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eMorph-p.hoc
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eMorph-p.hoc
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/* ================================================================================
Morphology related routines.
Add spines to a cell
1. by including a subsample of explicit spines
2. by corrections using Rm and Cm.
PARAMETERS
.sample_pct Percent of explicit spines to create
.g_type String array with dendritic label names for Gulyas cells
.g_den Array of densities for each dendritic type (#/um)
.type_pct Array of spine type densities for stub[0], mush[1] and thin[2] spines.
.head_dia Array of head diameters
.head_len Array of head lengths
.neck_dia Array of neck diameters
.neck_len Array of neck lengths
USAGE
load_file( "eMorph-template.hoc" )
.. // create soma and segments.
strdef cell_id
cell_id = "your-cell-identifier"
================================================================================ */
//--- Allow loading before cell
if( ! name_declared( "soma" )){
execute( "create soma" )
}
if( ! name_declared( "randSel" ) ){
execute("objref randSel" )
execute( "randSel = new Random(123)")
}
begintemplate String_array_aux_
public s
strdef s
endtemplate String_array_aux_
begintemplate String_array
objref s[1], strf
public s, n, set_size, split
proc init() { local i
n = $1
if( n > 0 ){
objref s[ n ]
for i=1, n s[i-1] = new String_array_aux_()
}
}
endtemplate String_array
//==========================================================================================
begintemplate eMorph
double type_pct[3], neck_dia[3], neck_len[3], head_dia[3], head_len[3], spine_area[3], type_added[3]
double g_den[9], dend_len[9], g_dend_len[9]
public RmCm_spine_gbar
strdef cmd_str
objref g_type, vSel, sec_list, this
public Add_spines_RmCm, append, spine_avgs, idebug
public Spine_Comp_RmCm_n400_BH, Spine_Comp_RmCm_n400
public Spine_Comp_RmCm_n400_JAI, sec_type_assignG_n400
public type_pct, neck_dia, neck_len, head_dia, head_len, type_added
public use_morpho_xyz
external randSel
//--------------------------------------------------------------------------------
proc init() {
todo_n400_types = 1
idebug = 0
sample_pct = 0.002
use_morpho_xyz = 0 // Flag to signal use of morpho coords instead of nrn's x3d, y3d, z3d coords
RmCm_spine_gbar = 0 // how to set spine_gbars flag 0=>gbar_spines=0; 1=>gbar_spines=gbar_dends
g_nType = 9 //-- Gulyas labeled cells
g_type = new String_array( g_nType )
g_type.s[0].s = "so_distal"
g_type.s[1].s = "so_proximal"
g_type.s[2].s = "sr_proximal"
g_type.s[3].s = "sr_medial"
g_type.s[4].s = "sr_distal"
g_type.s[5].s = "sr_thin"
g_type.s[6].s = "slm_thick"
g_type.s[7].s = "slm_medium"
g_type.s[8].s = "slm_thin"
double g_den[g_nType]
g_den[0] = 3.08 //-- Gulyas densities (#/um) per dend type
g_den[1] = 0.64
g_den[2] = 0.03
g_den[3] = 2.37
g_den[4] = 6.98
g_den[5] = 3.52
g_den[6] = 1.72
g_den[7] = 0.60
g_den[8] = 0.37
double g_dend_len[g_nType], dend_len[g_nType]
g_dend_len[0] = 33.0 //-- Gulyas per dend type as percent of total lenght
g_dend_len[1] = 3.3
g_dend_len[2] = 1.0
g_dend_len[3] = 1.0
g_dend_len[4] = 2.7
g_dend_len[5] = 35.5
g_dend_len[6] = 2.5
g_dend_len[7] = 5.3
g_dend_len[8] = 15.7
spine_nType = 3 //-- Spine types
double type_pct[spine_nType], spine_area[spine_nType], type_added[spine_nType]
double head_dia[spine_nType], head_len[spine_nType], neck_dia[spine_nType], neck_len[spine_nType]
// Based on data from Harris JNS 1992
//------ Stub spines
type_pct[0] = 0.07
neck_dia[0] = 0.27
neck_len[0] = 0.54/2
head_dia[0] = 0.27
head_len[0] = 0.54/2
//------ Mush spines
type_pct[1] = 0.25
neck_dia[1] = 0.32
neck_len[1] = 0.25
head_dia[1] = 0.45
head_len[1] = 1.70
//------ Thin spines
type_pct[2] = 0.68
neck_dia[2] = 0.19
neck_len[2] = 0.35
head_dia[2] = 0.30
head_len[2] = 0.42
}
//================================================================================
public comp_section_gbars
proc comp_section_gbars(){ local i, cF localobj mt, mL, sf, str
cF = $1
mL = new List()
sf = new StringFunctions()
mt = new MechanismType(0)
for i=0, mt.count-1 {
mt.select( i )
str = new str_obj()
mt.selected( str.s1 )
if( sf.substr( str.s1, "_ion" ) >=0 ) continue
if( sf.substr( str.s1, "morphology" ) >=0 ) continue
if( sf.substr( str.s1, "pas" ) >=0 ) continue
if( sf.substr( str.s1, "capacitance" ) >=0 ) continue
if( ismembrane( str.s1 )) {
mL.append( str )
if( idebug > 5 ) print str.s1
}
}
str = new str_obj()
for i=0, mL.count-1 {
execute( str.sPrint( "gbar_%s *= %g", mL.o(i).s1, cF ).s1 )
}
}
//================================================================================
// Perform spine compensation using 3d type assignment function
public Spine_Comp_RmCm_f3d, type
strdef f3d, buf // 3d type assign function
proc Spine_Comp_RmCm_f3d() { local i, comp_Fac, comp_gbar, dend_type, area_sec, area_spine
f3d = $s1
desired_nspn = 30000
if( numarg() > 1 ) desired_nspn = $2
for i=0, g_nType-1 dend_len[i] = 0
area_tot = 0
nspn_tot = 0
area_spn_tot = 0
spine_avgs()
distance( 0, 0.5 )
// forsec "dend" {
sec_list = new SectionList()
sprint( cmd_str, "forsec \"dend\" %s.append()", this )
execute( cmd_str )
len_tot = 0
vol_tot = 0
nspn = 0
type = 0
forsec sec_list {
// sprint( buf, "type = %s( %g, %g, %g )", f3d, x3d(0.5), y3d(0.5), z3d(0.5) )
sprint( buf, "%s.type = %s.%s( )", this, this, f3d )
execute( buf )
len_tot += L
vol_tot += PI / 4 * diam^2 * L
nspn += L * g_den[type]
}
len_adj_factor = desired_nspn / nspn
forsec sec_list {
area_sec = area_section()
L_adj = L * len_adj_factor
execute( buf )
nspn = L_adj * g_den[type]
area_spine = nspn * spine_area_avg_wgt
comp_Fac = 1 + area_spine / area_sec
cm = comp_Fac * cm
//g_pas = comp_Fac * g_pas
g_epasn = comp_Fac * g_epasn
comp_gbar = (area_spine + area_sec )/ area_sec
if( RmCm_spine_gbar ) comp_section_gbars( comp_gbar )
if( idebug > 5) printf( "name %s diam %g type %g area_sec %g dend_type %g area_spine %g comp_Fac %g\n", \
secname(), diam, type, area_sec, dend_type, area_spine, comp_Fac )
dend_len[type] += L
area_tot += area_sec
nspn_tot += nspn
area_spn_tot += area_spine
}
if( idebug ){
printf( "Spine_Comp_RmCm_morpho: len_tot %g area_tot %g vol_tot %g\n", len_tot, area_tot, vol_tot )
printf( "Spine_Comp_RmCm_morpho: len_adj_factor %g area_spn_tot %g nspn_tot %g\n", \
len_adj_factor, area_spn_tot, nspn_tot )
for i=0, g_nType-1 printf( "%20s %8.0f um %3.0f pct Gulyas %3.0f\n", \
g_type.s[i].s, dend_len[i], dend_len[i]/len_tot*100, g_dend_len[i] )
}
if( idebug > 5) printf( "exiting Spines_Comp_RmCm_morpho\n" )
}
//--------------------------------------------------------------------------------
// return the type of the currently accessed section using section name coupled to 3d location
public n400_af3d
func n400_af3d(){ local dist, ydist, pdist
//dist = distance( 1 )
//ydist = abs( y3d(0.5) )
//pdist = sqrt( x3d(0.5)^2 + z3d(0.5)^2 )
sec_type = 2 // default
ifsec "axon" sec_type = -2 // axon
ifsec "soma" sec_type = -1 // soma
ifsec "seg" {
ifsec "dend"{
dist=distance(1)
ydist=abs(y3d(0.5))
pdist=sqrt(x3d(0.5)^2+z3d(0.5)^2)
ifsec "dend_basal" {
if( dist > 30 ) { sec_type = 0 } // so_distal
if( dist <= 30 ) { sec_type = 1 } // so_proximal
}
ifsec "dend_apical" {
if( ydist < 50 && pdist <= 45 ) sec_type = 2 // sr_proximal
if( ydist >= 50 && ydist < 200 && pdist <= 45 ) sec_type = 3 // sr_medial
if( ydist >= 200 && ydist < 520 && pdist <= 45 ) sec_type = 4 // sr_distal
if( ydist < 520 && pdist > 45 ) sec_type = 5 // sr_thin
if( ydist >= 520 && pdist < 75 ) sec_type = 6 // slm_thick
if( ydist >= 520 && pdist >=75 && pdist < 125 ) sec_type = 7 // slm_medium
if( ydist >= 520 && pdist >= 125 ) sec_type = 8 // slm_thin
}
}
}
if( idebug > 5 ) printf( "af3d returning %g\n", sec_type )
return sec_type
}
//--------------------------------------------------------------------------------
// return the type of the currently accessed section using section name coupled to 3d location
public n420_af3d
func n420_af3d(){ local dist, ydist, pdist, so_pd_cut, sr_slm_cut
dist = distance( 1 )
ydist = abs( y3d(0.5) )
pdist = sqrt( x3d(0.5)^2 + z3d(0.5)^2 )
sec_type = 2 // default
ifsec "axon" sec_type = -2 // axon
ifsec "soma" sec_type = -1 // soma
so_pd_cut = 150
ifsec "dend_basal" {
if( dist > so_pd_cut ) { sec_type = 0 } // so_distal
if( dist <= so_pd_cut ) { sec_type = 1 } // so_proximal
}
sr_slm_cut = 460
sr_pm_cut = 50
sr_md_cut = 75
sr_pmd_t_cut = 28
slm_tm_cut = 25
slm_mt_cut = 71
ifsec "dend_apical" {
if( ydist < sr_pm_cut && pdist <= sr_pmd_t_cut ) sec_type = 2 // sr_proximal
if( ydist >= sr_pm_cut && ydist < sr_md_cut && pdist <= sr_pmd_t_cut ) sec_type = 3 // sr_medial
if( ydist >= sr_md_cut && ydist < sr_slm_cut && pdist <= sr_pmd_t_cut ) sec_type = 4 // sr_distal
if( ydist < sr_slm_cut && pdist > sr_pmd_t_cut ) sec_type = 5 // sr_thin
if( ydist >= sr_slm_cut && pdist < slm_tm_cut ) sec_type = 6 // slm_thick
if( ydist >= sr_slm_cut && pdist >= slm_tm_cut && pdist < slm_mt_cut ) sec_type = 7 // slm_medium
if( ydist >= sr_slm_cut && pdist >= slm_mt_cut ) sec_type = 8 // slm_thin
}
if( idebug > 5 ) printf( "af3d returning %g\n", sec_type )
return sec_type
}
//================================================================================
// Perform spine compensation using inserted morpho
public Spine_Comp_RmCm_morpho
proc Spine_Comp_RmCm_morpho() { local i, comp_Fac, dend_type, area_sec, area_spine
desired_nspn = 30000
if( numarg() > 0 ) desired_nspn = $1
for i=0, g_nType-1 dend_len[i] = 0
area_tot = 0
nspn_tot = 0
area_spn_tot = 0
spine_avgs()
distance( 0, 0.5 )
// forsec "dend" {
sec_list = new SectionList()
sprint( cmd_str, "forsec \"dend\" %s.append()", this )
execute( cmd_str )
len_tot = 0
vol_tot = 0
nspn = 0
forsec sec_list {
len_tot += L
vol_tot += PI / 4 * diam^2 * L
nspn += L * g_den[type_morpho]
}
len_adj_factor = desired_nspn / nspn
forsec sec_list {
area_sec = area_section()
L_adj = L * len_adj_factor
nspn = L_adj * g_den[type_morpho]
area_spine = nspn * spine_area_avg_wgt
comp_Fac = 1 + area_spine / area_sec
cm = comp_Fac * cm
g_pas = comp_Fac * g_pas
//ismembrane("Naf2_i1") {gbar_Naf2_i1=gbar_Naf2_i1*comp_Fac }
ismembrane("h_i0") { gbar_h_i0=gbar_h_i0*comp_Fac }
ismembrane("KDR_i1") { gbar_KDR_i1=gbar_KDR_i1*comp_Fac }
ismembrane("KA_i1") { gbar_KA_i1=gbar_KA_i1*comp_Fac }
if( idebug > 5) printf( "name %s diam %g area_sec %g dend_type %g area_spine %g comp_Fac %g\n", \
secname(), diam, area_sec, dend_type, area_spine, comp_Fac )
dend_len[type_morpho] += L
area_tot += area_sec
nspn_tot += nspn
area_spn_tot += area_spine
}
if( idebug ){
printf( "Spine_Comp_RmCm_morpho: len_tot %g area_tot %g vol_tot %g\n", len_tot, area_tot, vol_tot )
printf( "Spine_Comp_RmCm_morpho: len_adj_factor %g area_spn_tot %g nspn_tot %g\n", \
len_adj_factor, area_spn_tot, nspn_tot )
for i=0, g_nType-1 printf( "%20s %8.0f um %3.0f pct Gulyas %3.0f\n", \
g_type.s[i].s, dend_len[i], dend_len[i]/len_tot*100, g_dend_len[i] )
}
if( idebug > 5) printf( "exiting Spines_Comp_RmCm_morpho\n" )
}
//================================================================================
// assign type numbers consistent with Gulyas' code
// Added -1 for soma
proc sec_type_assignG_n400() { local sec_type, dist, diam_factor, adj_diam
sec_list = new SectionList()
sprint( cmd_str, "forall %s.append()", this )
execute( cmd_str )
forsec sec_list ifsec "soma" distance()
forsec sec_list {
if( ! ismembrane( "morpho" )){
continue_dialog("eMorph.sec_type_assignG_n400: requires insert morpho" )
break
}
ifsec "dend"{
if( use_morpho_xyz ){ // use morpho coordinates
xdist = abs( 0.5*(x0_morpho + x1_morpho) )
ydist = abs( 0.5*(y0_morpho + y1_morpho) )
zdist = abs( 0.5*(z0_morpho + z1_morpho) )
pdist = sqrt( xdist^2 + xdist^2 )
dist = sqrt( xdist^2 + ydist^2 + zdist^2 )
}else{
dist = distance( 1 )
ydist = abs( y3d(1) )
pdist = sqrt( x3d(1)^2 + z3d(1)^2 )
}
}
sec_type = 2 // default
ifsec "soma" sec_type = -1 // soma
ifsec "dend_basal" {
if( dist > 60 ) { sec_type = 0 } // so_distal
if( dist <= 60 ) { sec_type = 1 } // so_proximal
}
ifsec "dend_apical" {
if( ydist < 125 && pdist <= 45 ) sec_type = 2
if( ydist >= 125 && ydist < 250 && pdist <= 45 ) sec_type = 3
if( ydist >= 250 && ydist < 400 && pdist <= 45 ) sec_type = 4
if( ydist < 400 && pdist > 45 ) sec_type = 5
if( ydist >= 400 && pdist < 75 ) sec_type = 6
if( ydist >= 400 && pdist >=75 && pdist < 150 ) sec_type = 7
if( ydist >= 400 && pdist >= 150 ) sec_type = 8
// diam_factor = 1
// adj_diam = diam / diam_factor
//if( dist < 100 ) sec_type = 2 // sr_proximal
//if( dist >= 100 && dist < 500 ) sec_type = 3 // sr_medial
//if( dist >= 500 && dist < 850 ) sec_type = 4 // sr_distal
//if( dist < 850 && adj_diam < 0.6 ) sec_type = 5 // sr_thin (obliques)
//if( dist >= 850 ) {
// if( adj_diam > 0.6 ) sec_type = 6 // slm_thick
// if( adj_diam > 0.4 && adj_diam <= 0.6 ) sec_type = 7 // slm_medium
// if( adj_diam <= 0.4 ) sec_type = 8 // slm_thin
// }
}
// spf = g_den[ sec_type ] * sp_adj
// comp_Fac = ( area_sec + spf*L*ave_sp_area )/area_sec
// comp_Fac = RmCm_spine_factor( 0, g_den[sec_type], diam, L )
type_morpho = sec_type
}
}
//================================================================================
// assign type numbers consistent with Gulyas' code
// Added -1 for soma and -2 for axon
// Fine tuned to match Gulyas stats
proc sec_type_assignG_n400_2() { local sec_type, dist, diam_factor, adj_diam
sec_list = new SectionList()
sprint( cmd_str, "forall %s.append()", this )
execute( cmd_str )
forsec sec_list ifsec "soma" distance()
forsec sec_list {
if( ! ismembrane( "morpho" )){
continue_dialog("eMorph.sec_type_assignG_n400: requires insert morpho" )
break
}
if( use_morpho_xyz ){ // use morpho coordinates
xdist = abs( 0.5*(x0_morpho + x1_morpho) )
ydist = abs( 0.5*(y0_morpho + y1_morpho) )
zdist = abs( 0.5*(z0_morpho + z1_morpho) )
pdist = sqrt( xdist^2 + zdist^2 )
dist = sqrt( xdist^2 + ydist^2 + zdist^2 )
}else{
dist = distance( 1 )
ydist = abs( y3d(1) )
pdist = sqrt( x3d(1)^2 + z3d(1)^2 )
}
sec_type = 2 // default
ifsec "axon" sec_type = -2 // axon
ifsec "soma" sec_type = -1 // soma
ifsec "dend_basal" {
if( dist > 30 ) { sec_type = 0 } // so_distal
if( dist <= 30 ) { sec_type = 1 } // so_proximal
}
ifsec "dend_apical" {
if( ydist < 50 && pdist <= 45 ) sec_type = 2 // sr_proximal
if( ydist >= 50 && ydist < 200 && pdist <= 45 ) sec_type = 3 // sr_medial
if( ydist >= 200 && ydist < 520 && pdist <= 45 ) sec_type = 4 // sr_distal
if( ydist < 520 && pdist > 45 ) sec_type = 5 // sr_thin
if( ydist >= 520 && pdist < 75 ) sec_type = 6 // slm_thick
if( ydist >= 520 && pdist >=75 && pdist < 125 ) sec_type = 7 // slm_medium
if( ydist >= 520 && pdist >= 125 ) sec_type = 8 // slm_thin
}
type_morpho = sec_type
}
}
//================================================================================
// Perform spine compensation on cell n400
// Spine_Comp_RmCm_n400_BH( len_adj_factor )
public todo_n400_types
proc Spine_Comp_RmCm_n400_JAI() { local i, comp_Fac, dend_type, area_sec, area_spine
if( todo_n400_types == 1 ) sec_type_assignG_n400()
if( todo_n400_types == 2 ) sec_type_assignG_n400_2()
todo_n400_types = 0
Spine_Comp_RmCm_morpho( $1 )
}
//================================================================================
// Perform spine compensation on cell n400
// Spine_Comp_RmCm_n400_BH( len_adj_factor )
proc Spine_Comp_RmCm_n400_BH() { local i, comp_Fac, dend_type, area_sec, area_spine
if( numarg() > 0 ) len_adj_factor = $1
if( idebug > 5) printf( "entering Spines_Comp_RmCm_n400_BH\n" )
for i=0, g_nType-1 dend_len[i] = 0
area_tot = 0
nspn_tot = 0
area_spn_tot = 0
diam_factor = 1
spine_avgs()
distance( 0, 0.5 )
// forsec "dend" {
sec_list = new SectionList()
sprint( cmd_str, "forsec \"dend\" %s.append()", this )
execute( cmd_str )
len_tot = 0
forsec sec_list len_tot += L
if( numarg() <= 0 ) len_adj_factor = 11479/len_tot // normalize cell's length to Gulyas avg length
forsec sec_list {
dend_type = 2 // default
dist = distance( 1 )
adj_diam = diam / diam_factor
ifsec "dend_basal" {
if (adj_diam < 0.5 ) { dend_type = 0 } // so_distal
if (adj_diam >= 0.5) { dend_type = 1 } // so_proximal
}
ifsec "dend_apical" {
if( dist < 100 ) dend_type = 2 // sr_proximal
if( dist >= 100 && dist < 500 ) dend_type = 3 // sr_medial
if( dist >= 500 && dist < 850 ) dend_type = 4 // sr_distal
if( dist < 850 && adj_diam < 0.6 ) dend_type = 5 // sr_thin (obliques)
if( dist >= 850 ) {
if( adj_diam > 0.6 ) dend_type = 6 // slm_thick
if( adj_diam > 0.4 && adj_diam <= 0.6 ) dend_type = 7 // slm_medium
if( adj_diam <= 0.4 ) dend_type = 8 // slm_thin
}
}
// spf = g_den[ dend_type ] * sp_adj
// comp_Fac = ( area_sec + spf*L*ave_sp_area )/area_sec
// comp_Fac = RmCm_spine_factor( 0, g_den[dend_type], diam, L )
area_sec = area_section()
L_adj = L * len_adj_factor
nspn = L_adj * g_den[dend_type]
area_spine = nspn * spine_area_avg_wgt
comp_Fac = 1 + area_spine / area_sec
cm = comp_Fac * cm
g_pas = comp_Fac * g_pas
if( idebug > 5) printf( "name %s diam %g area_sec %g dend_type %g area_spine %g comp_Fac %g\n", \
secname(), diam, area_sec, dend_type, area_spine, comp_Fac )
dend_len[dend_type] += L
area_tot += area_sec
nspn_tot += nspn
area_spn_tot += area_spine
}
forall { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1 }
if( idebug ){
printf( "Spine_Comp_RmCm_n400_BH: len_adj_factor %g area_tot %g area_spn_tot %g nspn_tot %g\n", \
len_adj_factor, area_tot, area_spn_tot, nspn_tot )
printf( "len_tot %.0f\n", len_tot )
for i=0, g_nType-1 printf( "%20s %8.0f um %3.0f pct Gulyas %3.0f\n", \
g_type.s[i].s, dend_len[i], dend_len[i]/len_tot*100, g_dend_len[i] )
}
if( idebug > 5) printf( "exiting Spines_Comp_RmCm_n400_BH\n" )
}
//================================================================================
// Return the total area of the currently accessed section
func area_section() { local a, x
a = 0
for (x) { a += area(x) }
return a
}
//--------------------------------------------------------------------------------
func SpineTypeSelect() { local rStp, iStp
rStp = randSel.uniform( 0, type_pct_sum )
iStp = 0
while( rStp > type_pct[ iStp ] ){
rStp -= type_pct[ iStp ]
iStp += 1
}
return iStp
}
//--------------------------------------------------------------------------------
proc append() {
sec_list.append()
}
//--------------------------------------------------------------------------------
proc spine_avgs() { local iT
type_pct_sum = 0
spine_area_avg_wgt = 0
for( iT=0; iT < spine_nType; iT+=1 ) {
type_added[ iT] = 0
type_pct_sum += type_pct[iT]
spine_area[iT] = PI * neck_dia[iT] * neck_len[iT] + PI * head_dia[iT] * head_len[iT]
spine_area_avg_wgt += type_pct[iT] * spine_area[iT]
}
if( idebug ) print "spine_area_avg_wgt ", spine_area_avg_wgt
}
//--------------------------------------------------------------------------------
proc Add_spines_RmCm() { local iT, igT, len_sum, nSpine, iS, nNew, iNew, AddedArea
spine_avgs()
for( igT = 0; igT < g_nType; igT+=1 ){
sec_list = new SectionList()
sprint( cmd_str, "forsec \"%s\" %s.append()", g_type.s[ igT ].s, this )
execute( cmd_str )
len_sum = 0
forsec sec_list {
len_sum += L
}
nSpine = int( sample_pct * len_sum * g_den[ igT ] + 0.5 )
randSel.uniform( 0, len_sum )
vSel = new Vector( nSpine )
vSel.setrand( randSel )
vSel.sort()
len_curr = 0
iS = 0
forsec sec_list {
if( iS >= nSpine ) break
len_curr += L
nNew = 0
while( len_curr >= vSel.x[ iS+nNew ] ){
nNew += 1
if( iS+nNew >= nSpine ) break
}
AddedArea = 0
for( iNew=0; iNew < nNew; iNew+=1 ){
AddedArea += AddSpine( iNew, nNew )
iS += 1
}
Adjust_RmCm_section( AddedArea, g_den[igT] )
}
}
} //--- Add_spines_RmCm()
//--------------------------------------------------------------------------------
// return factor to correct section
func RmCm_spine_factor(){ local AddedSpineArea, spines_um, sec_diam, sec_len, Added_um2, spines_um2
AddedSpineArea = $1
spines_um = $2
sec_diam = $3
sec_len = $4
Added_um2 = AddedSpineArea / PI/sec_diam/sec_len //-- Added per um2
spines_um2 = spines_um / PI/sec_diam //-- convert desired density from linear to area
if( Added_um2 > spines_um2 ){
printf( "WARNING: eMorph: Too many explicit spines were added Added=%g ShouldHave=%g\n", \
Added_um2, spines_um2 )
abort( "" )
}
return 1 + (spines_um2 - Added_um2) * spine_area_avg_wgt
}
//--------------------------------------------------------------------------------
proc abort(){ //- abort( str ) [neuron's stop is a sham]
printf( "%s\n", $s1 )
execute( "aborting" ) //- generate execution error deliverately
}
//--------------------------------------------------------------------------------
// Adjust RmCm to reflect AddedSpineArea and spines_um density
proc Adjust_RmCm_section(){ adjustF
adjustF = RmCm_spine_factor( $1, $2 )
cm = cm * adjustF
g_pas = g_pas * adjustF
}
//--------------------------------------------------------------------------------
// Add a spine to the currently accessed section
func AddSpine(){ local iNew, nNew, iAddT
iNew = $1
nNew = $2
iAddT = SpineTypeSelect()
type_added[ iAddT ] += 1
sprint( cmd_str, "create spine_head_%s, spine_neck_%s", secname(), secname() )
execute( cmd_str )
sprint( cmd_str, "spine_neck_%s {diam=%g L=%g}", secname(), neck_dia[iAddT], neck_len[iAddT] )
execute( cmd_str )
sprint( cmd_str, "spine_head_%s {diam=%g L=%g}", secname(), head_dia[iAddT], head_len[iAddT] )
execute( cmd_str )
sprint( cmd_str, "connect spine_neck_%s(0), %s(%g)", secname(), secname(), (iNew+1)/(nNew+1) )
execute( cmd_str )
sprint( cmd_str, "connect spine_head_%s(0), spine_neck_%s(1)", secname(), secname() )
execute( cmd_str )
return( spine_area[ iAddT ] )
}
endtemplate eMorph
/*
objref sP, randSel
randSel = new Random( 123 )
sP = new eMorph()
load_file( "n400td-pc2.hoc" )
*/