adding point to make section shorter at %g with secL_add = %.3f\n",last_pt3d_i,secL_add)
		interp_pt = add_interp_pt(last_pt3d_i,secx,secy,secz,diamvec, secL_add, dir)		
		// replace old point to coordinate, length, and diameter vectors
		/*
		secx.x[last_pt3d_i] = interp_pt.x[0]
		secy.x[last_pt3d_i] = interp_pt.x[1]
		secz.x[last_pt3d_i] = interp_pt.x[2]
		length.x[last_pt3d_i] = length.x[last_pt3d_i-1] + sqrt( (secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2 ) 		
		*/
		// don't change diamvec entry, since this wasn't changed		
		
		secx.insrt(last_pt3d_i+1,interp_pt.x[0])
		secy.insrt(last_pt3d_i+1,interp_pt.x[1])
		secz.insrt(last_pt3d_i+1,interp_pt.x[2])
		length.insrt(last_pt3d_i+1,length.x[last_pt3d_i]+sqrt((secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2) ) // insert distnace of new point from first point
		//printf("Inserting length: %f + %f = %f\n",length.x[last_pt3d_i], sqrt( (secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2 ),length.x[last_pt3d_i] + sqrt( (secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2 ) )
		diamvec.insrt(last_pt3d_i+1,diamvec.x[last_pt3d_i]) // insert same diameter of previous point		
		
		return last_pt3d_i+1 // position of new point in modified coordinate vectors	
	} else if (length.x[last_pt3d_i] - length.x[first_pt3d_i] <= (secL - secerr) ) {
		// pt3d coordinates would make section too short
		// add additional point using existing coordinates direction		
		//printf("dist2: %f - %f = %f. secL = %f. secerr = %f\n",length.x[last_pt3d_i],length.x[first_pt3d_i],length.x[last_pt3d_i] - length.x[first_pt3d_i],secL,secerr)	
		assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz, diamvec) // add existing points (shortened)		
		secL_add = secL - (length.x[last_pt3d_i] - length.x[first_pt3d_i]) // distance of interpolated point from last existing point to make L=myelinL
		//printf("Adding point to make section longer at %g with secL_add = %.3f\n",last_pt3d_i,secL_add)	
		interp_pt = add_interp_pt(last_pt3d_i,secx,secy,secz,diamvec,secL_add,dir)						
		// insert new point to coordinate, length, and diameter vectors
		secx.insrt(last_pt3d_i+1,interp_pt.x[0])
		secy.insrt(last_pt3d_i+1,interp_pt.x[1])
		secz.insrt(last_pt3d_i+1,interp_pt.x[2])		
		//printf("Inserting length: %f + %f = %f\n",length.x[last_pt3d_i], sqrt( (secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2 ),length.x[last_pt3d_i] + sqrt( (secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2 ) )
		length.insrt(last_pt3d_i+1, length.x[last_pt3d_i] + sqrt( (secx.x[last_pt3d_i] - interp_pt.x[0])^2 + (secy.x[last_pt3d_i]-interp_pt.x[1])^2 + (secz.x[last_pt3d_i]-interp_pt.x[2])^2 )) // insert distnace of new point from first point
		diamvec.insrt(last_pt3d_i+1,diamvec.x[last_pt3d_i]) // insert same diameter of previous point
		return last_pt3d_i+1 // position of new point in modified coordinate vectors	
	} else {
		// just use existing points	
		//printf("dist: %f - %f = %f. secL = %f. secerr = %f\n",length.x[last_pt3d_i],length.x[first_pt3d_i],length.x[last_pt3d_i] - length.x[first_pt3d_i],secL,secerr)	
		assign_pts(first_pt3d_i,last_pt3d_i,secx,secy,secz,diamvec)						
		//printf("Used existing points, giving L= %.2f\n",L)
		return last_pt3d_i // position of new point in modified coordinate vectors		
	}	
}

// sets 2 comp per chunkSize in specified sectionList
// geom_nseg(chunkSize,secList)
proc geom_nseg() { local secIndex, chunkSize localobj seclist                                  
    chunkSize = 40                                                              
    if( numarg() > 0 ) {                                                        
        chunkSize = $1                                                          
    }  
    seclist = $o2                                                                             
    secIndex=0                                                                  
    forsec seclist {                                                                
        nseg = 1 + 2*int(L/chunkSize)                                           
        secIndex += 1                                                   
    }                                                                           
} 

obfunc get_arc3d() {local i, dist_i localobj x, y, z, length
	x = $o1
	y = $o2
	z = $o3
	length = new Vector(x.size())
	length.x[0] = 0 // first point starts at 0
	for i = 1, x.size() -1 {
		dist_i = sqrt( (x.x[i] - x.x[i-1])^2 + (y.x[i] - y.x[i-1])^2 + (z.x[i] - z.x[i-1])^2  )
		length.x[i] = length.x[i-1] + dist_i
	}
	return length
}

// input sectionlist and check if currently accessed section is a member
// in_secList = check_in_secList(SectionList) 
// returns 1 if in sectionlist
func check_in_secList() { localobj temp_secList
	// copy into new sectionlist
	temp_secList = new SectionList()
	forsec $o1 temp_secList.append()
	temp_secList.append() // append currently accessed section
	return (temp_secList.unique > 0)
}

// max_order = get_max_order(SectionList) 
// gets maximum branch order of input SectionList
// SectionList should have have xtra inserted and should have order_xtra defined (setpointers())
func get_max_order() { local max_order localobj seclist
	seclist = $o1
	max_order = 0
	forsec seclist {
		if (ismembrane("xtra")){
			if (order_xtra > max_order) max_order = order_xtra // get max order 
		} else {
			print "xtra not inserted in ", secname()
		}
	}
	return max_order
}

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