/*
CK Overstreet and JD Klein
Last Updated 12/20/2012
Major characteristics of cell bodies and axons reconstructed by hand from:
H.D. Schwark, “The distribution of intrinsic cortical axons in area 3b of cat primary somatosensory cortex”, Experimental Brain Research, vol. 78, no. 3, pp. 501-513, Aug. 1989. 
*/

load_file("nrngui.hoc")

NAPICAL=27
NBOUTON=12

create soma, ap[NAPICAL], bt[NBOUTON]

access soma

connect ap[0](0), soma(0)
connect ap[1](0), ap[0](1)
connect ap[2](0), ap[0](1)
connect ap[3](0), ap[2](1)
connect ap[4](0), ap[2](1)
connect ap[5](0), ap[4](1)
connect ap[6](0), ap[5](1)
connect ap[7](0), ap[5](1)
connect ap[8](0), ap[7](1)
connect ap[9](0), ap[7](1)
connect ap[10](0), ap[9](1)
connect ap[11](0), ap[5](1)
connect ap[12](0), ap[11](1)
connect ap[13](0), ap[12](1)
connect ap[14](0), ap[11](1)
connect ap[15](0), ap[14](1)
connect ap[16](0), ap[15](1)
connect ap[17](0), ap[15](1)
connect ap[18](0), ap[14](1)
connect ap[19](0), ap[18](1)
connect ap[20](0), ap[18](1)
connect ap[21](0), ap[2](1)
connect ap[22](0), ap[21](1)
connect ap[23](0), ap[22](1)
connect ap[24](0), ap[21](1)
connect ap[25](0), ap[24](1)
connect ap[26](0), ap[25](1)

connect bt[0](0), ap[1](1)
connect bt[1](0), ap[3](1)
connect bt[2](0), ap[6](1)
connect bt[3](0), ap[8](1)
connect bt[4](0), ap[10](1)
connect bt[5](0), ap[13](1)
connect bt[6](0), ap[16](1)
connect bt[7](0), ap[17](1)
connect bt[8](0), ap[19](1)
connect bt[9](0), ap[20](1)
connect bt[10](0), ap[23](1)
connect bt[11](0), ap[26](1)

forall pt3dclear()

soma {
	pt3dadd(0, 0, 0, 10)
	pt3dadd(0, 10, 0, 10)
	insert axnode
	insert extracellular
	insert xtra
	xraxial=1e+09 
	xg=1e+09 
	xc=0 
	e_extracellular=0
}

for i = 0, NAPICAL-1 ap[i] { 
	insert axnode
	insert extracellular 
	insert xtra
	xraxial=1e+09 
	xg=1e+09 
	xc=0 
	e_extracellular=0
} 

for i = 0, NBOUTON-1 bt[i] { 
	insert axnode
	insert extracellular 
	insert xtra
	xraxial=1e+09 
	xg=1e+09 
	xc=0 
	e_extracellular=0
}

ap[0] {
	pt3dadd(0, 10, 0, 1)
	pt3dadd(-25, -50, 0, 1)
}
ap[1] {
	pt3dadd(-25, -50, 0, .5)
	pt3dadd(-50, -75, 0, .25)
}
ap[2] {
	pt3dadd(-25, -50, 0, 1)
	pt3dadd(50, -25, 0, 1)
}
ap[3] {
	pt3dadd(50, -25, 0, .5)
	pt3dadd(125, -125, 0, .25)
}
ap[4] {
	pt3dadd(50, -25, 0, 1)
	pt3dadd(50, 100, 0, 1)
}
ap[5] {
	pt3dadd(50, 100, 0, .5)
	pt3dadd(30, 250, 0, .5)
}
ap[6] {
	pt3dadd(30, 250, 0, .5)
	pt3dadd(200, 400, 0, .25)
}
ap[7] {
	pt3dadd(30, 250, 0, .5)
	pt3dadd(40, 325, 0, .5)
}
ap[8] {
	pt3dadd(40, 325, 0, .25)
	pt3dadd(25, 350, 0, .25)
}
ap[9] {
	pt3dadd(40, 325, 0, .5)
	pt3dadd(40, 475, 0, .5)
}
ap[10] {
	pt3dadd(40, 475, 0, .25)
	pt3dadd(0, 500, 0, .25)
}
ap[11] {
	pt3dadd(50, 100, 0, .5)
	pt3dadd(75, 400, 0, .5)
}
ap[12] {
	pt3dadd(75, 400, 0, .25)
	pt3dadd(50, 450, 0, .25)
}
ap[13] {
	pt3dadd(50, 450, 0, .25)
	pt3dadd(50, 500, 0, .25)
}
ap[14] {
	pt3dadd(75, 400, 0, .5)
	pt3dadd(100, 650, 0, .5)
}
ap[15] {
	pt3dadd(100, 650, 0, .5)
	pt3dadd(75, 675, 0, .5)
}
ap[16] {
	pt3dadd(75, 675, 0, .25)
	pt3dadd(50, 700, 0, .25)
}
ap[17] {
	pt3dadd(75, 675, 0, .25)
	pt3dadd(100, 700, 0, .25)
}
ap[18] {
	pt3dadd(100, 650, 0, .5)
	pt3dadd(125, 675, 0, .5)
}
ap[19] {
	pt3dadd(125, 675, 0, .25)
	pt3dadd(100, 700, 0, .25)
}
ap[20] {
	pt3dadd(125, 675, 0, .25)
	pt3dadd(150, 700, 0, .25)
}
ap[21] {
	pt3dadd(50, -25, 0, 1)
	pt3dadd(75, -50, 0, 1)
}
ap[22] {
	pt3dadd(75, -50, 0, .5)
	pt3dadd(150, -25, 0, .5)
}
ap[23] {
	pt3dadd(150, -25, 0, .25)
	pt3dadd(225, -175, 0, .25)
}
ap[24] {
	pt3dadd(75, -50, 0, 1)
	pt3dadd(150, 200, 0, 1)
}
ap[25] {
	pt3dadd(150, 200, 0, .5)
	pt3dadd(250, 475, 0, .5)
}
ap[26] {
	pt3dadd(250, 475, 0, .5)
	pt3dadd(350, 600, 0, .25)
}

bt[0] {
	pt3dadd(-50, -75, 0, 0.25)
	pt3dadd(-53.5, -78.5, 0, 3)
}
bt[1] {
	pt3dadd(125, -125, 0, 0.25)
	pt3dadd(128.0, -129.0, 0, 3)
}
bt[2] {
	pt3dadd(200, 400, 0, 0.25)
	pt3dadd(203.7, 403.3, 0, 3)
}
bt[3] {
	pt3dadd(25, 350, 0, 0.25)
	pt3dadd(22.4, 354.3, 0, 3)
}
bt[4] {
	pt3dadd(0, 500, 0, 0.25)
	pt3dadd(-4.2, 502.6, 0, 3)
}
bt[5] {
	pt3dadd(50, 500, 0, 0.25)
	pt3dadd(50.0, 505.0, 0, 3)
}
bt[6] {
	pt3dadd(50, 700, 0, 0.25)
	pt3dadd(46.5, 703.5, 0, 3)
}
bt[7] {
	pt3dadd(100, 700, 0, 0.25)
	pt3dadd(103.5, 703.5, 0, 3)
}
bt[8] {
	pt3dadd(100, 700, 0, 0.25)
	pt3dadd(96.5, 703.5, 0, 3)
}
bt[9] {
	pt3dadd(150, 700, 0, 0.25)
	pt3dadd(153.5, 703.5, 0, 3)
}
bt[10] {
	pt3dadd(225, -175, 0, 0.25)
	pt3dadd(227.2, -179.5, 0, 3)
}
bt[11] {
	pt3dadd(350, 600, 0, 0.25)
	pt3dadd(353.1, 603.9, 0, 3)
}


XORIGIN = 0
YORIGIN = 0
ZORIGIN = 0

access soma
pt3dchange(0, x3d(0)+XORIGIN, y3d(0)+YORIGIN, z3d(0)+ZORIGIN, diam3d(0))
pt3dchange(1, x3d(1)+XORIGIN, y3d(1)+YORIGIN, z3d(1)+ZORIGIN, diam3d(1))
nseg=21

for(i=0; i<=NAPICAL-1; i=i+1){
	access ap[i]
	pt3dchange(0, x3d(0)+XORIGIN, y3d(0)+YORIGIN, z3d(0)+ZORIGIN, diam3d(0))
	pt3dchange(1, x3d(1)+XORIGIN, y3d(1)+YORIGIN, z3d(1)+ZORIGIN, diam3d(1))
	nseg=101
}

for(i=0; i<=NBOUTON-1; i=i+1){
	access bt[i]
	pt3dchange(0, x3d(0)+XORIGIN, y3d(0)+YORIGIN, z3d(0)+ZORIGIN, diam3d(0))
	pt3dchange(1, x3d(1)+XORIGIN, y3d(1)+YORIGIN, z3d(1)+ZORIGIN, diam3d(1))
	nseg=5
}

forall Ra=70
access ap[0]