# simplified corticostriatal cell model (6 compartment)
from neuron import h
h.load_file('stdrun.hoc')
Vrest = -90.7942106535
h.v_init = -75.8801688855
h.celsius = 34.0 # for in vitro opt
# these are to be used by h_kole.mod
h_aslope = 7.12195833953
h_ascale = 0.00276508832116
h_bslope = 28.5415800392
h_bscale = 0.154401580683
h_ashift = 118.919921764
# geom properties
somaL = 25.0612875049
somaDiam = 27.1149930518
axonL = 598.648623864
axonDiam = 0.552948640016
apicL = 294.615634554
apicDiam = 2.86090460606
bdendL = 265.920165144
bdendDiam = 1.02617341611
# passive properties
axonCap = 1.98999103645
somaCap = 1.98838095104
apicCap = 1.9931856141
bdendCap = 1.98526067401
rall = 88.8088669637
axonRM = 2426.70520092
somaRM = 11399.5571402
apicRM = 12053.0391655
bdendRM = 23023.3272552
# Na, K reversal potentials calculated from BenS internal/external solutions via Nernst eq.
p_ek = -104.0 # these reversal potentials for in vitro conditions
p_ena = 42.0
# h-current
h.erev_h = h.erev_ih = -37.0 # global
gbar_h = 9.99986721729e-06
# spiking currents
gbar_nax = 0.0345117294903
nax_gbar_axonm = 5.0
gbar_kdr = 0.0131103978049
kdr_gbar_axonm = 5.0
# A few kinetic params changed vis-a-vis kdr.mod defaults:
kdr_vhalfn = 11.6427471384
gbar_kap = 0.0898600246397
kap_gbar_axonm = 5.0
# A few kinetic params changed vis-a-vis kap.mod defaults:
kap_vhalfn = 32.7885075379
kap_tq = -52.0967985869
kap_vhalfl = -59.7867409796 #
# other ion channel parameters
cal_gcalbar = 4.41583533572e-06
can_gcanbar = 4.60717910591e-06
cat_gcatbar = 1.00149259311e-06
calginc = 1.0
kBK_gpeak = 5.09733585163e-05
kBK_caVhminShift = 43.8900261407
cadad_depth = 0.119408607923
cadad_taur = 99.1146852282
gbar_nap = 0.00301840094235
gbar_ican = 0.000106856758751
###############################################################################
# CSTR6 Cell
###############################################################################
class CSTR6 ():
"Simplified Corticostriatal Cell Model"
def __init__(self,x=0,y=0,z=0,ID=0,params=None):
self.x,self.y,self.z=x,y,z
self.ID=ID
self.all_sec = []
self.add_comp('soma')
self.set_morphology()
self.insert_conductances()
if params: self.set_params(params)
self.set_props()
def add_comp(self, name):
self.__dict__[name] = h.Section(name=name)#,cell=self)
self.all_sec.append(self.__dict__[name])
def set_morphology(self):
self.add_comp('axon')
self.add_comp('Bdend')
self.add_comp('Adend1')
self.add_comp('Adend2')
self.add_comp('Adend3')
self.apic = [self.Adend1, self.Adend2, self.Adend3]
self.basal = [self.Bdend]
self.alldend = [self.Adend1, self.Adend2, self.Adend3, self.Bdend]
self.set_geom()
self.axon.connect(self.soma, 0.0, 0.0)
self.Bdend.connect(self.soma, 0.5, 0.0) # soma 0.5 to Bdend 0
self.Adend1.connect(self.soma, 1.0, 0.0)
self.Adend2.connect(self.Adend1, 1.0, 0.0)
self.Adend3.connect(self.Adend2, 1.0, 0.0)
def set_geom (self):
self.axon.L = axonL; self.axon.diam = axonDiam;
self.soma.L = somaL; self.soma.diam = somaDiam
for sec in self.apic: sec.L,sec.diam = apicL,apicDiam
self.Bdend.L = bdendL; self.Bdend.diam = bdendDiam
def activeoff (self):
for sec in self.all_sec: sec.gbar_nax=sec.gbar_kdr=sec.gbar_kap=0.0
def set_axong (self):
axon = self.axon
axon.gbar_nax = gbar_nax * nax_gbar_axonm
axon.gbar_kdr = gbar_kdr * kdr_gbar_axonm
axon.gbar_kap = gbar_kap * kap_gbar_axonm
def set_calprops (self,sec):
sec.gcalbar_cal = cal_gcalbar
sec.gcanbar_can = can_gcanbar
sec.gcatbar_cat = cat_gcatbar
sec.gpeak_kBK = kBK_gpeak
sec.caVhmin_kBK = -46.08 + kBK_caVhminShift
sec.depth_cadad = cadad_depth
sec.taur_cadad = cadad_taur
#sec.gbar_ican = gbar_ican
def set_somag (self):
sec = self.soma
sec.gbar_ih = gbar_h # Ih
self.set_calprops(sec)
#sec.gbar_nap = gbar_nap
def set_bdendg (self):
sec = self.Bdend
sec.gbar_ih = gbar_h # Ih
#sec.gbar_nap = gbar_nap
self.set_calprops(sec)
def set_apicg (self):
for sec in self.apic:
self.set_calprops(sec)
sec.gbar_ih = gbar_h
#sec.gbar_nap = gbar_nap
self.apic[1].gcalbar_cal = cal_gcalbar * calginc # middle apical dend gets more iL
def set_ihkinetics (self):
for sec in [self.soma,self.Bdend,self.Adend1,self.Adend2,self.Adend3]:
sec.ascale_ih = h_ascale
sec.bscale_ih = h_bscale
sec.ashift_ih = h_ashift
sec.aslope_ih = h_aslope
sec.bslope_ih = h_bslope
# set properties
def set_props (self):
self.set_geom()
# cm - can differ across locations
self.axon.cm = axonCap
self.soma.cm = somaCap
self.Bdend.cm = bdendCap
for sec in self.apic: sec.cm = apicCap
# g_pas == 1.0/rm - can differ across locations
self.axon.g_pas = 1.0/axonRM
self.soma.g_pas = 1.0/somaRM
self.Bdend.g_pas = 1.0/bdendRM
for sec in self.apic: sec.g_pas = 1.0/apicRM
for sec in self.all_sec:
sec.ek = p_ek # K+ current reversal potential (mV)
sec.ena = p_ena # Na+ current reversal potential (mV)
sec.Ra = rall; sec.e_pas = Vrest # passive
sec.gbar_nax = gbar_nax # Na
sec.gbar_kdr = gbar_kdr # KDR
sec.vhalfn_kdr = kdr_vhalfn # KDR kinetics
sec.gbar_kap = gbar_kap # K-A
sec.vhalfn_kap = kap_vhalfn # K-A kinetics
sec.vhalfl_kap = kap_vhalfl
sec.tq_kap = kap_tq
self.set_somag()
self.set_bdendg()
self.set_apicg()
self.set_axong()
self.set_ihkinetics()
def insert_conductances (self):
for sec in self.all_sec:
sec.insert('k_ion')
sec.insert('na_ion')
sec.insert('pas') # passive
sec.insert('nax') # Na current
sec.insert('kdr') # K delayed rectifier current
sec.insert('kap') # K-A current
for sec in [self.Adend3, self.Adend2, self.Adend1, self.Bdend, self.soma]:
sec.insert('ih') # h-current
sec.insert('ca_ion') # calcium channels
sec.insert('cal') # cal_mig.mod
sec.insert('can') # can_mig.mod
sec.insert('cat') # cat_mig.mod
sec.insert('cadad') # cadad.mod - calcium decay
sec.insert('kBK') # kBK.mod - ca and v dependent k channel
#sec.insert('nap') # nap_sidi.mod
#sec.insert('ican') # ican_sidi.mod
# set parameters tuned to specific cell
def set_params(self, params):
global h
global axonRM
global somaRM
global apicRM
global bdendRM
global rall
global Vrest
global gbar_h
global axonCap
global somaCap
global apicCap
global bdendCap
global somaL
global somaDiam
global apicL
global apicDiam
global bdendL
global bdendDiam
global axonL
global axonDiam
global h_ascale
global h_bscale
global h_ashift
global h_aslope
global h_bslope
global gbar_nap
global gbar_ican
global kap_vhalfn
global kBK_caVhminShift
global kBK_gpeak
global kap_vhalfl
global gbar_kap
global gbar_kdr
global cal_gcalbar
global kap_tq
global gbar_nax
global can_gcanbar
global cat_gcatbar
if params == 'BS1578':
# properties from subthreshold fits
axonRM = 2822.01325416
somaRM = 10590.6461169
apicRM = 13889.6757076
bdendRM = 7068.31281683
rall = 70.0015514222
Vrest = -87.1335623948
h.v_init = -88.7986728464
gbar_h = 3.3176340367e-05
axonCap = 2.4630760526
somaCap = 2.4998269977
apicCap = 2.74242941886
bdendCap = 2.74086279376
somaL = 48.4123467666
somaDiam = 28.2149102762
apicL = 261.904636003
apicDiam = 1.5831889597
bdendL = 299.810775175
bdendDiam = 2.2799248874
axonL = 594.292937602
axonDiam = 1.40966286462
h_ascale = 0.00320887293027
h_bscale = 0.285307415701
h_ashift = 119.696272155
h_aslope = 7.09800576233
h_bslope = 23.2995848558
gbar_nap = 0.0
gbar_ican = 0.0
kap_vhalfn = 32.179925527
kBK_caVhminShift = 89.9991422912
# properties from evolution
kBK_gpeak = 4.45651933019e-05
kap_vhalfl = -36.7754836348
gbar_kap = 0.0240195239098
gbar_kdr = 0.00833766634808
cal_gcalbar = 2.39132864454e-06
kap_tq = -49.7149526489
gbar_nax = 0.0768253702194
can_gcanbar = 8.13137955053e-07
cat_gcatbar = 9.29455717585e-07
elif params == 'BS1579':
# properties from subthreshold fits
axonRM = 3120.59603524
somaRM = 25551.9729631
apicRM = 48333.5799025
bdendRM = 11763.9607778
rall = 114.969186163
Vrest = -79.8821836579
h.v_init = -92.8364820902
gbar_h = 3.13760461868e-05
axonCap = 1.87389705992
somaCap = 1.89133252551
apicCap = 2.49841939531
bdendCap = 2.46671987855
somaL = 48.4123467666
somaDiam = 28.2149102762
apicL = 261.904636003
apicDiam = 1.5831889597
bdendL = 299.810775175
bdendDiam = 2.2799248874
axonL = 594.292937602
axonDiam = 1.40966286462
h_ascale = 0.00365676240119
h_bscale = 0.26993550346
h_ashift = 115.040811905
h_aslope = 7.63692206734
h_bslope = 37.2740194128
gbar_nap = 0.0
gbar_ican = 0.0
# properties from evolution
kBK_gpeak = 4.2923494376e-05
kap_vhalfl = -78.3762490029
gbar_kap = 0.306752147542
gbar_kdr = 0.00501206206504
cal_gcalbar = 7.79902252875e-05
kap_tq = -55.772342395
gbar_nax = 0.146326621958
can_gcanbar = 8.43780573752e-05
cat_gcatbar = 5.85477866612e-05
#
def prmstr (p,s,fctr=2.0,shift=5.0):
if p == 0.0:
print (s,'=',str(p-shift),str(p+shift),str(p),'True')
elif p < 0.0:
print (s, '=',str(p*fctr),str(p/fctr),str(p),'True')
else:
print (s, ' = ' , str(p/fctr), str(p*fctr), str(p), 'True')