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 launching desired cell model, scaling diameters/lengths, and adding myelinated axon
* AUTHOR: Aman Aberra, Duke University
* CONTACT: aman.aberra@duke.edu
*/

cell_id = 0 // leave unset until user selects cell
objref cell_names, cell, nil
objref main_ax_list, strobj
objref secnames[numSect]
min_sec_ind = 0

cell_names = new List()
strdef tstr1, tstr2, cell_dir, current_dir,createsim_file // read Traub template names into cell_names List 
current_dir = getcwd()
for i=1,25 {getstr(tstr1,1) cell_names.append(new String(tstr1))}
L1_NGC-DA_bNAC219_1
L1_NGC-DA_bNAC219_2
L1_NGC-DA_bNAC219_3
L1_NGC-DA_bNAC219_4
L1_NGC-DA_bNAC219_5	
L23_PC_cADpyr229_1
L23_PC_cADpyr229_2
L23_PC_cADpyr229_3
L23_PC_cADpyr229_4
L23_PC_cADpyr229_5
L4_LBC_cACint209_1
L4_LBC_cACint209_2
L4_LBC_cACint209_3
L4_LBC_cACint209_4
L4_LBC_cACint209_5
L5_TTPC2_cADpyr232_1
L5_TTPC2_cADpyr232_2
L5_TTPC2_cADpyr232_3
L5_TTPC2_cADpyr232_4
L5_TTPC2_cADpyr232_5
L6_TPC_L4_cADpyr231_1
L6_TPC_L4_cADpyr231_2
L6_TPC_L4_cADpyr231_3
L6_TPC_L4_cADpyr231_4
L6_TPC_L4_cADpyr231_5

// cell_chooser(cell_id) 
proc cell_chooser() { local start_ind, synapses_enabled localobj terminal_sec_str, meth1cells
    cell_id = $1 // reset cell_id to input argument
    if (cell_id > 0){
        forall delete_section()    
        //cell = nil					
        // Launch cell using create_cell within Blue Brain code    
        synapses_enabled = 0 // turn off synapses
        sprint(cell_dir,"cells/%s",cell_names.o(cell_id-1).s)
        chdir(cell_dir) 				
        {load_file("createsimulation.hoc")}	// load cell-specific createsimulation.hoc file	
        create_cell(synapses_enabled)	
        printf("*---------*\nLoaded Blue Brain cell: %s\n",cell_names.o(cell_id-1).s)		        
        // insert xtra/extracellular and run setpointers/get secrefs()
        forall { // call setpointers() on original cell to get type_xtra of each original axon section
            insert xtra
            insert extracellular
        }    
        // Scale diameters and myelinate axon before setting pointers
        // Scale compartment diameters		
        if (scale_soma_area != 1) diam(0.5) = scale_soma_area*area(0.5)/(PI*L)
        if (scale_apic_diam != 1) scale_diam2(scale_apic_diam,cell.apical)
        if (scale_basal_diam != 1) scale_diam2(scale_basal_diam,cell.basal)		
        if (scale_basal_L != 1) forsec cell.basal L=L*scale_basal_L
        if (scale_axon_diam != 1) scale_diam2(scale_axon_diam,cell.axonal)
        // get coordinates and secrefs list        
        getSecRefs()
        // Get main axon of original axon
        // Prune axon if prune_ax >=1 for BLUE-BRAIN cells
        meth1cells = new Vector() // identify which main axon identification algorithm to use
        meth1cells.append(6,8,20,21,22,25) // method 1 cell ids
        // get main axon (most relevant for PCs) and prune sections (non-main axon axonal sections)
        objref main_ax_list 
        // defines main_ax_list and min_sec_ind (public variable)    
        if (!meth1cells.contains(cell_id)) { // use descending approach for most axons				
            main_ax_list = get_main_ax2()
            print "Got main axon (method 2)"
        } else { // for cell meth1cells use ascending approach				
            main_ax_list = get_main_ax()					
            print "Got main axon (method 1)"	
        }	          
        // Myelinate axon after getting main axon, pruning, and scaling diameter					
        if (myelinate_ax) {
            myelinate_axon(cell.axonal)	  
            numComp = 0
            forall {
                if (myelinate_ax){ // re-insert for myelin
                    insert xtra
                    insert extracellular
                } 			
                numComp+= nseg		 // save number of compartments	
            }	
            setpointers()	
            printf("Inserted xtra and extracellular in all %g compartments\n",numComp)														                     				        
            //setpointers()
            // get new main axon
            if (!meth1cells.contains(cell_id)) { // use descending approach for most axons				
                main_ax_list = get_main_ax2()
                print "Got main axon (method 2)"
            } else { // for meth1cells use ascending approach				
                setpointers()	
                main_ax_list = get_main_ax()		                		
                print "Got main axon (method 1)"	
            }	
        } else {
            // get numComp
            numComp = 0
            forall {            			
                numComp+= nseg		 // save number of compartments	
            }            
        }            
        chdir(current_dir) // switch back to parallel_plate     
        print "Cell Loaded"
        // Initilize potentials and waveform
        // getes() // set Ve(x,y,z)
        // setstim(DEL,DUR,AMP) // set waveform (current of E-field)  
        color_plotmax()
    } else {
        print "Cell model not selected"
    }     
}

// Get main axon using ascending approach - starting from lowest z point and going to AIS
// objref main_ax
// main_ax = get_main_ax()
// also outputs min_sec_ind, access using secrefs.o(min_sec_ind)
main_ax_rad = 500 // um main descending axon should be within this radius
obfunc get_main_ax() { local i, miny, min_ind, xi, yi, zi, at_root localobj main_ax, current_secref		
	main_ax = new SectionList() // main axon sections		
	// Find lowest point of axon (on z axis)	
	miny = 100 // initialize	
	for i = 0,numSect-1 {				
		if (yList.o(i).min < miny){
			min_ind = yList.o(i).min_ind
			xi = xList.o(i).x[min_ind]
			yi = yList.o(i).x[min_ind]
			rdist = sqrt((xi-secrefs.o(0).sec.x_xtra(0.5))^2+ (zi-secrefs.o(0).sec.y_xtra(0.5))^2 )
			if (rdist < main_ax_rad){ // make sure compartment is not an oblique, descending collateral by ensuring it's within a horizontal radius
				miny = yList.o(i).min
				min_sec_ind = i // get index of section with lowest z-value, corresponds to terminal compartment
			}			
		} 
	}
	// ascend axon 
	at_root = 0
	current_secref = secrefs.o(min_sec_ind)		
	while (!at_root) { // loop until reach root		
		if (current_secref.has_parent){	
			current_secref.sec main_ax.append() // add to SectionList
			current_secref.parent {
				current_secref = new SectionRef() // make parent current secref 
			}					
		} else {
			at_root = 1
		}
	}		
	return main_ax
}

// Get main axon using descending approach - choose biggest of branches
obfunc get_main_ax2() { local i, biggest_branch_diam, biggest_branch_ind, at_terminal localobj main_ax, current_secref, terminal_sec_str, current_sec_str		
	main_ax = new SectionList() // main axon sections		
	// descend axon 
	at_terminal = 0    
	cell.axon[0] current_secref = new SectionRef() // start at cell.axon[0] (initial segment/axon hillock)    
	while (!at_terminal) { // loop until reach root
		current_secref.sec main_ax.append() // add to SectionList        
		if (current_secref.nchild > 0){                       
			biggest_branch_diam = 0	// diameter of biggest child branch
			biggest_branch_ind = 0 // index of biggest child branch among current_secref's children
			for i = 0,current_secref.nchild - 1 {
				if(current_secref.child[i].diam(0) > biggest_branch_diam) {
					biggest_branch_diam = current_secref.child[i].diam(0)
					biggest_branch_ind = i
				}
			}			
			current_secref.child[biggest_branch_ind] { // make biggest child branch new current_sec, append to main-ax
				current_secref = new SectionRef() // make child current secref 
			}			            	
		} else {            
			at_terminal = 1
			terminal_sec_str = new String()
			current_secref.sec terminal_sec_str.s = secname()
			current_sec_str = new String()
			for i = 0, numSect - 1 {
				secrefs.o(i).sec current_sec_str.s = secname()  
				if (strcmp(current_sec_str.s,terminal_sec_str.s) == 0){ // compare each secname to terminal secname to get index - 0 means identical
					min_sec_ind = i
					//printf("Terminal section: %s, index: %g\n",terminal_sec_str.s,min_sec_ind)
				}
			}            
		}        
	}		
	return main_ax
}

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