/* TCR/TCR_template.hoc automatically written from f2nrn/neuron_code_writer.f via subroutines that were inserted into the fortran code e.g., TCR/integrate_TCR.hoc The template's form was derived by Tom Morse and Michael Hines from a template, pyr3_template created by Roger Traub and Maciej Lazarewicz when they ported Traub RD, Buhl EH, Gloveli T, Whittington MA. Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na(+) Conductance or by Blocking BK Channels.J Neurophysiol. 2003 Feb;89(2):909-21. to NEURON */ begintemplate TCR public type public name strdef name // parts of the template were lifted from a default // cell writing from Network Builder NetGUI[0] public is_art public init, topol, basic_shape, subsets public geom, biophys public synlist, x, y, z, position public connect2target public set_netcon_src_comp // the above function added to set neton // compartment source in the presyn cell public comp, level, Soma, Dendrites public Soma_Dendrites, Axon, all public presyn_comp, top_level // it is the responsibility of the calling // program to set the above presynapf_tcrtic // compartment number external traub_connect objref this create comp[ 137+1] objref level[ 4+1], Soma, Dendrites objref Soma_Dendrites, Axon objref synlist func type() {return 12 } proc init() { doubler = 1 comp[0] delete_section() // clean up for fortran code traub_connect( 137+1) titlePrint() presyn_comp = 135 // in Traub model;changed by calling prog. objref Soma, Axon, Dendrites, Soma_Dendrites objref level topol() shape1() shape2() geom() // the geometry and subsets() // subsets and biophys() // active currents synlist = new List() // list of synapses // NetGUI[0] stores synapses in the cell object, in // Traub model it is easier to store them outside set_doubler() // to double or not if (doubler) {double_dend_cond()} /* for taking spine membrane area correction into account (the method used doubles max cond's when spines present) */ more_adjustments() name = "TCR" } proc double_dend_cond() { /* this function gets replaced later with another one if double_dend_cond() is tacked on. */ } proc titlePrint() { /* print " print "-----" print " print "TCR Neuron Model based on " print "Traub RD et al (2005, 2003)" print " print "-----" Remove title printing with this comment for now. Printing otherwise repeats (for each cell) -too voluminous for a network creation */ } proc set_doubler() {doubler=1} // this function gets replaced with one that // sets doubler to 0 when there are no spines // in the cell (for no spines the additional // hoc code is written from integrate_cell.f // where cell is nRT, TCR. Woops I just // found that deepaxax, deepbask, deepLTS, // supaxax, supbask, supLTS all use the script // cell/run_fortran.sh to replace the =1's with // =0's. I will change the fortran code to // make it all run_fortran.sh replacements or // not for uniformity. proc topol() { // create comp[ 138] // note one greater than numcomp due to fortran indicies // last argument, parent location for connection // is overwritten to 1 for parents with connected children // in below traub_connect proc calls traub_connect(this, 1, 132, 0.0796751205, 0) traub_connect(this, 1, 2, 0.0946071642, 1) traub_connect(this, 1, 15, 0.0946071642, 1) traub_connect(this, 1, 28, 0.0946071642, 1) traub_connect(this, 1, 41, 0.0946071642, 1) traub_connect(this, 1, 54, 0.0946071642, 1) traub_connect(this, 1, 67, 0.0946071642, 1) traub_connect(this, 1, 80, 0.0946071642, 1) traub_connect(this, 1, 93, 0.0946071642, 1) traub_connect(this, 1, 106, 0.0946071642, 1) traub_connect(this, 1, 119, 0.0946071642, 1) traub_connect(this, 2, 3, 0.0174185429, 1.) traub_connect(this, 2, 4, 0.0174185429, 1.) traub_connect(this, 2, 5, 0.0174185429, 1.) traub_connect(this, 3, 6, 0.00766658232, 1) traub_connect(this, 3, 7, 0.00766658232, 1) traub_connect(this, 3, 8, 0.00766658232, 1) traub_connect(this, 4, 9, 0.00766658232, 1) traub_connect(this, 4, 10, 0.00766658232, 1) traub_connect(this, 4, 11, 0.00766658232, 1) traub_connect(this, 5, 12, 0.00766658232, 1) traub_connect(this, 5, 13, 0.00766658232, 1) traub_connect(this, 5, 14, 0.00766658232, 1) traub_connect(this, 6, 7, 0.00598951744, 1) traub_connect(this, 6, 8, 0.00598951744, 1) traub_connect(this, 7, 8, 0.00598951744, 1) traub_connect(this, 9, 10, 0.00598951744, 1) traub_connect(this, 9, 11, 0.00598951744, 1) traub_connect(this, 10, 11, 0.00598951744, 1) traub_connect(this, 12, 13, 0.00598951744, 1) traub_connect(this, 12, 14, 0.00598951744, 1) traub_connect(this, 13, 14, 0.00598951744, 1) traub_connect(this, 15, 16, 0.0174185429, 1.) traub_connect(this, 15, 17, 0.0174185429, 1.) traub_connect(this, 15, 18, 0.0174185429, 1.) traub_connect(this, 16, 19, 0.00766658232, 1) traub_connect(this, 16, 20, 0.00766658232, 1) traub_connect(this, 16, 21, 0.00766658232, 1) traub_connect(this, 17, 22, 0.00766658232, 1) traub_connect(this, 17, 23, 0.00766658232, 1) traub_connect(this, 17, 24, 0.00766658232, 1) traub_connect(this, 18, 25, 0.00766658232, 1) traub_connect(this, 18, 26, 0.00766658232, 1) traub_connect(this, 18, 27, 0.00766658232, 1) traub_connect(this, 19, 20, 0.00598951744, 1) traub_connect(this, 19, 21, 0.00598951744, 1) traub_connect(this, 20, 21, 0.00598951744, 1) traub_connect(this, 22, 23, 0.00598951744, 1) traub_connect(this, 22, 24, 0.00598951744, 1) traub_connect(this, 23, 24, 0.00598951744, 1) traub_connect(this, 25, 26, 0.00598951744, 1) traub_connect(this, 25, 27, 0.00598951744, 1) traub_connect(this, 26, 27, 0.00598951744, 1) traub_connect(this, 28, 29, 0.0174185429, 1.) traub_connect(this, 28, 30, 0.0174185429, 1.) traub_connect(this, 28, 31, 0.0174185429, 1.) traub_connect(this, 29, 32, 0.00766658232, 1) traub_connect(this, 29, 33, 0.00766658232, 1) traub_connect(this, 29, 34, 0.00766658232, 1) traub_connect(this, 30, 35, 0.00766658232, 1) traub_connect(this, 30, 36, 0.00766658232, 1) traub_connect(this, 30, 37, 0.00766658232, 1) traub_connect(this, 31, 38, 0.00766658232, 1) traub_connect(this, 31, 39, 0.00766658232, 1) traub_connect(this, 31, 40, 0.00766658232, 1) traub_connect(this, 32, 33, 0.00598951744, 1) traub_connect(this, 32, 34, 0.00598951744, 1) traub_connect(this, 33, 34, 0.00598951744, 1) traub_connect(this, 35, 36, 0.00598951744, 1) traub_connect(this, 35, 37, 0.00598951744, 1) traub_connect(this, 36, 37, 0.00598951744, 1) traub_connect(this, 38, 39, 0.00598951744, 1) traub_connect(this, 38, 40, 0.00598951744, 1) traub_connect(this, 39, 40, 0.00598951744, 1) traub_connect(this, 41, 42, 0.0174185429, 1.) traub_connect(this, 41, 43, 0.0174185429, 1.) traub_connect(this, 41, 44, 0.0174185429, 1.) traub_connect(this, 42, 45, 0.00766658232, 1) traub_connect(this, 42, 46, 0.00766658232, 1) traub_connect(this, 42, 47, 0.00766658232, 1) traub_connect(this, 43, 48, 0.00766658232, 1) traub_connect(this, 43, 49, 0.00766658232, 1) traub_connect(this, 43, 50, 0.00766658232, 1) traub_connect(this, 44, 51, 0.00766658232, 1) traub_connect(this, 44, 52, 0.00766658232, 1) traub_connect(this, 44, 53, 0.00766658232, 1) traub_connect(this, 45, 46, 0.00598951744, 1) traub_connect(this, 45, 47, 0.00598951744, 1) traub_connect(this, 46, 47, 0.00598951744, 1) traub_connect(this, 48, 49, 0.00598951744, 1) traub_connect(this, 48, 50, 0.00598951744, 1) traub_connect(this, 49, 50, 0.00598951744, 1) traub_connect(this, 51, 52, 0.00598951744, 1) traub_connect(this, 51, 53, 0.00598951744, 1) traub_connect(this, 52, 53, 0.00598951744, 1) traub_connect(this, 54, 55, 0.0174185429, 1.) traub_connect(this, 54, 56, 0.0174185429, 1.) traub_connect(this, 54, 57, 0.0174185429, 1.) traub_connect(this, 55, 58, 0.00766658232, 1) traub_connect(this, 55, 59, 0.00766658232, 1) traub_connect(this, 55, 60, 0.00766658232, 1) traub_connect(this, 56, 61, 0.00766658232, 1) traub_connect(this, 56, 62, 0.00766658232, 1) traub_connect(this, 56, 63, 0.00766658232, 1) traub_connect(this, 57, 64, 0.00766658232, 1) traub_connect(this, 57, 65, 0.00766658232, 1) traub_connect(this, 57, 66, 0.00766658232, 1) traub_connect(this, 58, 59, 0.00598951744, 1) traub_connect(this, 58, 60, 0.00598951744, 1) traub_connect(this, 59, 60, 0.00598951744, 1) traub_connect(this, 61, 62, 0.00598951744, 1) traub_connect(this, 61, 63, 0.00598951744, 1) traub_connect(this, 62, 63, 0.00598951744, 1) traub_connect(this, 64, 65, 0.00598951744, 1) traub_connect(this, 64, 66, 0.00598951744, 1) traub_connect(this, 65, 66, 0.00598951744, 1) traub_connect(this, 67, 68, 0.0174185429, 1.) traub_connect(this, 67, 69, 0.0174185429, 1.) traub_connect(this, 67, 70, 0.0174185429, 1.) traub_connect(this, 68, 71, 0.00766658232, 1) traub_connect(this, 68, 72, 0.00766658232, 1) traub_connect(this, 68, 73, 0.00766658232, 1) traub_connect(this, 69, 74, 0.00766658232, 1) traub_connect(this, 69, 75, 0.00766658232, 1) traub_connect(this, 69, 76, 0.00766658232, 1) traub_connect(this, 70, 77, 0.00766658232, 1) traub_connect(this, 70, 78, 0.00766658232, 1) traub_connect(this, 70, 79, 0.00766658232, 1) traub_connect(this, 71, 72, 0.00598951744, 1) traub_connect(this, 71, 73, 0.00598951744, 1) traub_connect(this, 72, 73, 0.00598951744, 1) traub_connect(this, 74, 75, 0.00598951744, 1) traub_connect(this, 74, 76, 0.00598951744, 1) traub_connect(this, 75, 76, 0.00598951744, 1) traub_connect(this, 77, 78, 0.00598951744, 1) traub_connect(this, 77, 79, 0.00598951744, 1) traub_connect(this, 78, 79, 0.00598951744, 1) traub_connect(this, 80, 81, 0.0174185429, 1.) traub_connect(this, 80, 82, 0.0174185429, 1.) traub_connect(this, 80, 83, 0.0174185429, 1.) traub_connect(this, 81, 84, 0.00766658232, 1) traub_connect(this, 81, 85, 0.00766658232, 1) traub_connect(this, 81, 86, 0.00766658232, 1) traub_connect(this, 82, 87, 0.00766658232, 1) traub_connect(this, 82, 88, 0.00766658232, 1) traub_connect(this, 82, 89, 0.00766658232, 1) traub_connect(this, 83, 90, 0.00766658232, 1) traub_connect(this, 83, 91, 0.00766658232, 1) traub_connect(this, 83, 92, 0.00766658232, 1) traub_connect(this, 84, 85, 0.00598951744, 1) traub_connect(this, 84, 86, 0.00598951744, 1) traub_connect(this, 85, 86, 0.00598951744, 1) traub_connect(this, 87, 88, 0.00598951744, 1) traub_connect(this, 87, 89, 0.00598951744, 1) traub_connect(this, 88, 89, 0.00598951744, 1) traub_connect(this, 90, 91, 0.00598951744, 1) traub_connect(this, 90, 92, 0.00598951744, 1) traub_connect(this, 91, 92, 0.00598951744, 1) traub_connect(this, 93, 94, 0.0174185429, 1.) traub_connect(this, 93, 95, 0.0174185429, 1.) traub_connect(this, 93, 96, 0.0174185429, 1.) traub_connect(this, 94, 97, 0.00766658232, 1) traub_connect(this, 94, 98, 0.00766658232, 1) traub_connect(this, 94, 99, 0.00766658232, 1) traub_connect(this, 95, 100, 0.00766658232, 1) traub_connect(this, 95, 101, 0.00766658232, 1) traub_connect(this, 95, 102, 0.00766658232, 1) traub_connect(this, 96, 103, 0.00766658232, 1) traub_connect(this, 96, 104, 0.00766658232, 1) traub_connect(this, 96, 105, 0.00766658232, 1) traub_connect(this, 97, 98, 0.00598951744, 1) traub_connect(this, 97, 99, 0.00598951744, 1) traub_connect(this, 98, 99, 0.00598951744, 1) traub_connect(this, 100, 101, 0.00598951744, 1) traub_connect(this, 100, 102, 0.00598951744, 1) traub_connect(this, 101, 102, 0.00598951744, 1) traub_connect(this, 103, 104, 0.00598951744, 1) traub_connect(this, 103, 105, 0.00598951744, 1) traub_connect(this, 104, 105, 0.00598951744, 1) traub_connect(this, 106, 107, 0.0174185429, 1.) traub_connect(this, 106, 108, 0.0174185429, 1.) traub_connect(this, 106, 109, 0.0174185429, 1.) traub_connect(this, 107, 110, 0.00766658232, 1) traub_connect(this, 107, 111, 0.00766658232, 1) traub_connect(this, 107, 112, 0.00766658232, 1) traub_connect(this, 108, 113, 0.00766658232, 1) traub_connect(this, 108, 114, 0.00766658232, 1) traub_connect(this, 108, 115, 0.00766658232, 1) traub_connect(this, 109, 116, 0.00766658232, 1) traub_connect(this, 109, 117, 0.00766658232, 1) traub_connect(this, 109, 118, 0.00766658232, 1) traub_connect(this, 110, 111, 0.00598951744, 1) traub_connect(this, 110, 112, 0.00598951744, 1) traub_connect(this, 111, 112, 0.00598951744, 1) traub_connect(this, 113, 114, 0.00598951744, 1) traub_connect(this, 113, 115, 0.00598951744, 1) traub_connect(this, 114, 115, 0.00598951744, 1) traub_connect(this, 116, 117, 0.00598951744, 1) traub_connect(this, 116, 118, 0.00598951744, 1) traub_connect(this, 117, 118, 0.00598951744, 1) traub_connect(this, 119, 120, 0.0174185429, 1.) traub_connect(this, 119, 121, 0.0174185429, 1.) traub_connect(this, 119, 122, 0.0174185429, 1.) traub_connect(this, 120, 123, 0.00766658232, 1) traub_connect(this, 120, 124, 0.00766658232, 1) traub_connect(this, 120, 125, 0.00766658232, 1) traub_connect(this, 121, 126, 0.00766658232, 1) traub_connect(this, 121, 127, 0.00766658232, 1) traub_connect(this, 121, 128, 0.00766658232, 1) traub_connect(this, 122, 129, 0.00766658232, 1) traub_connect(this, 122, 130, 0.00766658232, 1) traub_connect(this, 122, 131, 0.00766658232, 1) traub_connect(this, 123, 124, 0.00598951744, 1) traub_connect(this, 123, 125, 0.00598951744, 1) traub_connect(this, 124, 125, 0.00598951744, 1) traub_connect(this, 126, 127, 0.00598951744, 1) traub_connect(this, 126, 128, 0.00598951744, 1) traub_connect(this, 127, 128, 0.00598951744, 1) traub_connect(this, 129, 130, 0.00598951744, 1) traub_connect(this, 129, 131, 0.00598951744, 1) traub_connect(this, 130, 131, 0.00598951744, 1) traub_connect(this, 132, 133, 0.0348744292, 1.) traub_connect(this, 133, 134, 0.0208024203, 1) traub_connect(this, 133, 136, 0.0208024203, 1) traub_connect(this, 134, 135, 0.01570795, 1.) traub_connect(this, 134, 136, 0.01570795, 1) traub_connect(this, 136, 137, 0.01570795, 1.) access comp[1] // handy statement if want to start gui's from nrnmainmenu } proc geom() { // the "traub level" subsets are created and defined below top_level = 4 objref level[top_level+1] for i=0,top_level { level[i] = new SectionList() } comp[ 1] { level[ 1].append() L= 42. diam = 2* 10. } comp[ 2] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 3] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 4] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 5] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 6] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 7] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 8] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 9] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 10] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 11] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 12] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 13] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 14] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 15] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 16] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 17] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 18] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 19] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 20] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 21] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 22] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 23] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 24] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 25] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 26] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 27] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 28] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 29] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 30] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 31] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 32] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 33] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 34] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 35] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 36] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 37] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 38] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 39] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 40] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 41] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 42] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 43] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 44] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 45] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 46] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 47] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 48] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 49] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 50] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 51] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 52] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 53] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 54] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 55] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 56] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 57] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 58] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 59] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 60] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 61] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 62] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 63] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 64] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 65] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 66] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 67] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 68] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 69] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 70] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 71] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 72] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 73] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 74] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 75] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 76] { level[ 4].append() L= 57.5 diam = 2* 0.438 } geom1() /* arbitrary subdivision of geom helps to large a function problem in tcr_template */ } proc geom1() { comp[ 77] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 78] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 79] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 80] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 81] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 82] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 83] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 84] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 85] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 86] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 87] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 88] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 89] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 90] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 91] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 92] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 93] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 94] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 95] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 96] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 97] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 98] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 99] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 100] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 101] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 102] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 103] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 104] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 105] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 106] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 107] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 108] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 109] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 110] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 111] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 112] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 113] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 114] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 115] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 116] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 117] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 118] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 119] { level[ 2].append() L= 20. diam = 2* 0.73 } comp[ 120] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 121] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 122] { level[ 3].append() L= 57.5 diam = 2* 0.584 } comp[ 123] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 124] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 125] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 126] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 127] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 128] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 129] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 130] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 131] { level[ 4].append() L= 57.5 diam = 2* 0.438 } comp[ 132] { level[ 0].append() L= 50. diam = 2* 0.8 } comp[ 133] { level[ 0].append() L= 50. diam = 2* 0.7 } comp[ 134] { level[ 0].append() L= 50. diam = 2* 0.5 } comp[ 135] { level[ 0].append() L= 50. diam = 2* 0.5 } comp[ 136] { level[ 0].append() L= 50. diam = 2* 0.5 } comp[ 137] { level[ 0].append() L= 50. diam = 2* 0.5 } } // Here are some commonly used subsets of sections objref all proc subsets() { local i objref Soma, Dendrites, Soma_Dendrites, Axon objref all Soma = new SectionList() Dendrites = new SectionList() Soma_Dendrites = new SectionList() Axon = new SectionList() for i=1,top_level { forsec level[i] { // recall level 0 is axon, 1 is soma, higher are dends Soma_Dendrites.append() if (i>1) {Dendrites.append()} } } forsec level[1] { Soma.append() } forsec level[0] { Axon.append() } all = new SectionList() for i=1, 137 comp[i] all.append() } proc shape1() { comp[1] {pt3dclear() pt3dadd(0.0, 0.0, 0.0, 20.0) pt3dadd(0.0, 21.0, 0.0, 20.0)} comp[1] {pt3dadd(-9.179392E-7, 42.0, 0.0, 20.0)} comp[132] {pt3dclear() pt3dadd(9.179392E-7, 0.0, 0.0, 1.6) pt3dadd(-1.7484616E-7, -25.0, 0.0, 1.6)} comp[132] {pt3dadd(-1.2676315E-6, -50.0, 0.0, 1.6)} comp[119] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(-5.87726, 42.0, 8.089361, 1.46)} comp[119] {pt3dadd(-11.7550955, 42.000004, 16.179533, 1.46)} comp[106] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(5.877265, 42.0, -8.08936, 1.46)} comp[106] {pt3dadd(11.75513, 42.00003, -16.17959, 1.46)} comp[93] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(9.509614, 42.0, 3.08986, 1.46)} comp[93] {pt3dadd(19.020178, 42.00001, 6.180023, 1.46)} comp[80] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(5.877265, 42.0, 8.089361, 1.46)} comp[80] {pt3dadd(11.7551365, 42.000015, 16.179583, 1.46)} comp[67] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(0.44429666, 42.0, -9.99, 1.46)} comp[67] {pt3dadd(0.88859874, 42.0, -19.9802, 1.46)} comp[54] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(-0.44429934, 42.0, 9.99, 1.46)} comp[54] {pt3dadd(-0.8886023, 42.0, 19.9802, 1.46)} comp[41] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(-9.50961, 42.0, -3.089861, 1.46)} comp[41] {pt3dadd(-19.020224, 42.000023, -6.1800547, 1.46)} comp[28] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(-5.87726, 42.0, -8.08936, 1.46)} comp[28] {pt3dadd(-11.755103, 42.000008, -16.179535, 1.46)} comp[15] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(-9.50961, 42.0, 3.089861, 1.46)} comp[15] {pt3dadd(-19.020226, 42.00004, 6.1800585, 1.46)} comp[2] {pt3dclear() pt3dadd(-9.179392E-7, 42.0, 0.0, 1.46) pt3dadd(9.509614, 42.0, -3.089861, 1.46)} comp[2] {pt3dadd(19.020168, 41.999996, -6.1800375, 1.46)} comp[133] {pt3dclear() pt3dadd(-1.2676315E-6, -50.0, 0.0, 1.4) pt3dadd(-3.9497368E-6, -75.0, 0.0, 1.4)} comp[133] {pt3dadd(-6.6318216E-6, -100.0, 0.0, 1.4)} comp[122] {pt3dclear() pt3dadd(-11.7550955, 42.000004, 16.179533, 1.168) pt3dadd(-18.567154, 44.880123, 43.961975, 1.168)} comp[122] {pt3dadd(-25.37945, 47.760193, 71.744415, 1.168)} comp[121] {pt3dclear() pt3dadd(-11.7550955, 42.000004, 16.179533, 1.168) pt3dadd(-28.653934, 41.999992, 39.438736, 1.168)} comp[121] {pt3dadd(-45.552567, 42.000015, 62.6979, 1.168)} comp[120] {pt3dclear() pt3dadd(-11.7550955, 42.000004, 16.179533, 1.168) pt3dadd(-36.072685, 39.119892, 31.243484, 1.168)} comp[120] {pt3dadd(-60.39009, 36.239807, 46.307327, 1.168)} comp[109] {pt3dclear() pt3dadd(11.75513, 42.00003, -16.17959, 1.168) pt3dadd(33.232132, 33.51822, -33.30729, 1.168)} comp[109] {pt3dadd(54.709126, 25.036484, -50.43508, 1.168)} comp[108] {pt3dclear() pt3dadd(11.75513, 42.00003, -16.17959, 1.168) pt3dadd(28.653934, 42.000042, -39.438816, 1.168)} comp[108] {pt3dadd(45.55289, 42.00022, -62.698498, 1.168)} comp[107] {pt3dclear() pt3dadd(11.75513, 42.00003, -16.17959, 1.168) pt3dadd(21.407784, 50.481857, -41.898212, 1.168)} comp[107] {pt3dadd(31.060482, 58.963715, -67.616936, 1.168)} comp[96] {pt3dclear() pt3dadd(19.020178, 42.00001, 6.180023, 1.168) pt3dadd(43.342514, 31.157368, 17.016235, 1.168)} comp[96] {pt3dadd(67.66503, 20.31482, 27.852478, 1.168)} comp[95] {pt3dclear() pt3dadd(19.020178, 42.00001, 6.180023, 1.168) pt3dadd(46.363018, 41.999996, 15.064248, 1.168)} comp[95] {pt3dadd(73.705666, 41.99999, 23.948406, 1.168)} comp[94] {pt3dclear() pt3dadd(19.020178, 42.00001, 6.180023, 1.168) pt3dadd(45.066757, 52.842632, 11.709659, 1.168)} comp[94] {pt3dadd(71.11335, 63.685265, 17.239292, 1.168)} comp[83] {pt3dclear() pt3dadd(11.7551365, 42.000015, 16.179583, 1.168) pt3dadd(34.056313, 34.515747, 32.708527, 1.168)} comp[83] {pt3dadd(56.35762, 27.031525, 49.23774, 1.168)} comp[82] {pt3dclear() pt3dadd(11.7551365, 42.000015, 16.179583, 1.168) pt3dadd(28.653938, 42.000027, 39.438812, 1.168)} comp[82] {pt3dadd(45.552658, 42.000065, 62.697968, 1.168)} comp[81] {pt3dclear() pt3dadd(11.7551365, 42.000015, 16.179583, 1.168) pt3dadd(20.583645, 49.48428, 42.496964, 1.168)} comp[81] {pt3dadd(29.412083, 56.96856, 68.81427, 1.168)} comp[70] {pt3dclear() pt3dadd(0.88859874, 42.0, -19.9802, 1.168) pt3dadd(13.205743, 41.007107, -45.939056, 1.168)} comp[70] {pt3dadd(25.522982, 40.014202, -71.897804, 1.168)} comp[69] {pt3dclear() pt3dadd(0.88859874, 42.0, -19.9802, 1.168) pt3dadd(2.1659646, 42.000004, -48.701797, 1.168)} comp[69] {pt3dadd(3.4433362, 42.0, -77.42289, 1.168)} comp[68] {pt3dclear() pt3dadd(0.88859874, 42.0, -19.9802, 1.168) pt3dadd(-9.075516, 42.9929, -46.92994, 1.168)} comp[68] {pt3dadd(-19.039633, 43.9858, -73.87999, 1.168)} comp[57] {pt3dclear() pt3dadd(-0.8886023, 42.0, 19.9802, 1.168) pt3dadd(9.07551, 42.9929, 46.92994, 1.168)} comp[57] {pt3dadd(19.039625, 43.985806, 73.87999, 1.168)} comp[56] {pt3dclear() pt3dadd(-0.8886023, 42.0, 19.9802, 1.168) pt3dadd(-2.1659708, 42.0, 48.701797, 1.168)} comp[56] {pt3dadd(-3.4433446, 42.0, 77.42289, 1.168)} comp[55] {pt3dclear() pt3dadd(-0.8886023, 42.0, 19.9802, 1.168) pt3dadd(-13.205749, 41.007103, 45.939056, 1.168)} comp[55] {pt3dadd(-25.52299, 40.0142, 71.897804, 1.168)} comp[44] {pt3dclear() pt3dadd(-19.020224, 42.000023, -6.1800547, 1.168) pt3dadd(-43.263966, 52.77403, -17.258093, 1.168)} comp[44] {pt3dadd(-67.507614, 63.54805, -28.336105, 1.168)} comp[43] {pt3dclear() pt3dadd(-19.020224, 42.000023, -6.1800547, 1.168) pt3dadd(-46.363075, 42.000042, -15.064296, 1.168)} comp[43] {pt3dadd(-73.705826, 42.000095, -23.948511, 1.168)} comp[42] {pt3dclear() pt3dadd(-19.020224, 42.000023, -6.1800547, 1.168) pt3dadd(-45.145355, 31.226013, -11.467863, 1.168)} comp[42] {pt3dadd(-71.27077, 20.452072, -16.755781, 1.168)} comp[31] {pt3dclear() pt3dadd(-11.755103, 42.000008, -16.179535, 1.168) pt3dadd(-20.992151, 50.010513, -42.200153, 1.168)} comp[31] {pt3dadd(-30.229197, 58.021027, -68.22078, 1.168)} comp[30] {pt3dclear() pt3dadd(-11.755103, 42.000008, -16.179535, 1.168) pt3dadd(-28.653908, 41.999996, -39.438744, 1.168)} comp[30] {pt3dadd(-45.55259, 41.99999, -62.697796, 1.168)} comp[29] {pt3dclear() pt3dadd(-11.755103, 42.000008, -16.179535, 1.168) pt3dadd(-33.647755, 33.989483, -33.005283, 1.168)} comp[29] {pt3dadd(-55.54046, 25.979021, -49.831215, 1.168)} comp[18] {pt3dclear() pt3dadd(-19.020226, 42.00004, 6.1800585, 1.168) pt3dadd(-43.416378, 52.90137, 16.789074, 1.168)} comp[18] {pt3dadd(-67.81264, 63.80274, 27.398129, 1.168)} comp[17] {pt3dclear() pt3dadd(-19.020226, 42.00004, 6.1800585, 1.168) pt3dadd(-46.36307, 42.000057, 15.064298, 1.168)} comp[17] {pt3dadd(-73.70635, 42.00029, 23.948729, 1.168)} comp[16] {pt3dclear() pt3dadd(-19.020226, 42.00004, 6.1800585, 1.168) pt3dadd(-44.992924, 31.098736, 11.9368925, 1.168)} comp[16] {pt3dadd(-70.96569, 20.197525, 17.693771, 1.168)} comp[5] {pt3dclear() pt3dadd(19.020168, 41.999996, -6.1800375, 1.168) pt3dadd(47.39121, 46.359837, -4.555674, 1.168)} comp[5] {pt3dadd(75.76205, 50.719646, -2.9313235, 1.168)} comp[4] {pt3dclear() pt3dadd(19.020168, 41.999996, -6.1800375, 1.168) pt3dadd(46.36304, 42.00001, -15.064235, 1.168)} comp[4] {pt3dadd(73.70571, 41.999973, -23.948502, 1.168)} comp[3] {pt3dclear() pt3dadd(19.020168, 41.999996, -6.1800375, 1.168) pt3dadd(41.018032, 37.640137, -24.170292, 1.168)} comp[3] {pt3dadd(63.016083, 33.280357, -42.160416, 1.168)} comp[136] {pt3dclear() pt3dadd(-6.6318216E-6, -100.0, 0.0, 1.0) pt3dadd(-9.735474, -123.02701, 0.0, 1.0)} comp[136] {pt3dadd(-19.470892, -146.053, 0.0, 1.0)} comp[134] {pt3dclear() pt3dadd(-6.6318216E-6, -100.0, 0.0, 1.0) pt3dadd(9.735456, -123.02701, 0.0, 1.0)} comp[134] {pt3dadd(19.470907, -146.053, 0.0, 1.0)} comp[131] {pt3dclear() pt3dadd(-25.37945, 47.760193, 71.744415, 0.876) pt3dadd(-21.029491, 53.065697, 99.66395, 0.876)} comp[131] {pt3dadd(-16.678543, 58.371376, 127.58321, 0.876)} comp[130] {pt3dclear() pt3dadd(-25.37945, 47.760193, 71.744415, 0.876) pt3dadd(-32.19127, 50.640335, 99.52668, 0.876)} comp[130] {pt3dadd(-39.003105, 53.520477, 127.30895, 0.876)} comp[129] {pt3dclear() pt3dadd(-25.37945, 47.760193, 71.744415, 0.876) pt3dadd(-42.277824, 47.760246, 95.00342, 0.876)} comp[129] {pt3dadd(-59.177048, 47.760204, 118.26294, 0.876)} comp[128] {pt3dclear() pt3dadd(-45.552567, 42.000015, 62.6979, 0.876) pt3dadd(-52.365227, 44.880062, 90.48068, 0.876)} comp[128] {pt3dadd(-59.177048, 47.760204, 118.26294, 0.876)} comp[127] {pt3dclear() pt3dadd(-45.552567, 42.000015, 62.6979, 0.876) pt3dadd(-62.45179, 41.999973, 85.95743, 0.876)} comp[127] {pt3dadd(-79.35017, 42.000027, 109.216415, 0.876)} comp[126] {pt3dclear() pt3dadd(-45.552567, 42.000015, 62.6979, 0.876) pt3dadd(-69.87015, 39.119907, 77.76185, 0.876)} comp[126] {pt3dadd(-94.18774, 36.2398, 92.8258, 0.876)} comp[125] {pt3dclear() pt3dadd(-60.39009, 36.239807, 46.307327, 0.876) pt3dadd(-77.289345, 36.239746, 69.56679, 0.876)} comp[125] {pt3dadd(-94.18774, 36.2398, 92.8258, 0.876)} comp[124] {pt3dclear() pt3dadd(-60.39009, 36.239807, 46.307327, 0.876) pt3dadd(-84.70768, 33.359695, 61.371277, 0.876)} comp[124] {pt3dadd(-109.02527, 30.479588, 76.43523, 0.876)} comp[123] {pt3dclear() pt3dadd(-60.39009, 36.239807, 46.307327, 0.876) pt3dadd(-88.28765, 30.934244, 50.797966, 0.876)} comp[123] {pt3dadd(-116.18438, 25.62878, 55.288086, 0.876)} comp[118] {pt3dclear() pt3dadd(54.709126, 25.036484, -50.43508, 0.876) pt3dadd(77.37341, 9.411922, -58.72691, 0.876)} comp[118] {pt3dadd(100.03817, -6.212467, -67.01964, 0.876)} comp[117] {pt3dclear() pt3dadd(54.709126, 25.036484, -50.43508, 0.876) pt3dadd(76.18608, 16.554726, -67.5628, 0.876)} comp[117] {pt3dadd(97.66311, 8.072891, -84.6905, 0.876)} comp[116] {pt3dclear() pt3dadd(54.709126, 25.036484, -50.43508, 0.876) pt3dadd(71.60803, 25.036524, -73.694496, 0.876)} comp[116] {pt3dadd(88.50687, 25.036634, -96.9539, 0.876)} comp[115] {pt3dclear() pt3dadd(45.55289, 42.00022, -62.698498, 0.876) pt3dadd(67.029915, 33.518394, -79.826195, 0.876)} comp[115] {pt3dadd(88.50687, 25.036634, -96.9539, 0.876)} comp[114] {pt3dclear() pt3dadd(45.55289, 42.00022, -62.698498, 0.876) pt3dadd(62.4514, 42.00003, -85.957016, 0.876)} comp[114] {pt3dadd(79.350235, 42.00014, -109.21642, 0.876)} comp[113] {pt3dclear() pt3dadd(45.55289, 42.00022, -62.698498, 0.876) pt3dadd(55.20534, 50.481945, -88.41669, 0.876)} comp[113] {pt3dadd(64.85825, 58.963825, -114.135735, 0.876)} comp[112] {pt3dclear() pt3dadd(31.060482, 58.963715, -67.616936, 0.876) pt3dadd(47.959354, 58.963787, -90.876335, 0.876)} comp[112] {pt3dadd(64.85825, 58.963825, -114.135735, 0.876)} comp[111] {pt3dclear() pt3dadd(31.060482, 58.963715, -67.616936, 0.876) pt3dadd(40.712944, 67.44543, -93.33511, 0.876)} comp[111] {pt3dadd(50.365795, 75.92737, -119.05418, 0.876)} comp[110] {pt3dclear() pt3dadd(31.060482, 58.963715, -67.616936, 0.876) pt3dadd(31.943047, 74.58819, -91.734436, 0.876)} comp[110] {pt3dadd(32.825565, 90.2127, -115.85193, 0.876)} comp[105] {pt3dclear() pt3dadd(67.66503, 20.31482, 27.852478, 0.876) pt3dadd(85.12662, 0.34132385, 38.929787, 0.876)} comp[105] {pt3dadd(102.58821, -19.63216, 50.0071, 0.876)} comp[104] {pt3dclear() pt3dadd(67.66503, 20.31482, 27.852478, 0.876) pt3dadd(91.98754, 9.4722595, 38.688717, 0.876)} comp[104] {pt3dadd(116.31006, -1.3702888, 49.524956, 0.876)} comp[103] {pt3dclear() pt3dadd(67.66503, 20.31482, 27.852478, 0.876) pt3dadd(95.00786, 20.314846, 36.736683, 0.876)} comp[103] {pt3dadd(122.35069, 20.314882, 45.620888, 0.876)} comp[102] {pt3dclear() pt3dadd(73.705666, 41.99999, 23.948406, 0.876) pt3dadd(98.028175, 31.157429, 34.78465, 0.876)} comp[102] {pt3dadd(122.3507, 20.314789, 45.62092, 0.876)} comp[101] {pt3dclear() pt3dadd(73.705666, 41.99999, 23.948406, 0.876) pt3dadd(101.0485, 41.999924, 32.83264, 0.876)} comp[101] {pt3dadd(128.39134, 41.999954, 41.71685, 0.876)} comp[100] {pt3dclear() pt3dadd(73.705666, 41.99999, 23.948406, 0.876) pt3dadd(99.75235, 52.842606, 29.478073, 0.876)} comp[100] {pt3dadd(125.79903, 63.68526, 35.00773, 0.876)} comp[99] {pt3dclear() pt3dadd(71.11335, 63.685265, 17.239292, 0.876) pt3dadd(98.456184, 63.68526, 26.123516, 0.876)} comp[99] {pt3dadd(125.79903, 63.68526, 35.00773, 0.876)} comp[98] {pt3dclear() pt3dadd(71.11335, 63.685265, 17.239292, 0.876) pt3dadd(97.16003, 74.52787, 22.768963, 0.876)} comp[98] {pt3dadd(123.206696, 85.37058, 28.298603, 0.876)} comp[97] {pt3dclear() pt3dadd(71.11335, 63.685265, 17.239292, 0.876) pt3dadd(91.75117, 83.658615, 18.541252, 0.876)} comp[97] {pt3dadd(112.38899, 103.63197, 19.843212, 0.876)} comp[92] {pt3dclear() pt3dadd(56.35762, 27.031525, 49.23774, 0.876) pt3dadd(80.54034, 13.244663, 56.427048, 0.876)} comp[92] {pt3dadd(104.72254, -0.5422821, 63.61551, 0.876)} comp[91] {pt3dclear() pt3dadd(56.35762, 27.031525, 49.23774, 0.876) pt3dadd(78.65866, 19.547329, 65.76663, 0.876)} comp[91] {pt3dadd(100.95976, 12.063074, 82.29551, 0.876)} comp[90] {pt3dclear() pt3dadd(56.35762, 27.031525, 49.23774, 0.876) pt3dadd(73.25647, 27.031612, 72.49717, 0.876)} comp[90] {pt3dadd(90.15488, 27.031548, 95.75571, 0.876)} comp[89] {pt3dclear() pt3dadd(45.552658, 42.000065, 62.697968, 0.876) pt3dadd(67.85377, 34.51581, 79.22684, 0.876)} comp[89] {pt3dadd(90.15488, 27.031548, 95.75571, 0.876)} comp[88] {pt3dclear() pt3dadd(45.552658, 42.000065, 62.697968, 0.876) pt3dadd(62.451576, 42.000088, 85.957375, 0.876)} comp[88] {pt3dadd(79.35048, 42.000114, 109.21677, 0.876)} comp[87] {pt3dclear() pt3dadd(45.552658, 42.000065, 62.697968, 0.876) pt3dadd(54.381298, 49.48432, 89.01551, 0.876)} comp[87] {pt3dadd(63.2099, 56.968613, 115.33306, 0.876)} comp[86] {pt3dclear() pt3dadd(29.412083, 56.96856, 68.81427, 0.876) pt3dadd(46.311005, 56.968575, 92.07366, 0.876)} comp[86] {pt3dadd(63.209904, 56.968605, 115.33306, 0.876)} comp[85] {pt3dclear() pt3dadd(29.412083, 56.96856, 68.81427, 0.876) pt3dadd(38.240707, 64.452835, 95.13181, 0.876)} comp[85] {pt3dadd(47.069324, 71.9371, 121.449356, 0.876)} comp[84] {pt3dclear() pt3dadd(29.412083, 56.96856, 68.81427, 0.876) pt3dadd(28.776363, 70.75544, 94.03465, 0.876)} comp[84] {pt3dadd(28.141151, 84.54241, 119.25589, 0.876)} comp[79] {pt3dclear() pt3dadd(25.522982, 40.014202, -71.897804, 0.876) pt3dadd(46.935406, 38.185158, -90.995415, 0.876)} comp[79] {pt3dadd(68.347725, 36.35613, -110.094, 0.876)} comp[78] {pt3dclear() pt3dadd(25.522982, 40.014202, -71.897804, 0.876) pt3dadd(37.840126, 39.02131, -97.856766, 0.876)} comp[78] {pt3dadd(50.15736, 38.028408, -123.81572, 0.876)} comp[77] {pt3dclear() pt3dadd(25.522982, 40.014202, -71.897804, 0.876) pt3dadd(26.800293, 40.01421, -100.619804, 0.876)} comp[77] {pt3dadd(28.077707, 40.014206, -129.34082, 0.876)} comp[76] {pt3dclear() pt3dadd(3.4433362, 42.0, -77.42289, 0.876) pt3dadd(15.760565, 41.0071, -103.38186, 0.876)} comp[76] {pt3dadd(28.077707, 40.014206, -129.34082, 0.876)} comp[75] {pt3dclear() pt3dadd(3.4433362, 42.0, -77.42289, 0.876) pt3dadd(4.720708, 42.000004, -106.144905, 0.876)} comp[75] {pt3dadd(5.9980702, 42.000008, -134.86691, 0.876)} comp[74] {pt3dclear() pt3dadd(3.4433362, 42.0, -77.42289, 0.876) pt3dadd(-6.5207815, 42.9929, -104.37295, 0.876)} comp[74] {pt3dadd(-16.484907, 43.9858, -131.32298, 0.876)} comp[73] {pt3dclear() pt3dadd(-19.039633, 43.9858, -73.87999, 0.876) pt3dadd(-17.762222, 43.985794, -102.60098, 0.876)} comp[73] {pt3dadd(-16.484907, 43.9858, -131.32298, 0.876)} comp[72] {pt3dclear() pt3dadd(-19.039633, 43.9858, -73.87999, 0.876) pt3dadd(-29.003752, 44.978703, -100.83003, 0.876)} comp[72] {pt3dadd(-38.96787, 45.9716, -127.77908, 0.876)} comp[71] {pt3dclear() pt3dadd(-19.039633, 43.9858, -73.87999, 0.876) pt3dadd(-38.67214, 45.814846, -94.80339, 0.876)} comp[71] {pt3dadd(-58.30465, 47.64389, -115.72679, 0.876)} comp[66] {pt3dclear() pt3dadd(19.039625, 43.985806, 73.87999, 0.876) pt3dadd(38.67213, 45.81485, 94.80339, 0.876)} comp[66] {pt3dadd(58.304634, 47.643898, 115.72679, 0.876)} comp[65] {pt3dclear() pt3dadd(19.039625, 43.985806, 73.87999, 0.876) pt3dadd(29.00374, 44.978706, 100.83003, 0.876)} comp[65] {pt3dadd(38.967854, 45.971603, 127.77908, 0.876)} comp[64] {pt3dclear() pt3dadd(19.039625, 43.985806, 73.87999, 0.876) pt3dadd(17.76221, 43.985798, 102.60098, 0.876)} comp[64] {pt3dadd(16.484896, 43.985806, 131.32298, 0.876)} } proc shape2() { comp[63] {pt3dclear() pt3dadd(-3.4433446, 42.0, 77.42289, 0.876) pt3dadd(6.520771, 42.9929, 104.37295, 0.876)} comp[63] {pt3dadd(16.484896, 43.985806, 131.32298, 0.876)} comp[62] {pt3dclear() pt3dadd(-3.4433446, 42.0, 77.42289, 0.876) pt3dadd(-4.7207193, 42.000004, 106.144905, 0.876)} comp[62] {pt3dadd(-5.9980836, 42.000004, 134.86691, 0.876)} comp[61] {pt3dclear() pt3dadd(-3.4433446, 42.0, 77.42289, 0.876) pt3dadd(-15.760576, 41.007095, 103.38186, 0.876)} comp[61] {pt3dadd(-28.077719, 40.014202, 129.34082, 0.876)} comp[60] {pt3dclear() pt3dadd(-25.52299, 40.0142, 71.897804, 0.876) pt3dadd(-26.800304, 40.014206, 100.619804, 0.876)} comp[60] {pt3dadd(-28.077719, 40.014202, 129.34082, 0.876)} comp[59] {pt3dclear() pt3dadd(-25.52299, 40.0142, 71.897804, 0.876) pt3dadd(-37.840134, 39.0213, 97.856766, 0.876)} comp[59] {pt3dadd(-50.157375, 38.0284, 123.81572, 0.876)} comp[58] {pt3dclear() pt3dadd(-25.52299, 40.0142, 71.897804, 0.876) pt3dadd(-46.935413, 38.18515, 90.995415, 0.876)} comp[58] {pt3dadd(-68.34774, 36.356117, 110.094, 0.876)} comp[53] {pt3dclear() pt3dadd(-67.507614, 63.54805, -28.336105, 0.876) pt3dadd(-84.82448, 83.39501, -39.85888, 0.876)} comp[53] {pt3dadd(-102.14227, 103.242096, -51.38199, 0.876)} comp[52] {pt3dclear() pt3dadd(-67.507614, 63.54805, -28.336105, 0.876) pt3dadd(-91.75155, 74.32207, -39.414207, 0.876)} comp[52] {pt3dadd(-115.995476, 85.09608, -50.49231, 0.876)} comp[51] {pt3dclear() pt3dadd(-67.507614, 63.54805, -28.336105, 0.876) pt3dadd(-94.85066, 63.548077, -37.220413, 0.876)} comp[51] {pt3dadd(-122.193695, 63.54812, -46.10472, 0.876)} comp[50] {pt3dclear() pt3dadd(-73.705826, 42.000095, -23.948511, 0.876) pt3dadd(-97.94977, 52.77409, -35.02661, 0.876)} comp[50] {pt3dadd(-122.19369, 63.54813, -46.10472, 0.876)} comp[49] {pt3dclear() pt3dadd(-73.705826, 42.000095, -23.948511, 0.876) pt3dadd(-101.048874, 42.00013, -32.832825, 0.876)} comp[49] {pt3dadd(-128.3919, 42.000164, -41.717125, 0.876)} comp[48] {pt3dclear() pt3dadd(-73.705826, 42.000095, -23.948511, 0.876) pt3dadd(-99.830864, 31.226103, -29.236294, 0.876)} comp[48] {pt3dadd(-125.9559, 20.452112, -34.52408, 0.876)} comp[47] {pt3dclear() pt3dadd(-71.27077, 20.452072, -16.755781, 0.876) pt3dadd(-98.61379, 20.452206, -25.64011, 0.876)} comp[47] {pt3dadd(-125.9559, 20.452112, -34.52408, 0.876)} comp[46] {pt3dclear() pt3dadd(-71.27077, 20.452072, -16.755781, 0.876) pt3dadd(-97.395775, 9.678177, -22.043583, 0.876)} comp[46] {pt3dadd(-123.52082, -1.0958176, -27.331366, 0.876)} comp[45] {pt3dclear() pt3dadd(-71.27077, 20.452072, -16.755781, 0.876) pt3dadd(-92.053764, 0.6051483, -17.612423, 0.876)} comp[45] {pt3dadd(-112.83584, -19.241909, -18.468721, 0.876)} comp[40] {pt3dclear() pt3dadd(-30.229197, 58.021027, -68.22078, 0.876) pt3dadd(-30.346024, 72.7773, -92.89441, 0.876)} comp[40] {pt3dadd(-30.46285, 87.533585, -117.568054, 0.876)} comp[39] {pt3dclear() pt3dadd(-30.229197, 58.021027, -68.22078, 0.876) pt3dadd(-39.466316, 66.031525, -94.24147, 0.876)} comp[39] {pt3dadd(-48.703354, 74.0421, -120.26219, 0.876)} comp[38] {pt3dclear() pt3dadd(-30.229197, 58.021027, -68.22078, 0.876) pt3dadd(-47.12799, 58.021027, -91.47999, 0.876)} comp[38] {pt3dadd(-64.02679, 58.021027, -114.739204, 0.876)} comp[37] {pt3dclear() pt3dadd(-45.55259, 41.99999, -62.697796, 0.876) pt3dadd(-54.789703, 50.01049, -88.7185, 0.876)} comp[37] {pt3dadd(-64.02679, 58.021027, -114.739204, 0.876)} comp[36] {pt3dclear() pt3dadd(-45.55259, 41.99999, -62.697796, 0.876) pt3dadd(-62.451424, 41.99994, -85.956985, 0.876)} comp[36] {pt3dadd(-79.3502, 41.99996, -109.2162, 0.876)} comp[35] {pt3dclear() pt3dadd(-45.55259, 41.99999, -62.697796, 0.876) pt3dadd(-67.44529, 33.989525, -79.52372, 0.876)} comp[35] {pt3dadd(-89.338066, 25.978994, -96.349625, 0.876)} comp[34] {pt3dclear() pt3dadd(-55.54046, 25.979021, -49.831215, 0.876) pt3dadd(-72.439224, 25.979042, -73.09043, 0.876)} comp[34] {pt3dadd(-89.338, 25.979063, -96.34965, 0.876)} comp[33] {pt3dclear() pt3dadd(-55.54046, 25.979021, -49.831215, 0.876) pt3dadd(-77.43316, 17.968561, -66.65714, 0.876)} comp[33] {pt3dadd(-99.325874, 9.958099, -83.48307, 0.876)} comp[32] {pt3dclear() pt3dadd(-55.54046, 25.979021, -49.831215, 0.876) pt3dadd(-78.97044, 11.222641, -57.56683, 0.876)} comp[32] {pt3dadd(-102.40043, -3.533741, -65.30246, 0.876)} comp[27] {pt3dclear() pt3dadd(-67.81264, 63.80274, 27.398129, 0.876) pt3dadd(-85.4104, 83.8842, 38.05694, 0.876)} comp[27] {pt3dadd(-103.00813, 103.96572, 48.715744, 0.876)} comp[26] {pt3dclear() pt3dadd(-67.81264, 63.80274, 27.398129, 0.876) pt3dadd(-92.20835, 74.70392, 38.006966, 0.876)} comp[26] {pt3dadd(-116.60495, 85.60541, 48.616158, 0.876)} comp[25] {pt3dclear() pt3dadd(-67.81264, 63.80274, 27.398129, 0.876) pt3dadd(-95.155655, 63.802834, 36.28244, 0.876)} comp[25] {pt3dadd(-122.49869, 63.802887, 45.166748, 0.876)} comp[24] {pt3dclear() pt3dadd(-73.70635, 42.00029, 23.948729, 0.876) pt3dadd(-98.102066, 52.901485, 34.557564, 0.876)} comp[24] {pt3dadd(-122.49869, 63.802887, 45.166748, 0.876)} comp[23] {pt3dclear() pt3dadd(-73.70635, 42.00029, 23.948729, 0.876) pt3dadd(-101.04851, 42.00005, 32.83268, 0.876)} comp[23] {pt3dadd(-128.39151, 42.00019, 41.716995, 0.876)} comp[22] {pt3dclear() pt3dadd(-73.70635, 42.00029, 23.948729, 0.876) pt3dadd(-99.67906, 31.098963, 29.705559, 0.876)} comp[22] {pt3dadd(-125.65174, 20.19772, 35.462402, 0.876)} comp[21] {pt3dclear() pt3dadd(-70.96569, 20.197525, 17.693771, 0.876) pt3dadd(-98.30874, 20.19758, 26.578083, 0.876)} comp[21] {pt3dadd(-125.65174, 20.19772, 35.462402, 0.876)} comp[20] {pt3dclear() pt3dadd(-70.96569, 20.197525, 17.693771, 0.876) pt3dadd(-96.93838, 9.296288, 23.450617, 0.876)} comp[20] {pt3dadd(-122.911095, -1.6050453, 29.207449, 0.876)} comp[19] {pt3dclear() pt3dadd(-70.96569, 20.197525, 17.693771, 0.876) pt3dadd(-91.46744, 0.11594391, 19.414223, 0.876)} comp[19] {pt3dadd(-111.9701, -19.96542, 21.135023, 0.876)} comp[14] {pt3dclear() pt3dadd(75.76205, 50.719646, -2.9313235, 0.876) pt3dadd(100.68256, 58.75108, 8.945222, 0.876)} comp[14] {pt3dadd(125.60211, 66.782364, 20.82172, 0.876)} comp[13] {pt3dclear() pt3dadd(75.76205, 50.719646, -2.9313235, 0.876) pt3dadd(104.13309, 55.079487, -1.3069592, 0.876)} comp[13] {pt3dadd(132.50412, 59.439327, 0.3174057, 0.876)} comp[12] {pt3dclear() pt3dadd(75.76205, 50.719646, -2.9313235, 0.876) pt3dadd(103.10539, 50.719734, -11.815488, 0.876)} comp[12] {pt3dadd(130.4478, 50.719654, -20.699776, 0.876)} comp[11] {pt3dclear() pt3dadd(73.70571, 41.999973, -23.948502, 0.876) pt3dadd(102.07675, 46.359814, -22.32414, 0.876)} comp[11] {pt3dadd(130.4478, 50.719654, -20.699776, 0.876)} comp[10] {pt3dclear() pt3dadd(73.70571, 41.999973, -23.948502, 0.876) pt3dadd(101.04909, 42.00004, -32.832737, 0.876)} comp[10] {pt3dadd(128.39146, 41.999954, -41.717026, 0.876)} comp[9] {pt3dclear() pt3dadd(73.70571, 41.999973, -23.948502, 0.876) pt3dadd(95.704254, 37.64023, -41.93869, 0.876)} comp[9] {pt3dadd(117.70182, 33.280334, -59.92894, 0.876)} comp[8] {pt3dclear() pt3dadd(63.016083, 33.280357, -42.160416, 0.876) pt3dadd(90.35845, 33.28027, -51.04471, 0.876)} comp[8] {pt3dadd(117.70182, 33.280334, -59.92894, 0.876)} comp[7] {pt3dclear() pt3dadd(63.016083, 33.280357, -42.160416, 0.876) pt3dadd(85.01363, 28.92046, -60.150665, 0.876)} comp[7] {pt3dadd(107.01119, 24.560566, -78.14091, 0.876)} comp[6] {pt3dclear() pt3dadd(63.016083, 33.280357, -42.160416, 0.876) pt3dadd(76.19619, 25.249002, -66.416405, 0.876)} comp[6] {pt3dadd(89.37534, 17.217388, -90.67273, 0.876)} comp[137] {pt3dclear() pt3dadd(-19.470892, -146.053, 0.0, 1.0) pt3dadd(-29.206392, -169.08, 0.0, 1.0)} comp[137] {pt3dadd(-38.94189, -192.106, 0.0, 1.0)} comp[135] {pt3dclear() pt3dadd(19.470907, -146.053, 0.0, 1.0) pt3dadd(29.206408, -169.08, 0.0, 1.0)} comp[135] {pt3dadd(38.941807, -192.106, 0.0, 1.0)} } proc biophys() { // // insert the mechanisms and assign max conductances // forsec all { insert pas insert extracellular xraxial=1e+09 xg=1e+09 xc=0 e_extracellular } // g_pas has two values; soma-dend,axon forsec level[ 0] { insert naf_tcr gbar_naf_tcr = 0.4 // shift_hnaf_naf_tcr = JfgNaS insert napf_tcr gbar_napf_tcr = 0.0008 insert kdr gbar_kdr = 0.18 insert ka gbar_ka = 0.001 insert k2 gbar_k2 = 0.0005 } forsec level[ 1] { insert naf_tcr gbar_naf_tcr = 0.1 insert napf_tcr gbar_napf_tcr = 0.0002 insert kdr gbar_kdr = 0.03375 insert kc gbar_kc = 0.012 insert ka gbar_ka = 0.006 insert km gbar_km = 0.0005 insert k2 gbar_k2 = 0.002 insert kahp_slower gbar_kahp_slower = 0.00005 insert cal gbar_cal = 0.0005 insert cat gbar_cat = 0.0005 insert ar gbar_ar = 0.00025 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.02 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 52000. } forsec level[ 2] { insert naf_tcr gbar_naf_tcr = 0.1 insert napf_tcr gbar_napf_tcr = 0.0002 insert kdr gbar_kdr = 0.0225 insert kc gbar_kc = 0.012 insert ka gbar_ka = 0.006 insert km gbar_km = 0.0005 insert k2 gbar_k2 = 0.002 insert kahp_slower gbar_kahp_slower = 0.00005 insert cal gbar_cal = 0.0005 insert cat gbar_cat = 0.005 insert ar gbar_ar = 0.0005 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.05 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 104000. } forsec level[ 3] { insert naf_tcr gbar_naf_tcr = 0.005 insert napf_tcr gbar_napf_tcr = 0.00001 insert kc gbar_kc = 0.02 insert ka gbar_ka = 0.0002 insert km gbar_km = 0.0005 insert k2 gbar_k2 = 0.002 insert kahp_slower gbar_kahp_slower = 0.00005 insert cal gbar_cal = 0.00025 insert cat gbar_cat = 0.003 insert ar gbar_ar = 0.0003 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.05 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 104000. } forsec level[ 4] { insert naf_tcr gbar_naf_tcr = 0.005 insert napf_tcr gbar_napf_tcr = 0.00001 insert kc gbar_kc = 0.02 insert ka gbar_ka = 0.0002 insert km gbar_km = 0.0005 insert k2 gbar_k2 = 0.002 insert kahp_slower gbar_kahp_slower = 0.00005 insert cal gbar_cal = 0.00025 insert cat gbar_cat = 0.0005 insert ar gbar_ar = 0.0003 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.05 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 104000. } forsec all { cm = 0.9 // assign global specific capac. } // // passive membrane resistance (leak) and axial resistance // forsec Soma_Dendrites { g_pas = 3.78787879E-05 Ra = 175. } forsec Axon { g_pas = 0.001 Ra = 100. } ceiling_cad = 1e6 // nearly unlimited Ca concentration // print "made it to end of initialization from SCORTMAJ_FRB()" } // end of biophys // Compartment Area: Dendritic.spines double area of // dend. membrane, which in Traubs method is equivalent to // only multiplying all dend. max conductances by two // (the area is doubled but the volume is const.) proc double_dend_cond() { spine_area_multiplier = 2 forsec Dendrites { if (ismembrane("napf_tcr")) { gbar_napf_tcr *= spine_area_multiplier } if (ismembrane("napf_tcrf")) { gbar_napf_tcrf *= spine_area_multiplier } if (ismembrane("napf_tcrf_tcr")) { gbar_napf_tcrf_tcr *= spine_area_multiplier } if (ismembrane("naf_tcr")) { gbar_naf_tcr *= spine_area_multiplier } if (ismembrane("naf_tcr_tcr")) { gbar_naf_tcr_tcr *= spine_area_multiplier } if (ismembrane("naf_tcr2")) { gbar_naf_tcr2 *= spine_area_multiplier } if (ismembrane("kc")) { gbar_kc *= spine_area_multiplier } if (ismembrane("kc_fast")) { gbar_kc_fast *= spine_area_multiplier } if (ismembrane("kahp")) { gbar_kahp *= spine_area_multiplier } if (ismembrane("kahp_slower")) { gbar_kahp_slower *= spine_area_multiplier } if (ismembrane("km")) { gbar_km *= spine_area_multiplier } if (ismembrane("kdr")) { gbar_kdr *= spine_area_multiplier } if (ismembrane("kdr_fs")) { gbar_kdr_fs *= spine_area_multiplier } if (ismembrane("ka")) { gbar_ka *= spine_area_multiplier } if (ismembrane("ka_ib")) { gbar_ka_ib *= spine_area_multiplier } if (ismembrane("k2")) { gbar_k2 *= spine_area_multiplier } if (ismembrane("cal")) { gbar_cal *= spine_area_multiplier } if (ismembrane("cat")) { gbar_cat *= spine_area_multiplier } if (ismembrane("cat_a")) { gbar_cat_a *= spine_area_multiplier } if (ismembrane("ar")) { gbar_ar *= spine_area_multiplier } if (ismembrane("pas")) { g_pas *= spine_area_multiplier } cm = cm * spine_area_multiplier } } // double_dend_cond() // run for cells w/ spines proc position() { local i // comp switched to comp[1] since 0 deleted forsec all { for i = 0, n3d()-1 { pt3dchange(i, $1-x+x3d(i), \ $2-y+y3d(i), $3-z+z3d(i),diam3d(i)) } } x=$1 y=$2 z=$3 } proc connect2target() { // $o1 targ point process, $o2 returned NetCon comp[presyn_comp] $o2 = new NetCon(&v(1),$o1) $o2.threshold = 0 } objref syn_ proc synapses() { // place for each compartment that has input // statements like //comp[3] syn_=new AlphaSynKinT(1) synlist.append(syn_) //comp[4] syn_=new NMDA(1) synlist.append(syn_) } // is not an artificial cell: func is_art() { return 0 } proc more_adjustments() { forsec all { // global reversal potentials ek = -95. e_pas = -70. ena = 50. vca = 125. forsec all if (ismembrane("ar")) erev_ar = -35. e_gaba_a = -81. } //extended initializations // for i=1,137 { // comp[i] if (ismembrane("ka")) {gbar_ka*=0.2} // } // for i = 132, 137 { // axon // comp[i] gbar_kdr *= 0.45 // } // comp[1] gbar_kdr *= 0.45 // for (i = 2; i<=119; i += 13) { // level 2 // comp[i] gbar_kdr *= 0.45 // } persistentNa_shift = 7 // in the fortran code the napf_tcrf has a 10 mV shift // but uses the naf_tcr rates (apham_...) which were // created with a -3 mV shift for total 7 mV forsec all { if (ismembrane("napf_tcr")){ fastNa_shift_napf_tcr = 0.0} } } proc set_doubler() {doubler=0} // this function sets doubler to 0 // because there are no spines // in the cell, replacing earlier fnc. endtemplate TCR