# $Id: geom.py,v 1.38 2012/11/09 21:00:26 samn Exp $
from pyinit import *
h.celsius = 37
from conf import *
########### the following allows for setting and reading the config file ###########
def setfcfg ():
'''determine config file'''
# fcfg = "netcfg.cfg" # default config file name
fcfg = 'fig1simulationConfig.cfg'
for i in range(len(sys.argv)):
if sys.argv[i].endswith(".cfg") and os.path.exists(sys.argv[i]):
fcfg = sys.argv[i]
print ("config file is " , fcfg)
return fcfg
fcfg=setfcfg() # config file name
dconf = readconf(fcfg)
########### h currents for different cells ###########
hCurrent_g_pv_scaling = dconf['hCurrent_g_pv_scaling']
hCurrent_g_olm_scaling = dconf['hCurrent_g_olm_scaling']
hCurrent_g_pyr_scaling = dconf['hCurrent_g_pyr_scaling']
hCurrent_g_cck_scaling = dconf['hCurrent_g_cck_scaling']
########### code for defining cells and synapses ###########
# h('load_file("./hoc_files/pywrap.hoc")')
class Synapse:
def __init__(self, sect, loc, tau1, tau2, e):
self.syn = h.MyExp2SynBB(loc, sec=sect)
self.syn.tau1 = tau1
self.syn.tau2 = tau2
self.syn.e = e
class SynapseNMDA:
def __init__(self, sect, loc, tau1, tau2, tau1NMDA, tau2NMDA, r, e):
self.syn = h.MyExp2SynNMDABB(loc, sec=sect)
self.syn.tau1 = tau1
self.syn.tau2 = tau2
self.syn.tau1NMDA = tau1NMDA
self.syn.tau2NMDA = tau2NMDA
self.syn.r = r
self.syn.e = e
class SynapseSTDP:
def __init__(self, sect, loc, tau, e, dtau, ptau, d, p):
self.syn = h.ExpSynSTDP(loc, sec=sect)
self.syn.tau = tau
self.syn.e = e
self.syn.dtau = dtau
self.syn.ptau = ptau
self.syn.d = d
self.syn.p = p
###############################################################################
#
# General Cell
#
###############################################################################
class Cell(object):
"General cell"
def __init__(self,x,y,z,id):
self.x=x
self.y=y
self.z=z
self.id=id
self.all_sec = []
self.add_comp('soma',True)
self.set_morphology()
self.set_conductances()
self.set_synapses()
self.set_inj()
self.calc_area()
def __repr__(self):
return str(type(self)) + str(self.id)
def set_morphology(self):
pass
def set_conductances(self):
pass
def set_synapses(self):
pass
def set_inj(self):
self.somaInj = h.IClamp(0.5, sec=self.soma)
def add_comp(self, name, rec):
self.__dict__[name] = h.Section()
self.all_sec.append(self.__dict__[name])
# Record voltage
if rec:
self.__dict__[name+"_volt"] = h.Vector(int(h.tstop/h.dt)+1)
self.__dict__[name+"_volt"].record(self.__dict__[name](0.5)._ref_v)
def plot_volt(self, name, myax, *args, **kwargs):
# figure(fig)
volt = self.__dict__[name+"_volt"].to_python()
myax.plot(arange(len(volt))*h.dt, volt, *args, **kwargs)
myax.set_xlabel('time (ms)')
myax.set_ylabel('voltage (mV)')
def clear_volt(self):
self.soma_volt.resize(0)
def calc_area(self):
self.total_area = 0
self.n = 0
for sect in self.all_sec:
self.total_area += h.area(0.5,sec=sect)
self.n+=1
def insert_gfluct_noise(self):
self.Gfluctp = h.Gfluctp(self.soma(0.5))
###############################################################################
#
# PV Basket Cell -- PVC
# (was called Bwb before)
#
###############################################################################
class PVC(Cell):
"PV Basket cell"
def set_morphology(self):
total_area = 10000 # um2
self.soma.nseg = 1
self.soma.cm = 1 # uF/cm2
diam = sqrt(total_area) # um
L = diam/pi # um
h.pt3dclear(sec=self.soma)
h.pt3dadd(self.x, self.y, self.z, diam, sec=self.soma)
h.pt3dadd(self.x, self.y, self.z+L, diam, sec=self.soma)
def set_conductances(self):
self.soma.insert('pas')
self.soma.e_pas = -65 # mV
self.soma.g_pas = 0.1e-3 #*2.5 # default: 0.1e-3 # S/cm2
self.soma.insert('Nafbwb')
self.soma(0.5).Nafbwb.gna = 35 # default == 35
self.soma.insert('Kdrbwb')
self.soma(0.5).Kdrbwb.gkdr = 9 #*1.2# *2 # default is 9
self.soma.insert('HCN1')
self.soma(0.5).HCN1.htaufactor = 1
self.soma(0.5).HCN1.gbar = 0.0001 * 0.2 * hCurrent_g_pv_scaling # (0.074 / 0.175) * 0.5
def set_synapses(self):
self.somaAMPAf = Synapse(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.somaGABAf = Synapse(sect=self.soma, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
self.somaGABAss = Synapse(sect=self.soma, loc=0.5, tau1=20, tau2=40, e=-80)#only for septal input
self.somaNMDA = SynapseNMDA(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
self.somaAMPASTDP = SynapseSTDP(sect=self.soma,loc=0.5,tau=5.35,e=0,dtau=34,ptau=17,d=0.5,p=0.5)
###############################################################################
#
# CCK Basket Cell -- Cck
#
###############################################################################
class CCKC(Cell):
"CCK Basket cell"
def set_morphology(self):
total_area = 10000 # um2
self.soma.nseg = 1
self.soma.cm = 1 # uF/cm2
diam = sqrt(total_area) # um
L = diam/pi # um
h.pt3dclear(sec=self.soma)
h.pt3dadd(self.x, self.y, self.z, diam, sec=self.soma)
h.pt3dadd(self.x, self.y, self.z+L, diam, sec=self.soma)
def set_conductances(self):
self.soma.insert('pas')
self.soma.e_pas = -65 # mV
self.soma.g_pas = 0.1e-3 # 0.3e-3 # S/cm2
self.soma.insert('Nafbwb')
self.soma(0.5).Nafbwb.gna = 35 * 1.5 # 2 # default == 35
self.soma.insert('Kdrbwb')
self.soma.insert('Iholmw')
self.soma(0.5).Iholmw.gbar = 0.00015 * hCurrent_g_cck_scaling # default in mod file is 0.00015
self.soma.insert('Caolmw')
self.soma(0.5).Caolmw.tau = 400
self.soma.insert('ICaolmw')
self.soma.insert('KCaolmw')
self.soma(0.5).KCaolmw.gkca = 3 # 10 * 0.3 # default is 10
self.soma.insert('km')
self.soma(0.5).km.gbar = 10* 0.5 # 2 #* 1.5 # default is 10
def set_synapses(self):
self.somaAMPAf = Synapse(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.somaGABAf = Synapse(sect=self.soma, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
self.somaGABAss = Synapse(sect=self.soma, loc=0.5, tau1=20, tau2=40, e=-80)#only for septal input
self.somaNMDA = SynapseNMDA(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
self.somaAMPASTDP = SynapseSTDP(sect=self.soma,loc=0.5,tau=5.35,e=0,dtau=34,ptau=17,d=0.5,p=0.5)
###############################################################################
#
# OLM Cell -- Ow
#
###############################################################################
class Ow(Cell):
"OLM cell"
def set_morphology(self):
total_area = 10000 # um2
self.soma.nseg = 1
self.soma.cm = 1 # uF/cm2
diam = sqrt(total_area) # um
L = diam/pi # um
h.pt3dclear(sec=self.soma)
h.pt3dadd(self.x, self.y, self.z, diam, sec=self.soma)
h.pt3dadd(self.x, self.y, self.z+L, diam, sec=self.soma)
def set_conductances(self):
self.soma.insert('pas')
self.soma.e_pas = -65 # mV
self.soma.g_pas = 0.1e-3 # S/cm2
self.soma.insert('Nafbwb')
self.soma.insert('Kdrbwb')
self.soma.insert('Iholmw')
self.soma(0.5).Iholmw.gbar = 0.00015 * hCurrent_g_olm_scaling # default in mod file is 0.00015
# self.soma.insert('HCN1')
# self.soma.insert('HCN2')
self.soma.insert('Caolmw')
self.soma.insert('ICaolmw')
self.soma.insert('KCaolmw')
def set_synapses(self):
self.somaGABAf = Synapse(sect=self.soma, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
self.somaAMPAf = Synapse( sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.somaGABAss = Synapse( sect=self.soma, loc=0.5, tau1=20, tau2=40, e=-80)#only for septal input
self.somaNMDA = SynapseNMDA(sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
self.somaAMPASTDP = SynapseSTDP(sect=self.soma,loc=0.5,tau=5.35,e=0,dtau=34,ptau=17,d=0.5,p=0.5)
###############################################################################
#
# Pyramidal Cell -- KopAdr
#
###############################################################################
class PyrAdr(Cell):
"Pyramidal cell"
def set_morphology(self):
self.add_comp('Bdend',True)
self.add_comp('Adend1',False)
self.add_comp('Adend2',False)
self.add_comp('Adend3',True)
h.pt3dclear(sec=self.soma)
h.pt3dadd(self.x, self.y, self.z, 20, sec=self.soma)
h.pt3dadd(self.x, self.y, self.z+20, 20, sec=self.soma)
h.pt3dclear(sec=self.Bdend)
h.pt3dadd(self.x, self.y, self.z, 2, sec=self.Bdend)
h.pt3dadd(self.x, self.y, self.z-200, 2, sec=self.Bdend)
h.pt3dclear(sec=self.Adend1)
h.pt3dadd(self.x, self.y, self.z+20, 2, sec=self.Adend1)
h.pt3dadd(self.x, self.y, self.z+20+150, 2, sec=self.Adend1)
h.pt3dclear(sec=self.Adend2)
h.pt3dadd(self.x, self.y, self.z+20+150, 2, sec=self.Adend2)
h.pt3dadd(self.x, self.y, self.z+20+150*2, 2, sec=self.Adend2)
h.pt3dclear(sec=self.Adend3)
h.pt3dadd(self.x, self.y, self.z+20+150*2, 2, sec=self.Adend3)
h.pt3dadd(self.x, self.y, self.z+20+150*3, 2, sec=self.Adend3)
self.Bdend.connect(self.soma, 0, 0)
self.Adend1.connect(self.soma, 0.5, 0)
self.Adend2.connect(self.Adend1, 1, 0)
self.Adend3.connect(self.Adend2, 1, 0)
def clear_volt(self):
self.soma_volt.resize(0)
self.Bdend_volt.resize(0)
self.Adend3_volt.resize(0)
def set_conductances(self):
for sect in self.all_sec:
sect.insert('pas')
sect(0.5).pas.g = 0.0000357
sect.insert('nacurrent')
sect.insert('kacurrent')
sect.insert('kdrcurrent')
sect.insert('hcurrent')
# sect.insert('HCN2')
sect(0.5).pas.e = -70 # mV
sect.cm = 1
sect.Ra = 150
# sect(0.5).HCN2.v50 = -92
# sect(0.5).HCN2.gbar = 0.0007
self.soma(0.5).hcurrent.gbar = 0.0001 * hCurrent_g_pyr_scaling # default from CA1ih.mod file is 0.0001
self.Adend1(0.5).nacurrent.ki = 0.5
self.Adend1(0.5).kacurrent.g = 0.072
self.Adend1(0.5).hcurrent.v50 = -82
self.Adend1(0.5).hcurrent.gbar = 0.0002 * hCurrent_g_pyr_scaling
self.Adend2(0.5).nacurrent.ki = 0.5
self.Adend2(0.5).kacurrent.g = 0
self.Adend2(0.5).kacurrent.gd = 0.120
self.Adend2(0.5).hcurrent.v50 = -90
self.Adend2(0.5).hcurrent.gbar = 0.0004 * hCurrent_g_pyr_scaling
self.Adend3(0.5).cm = 2
self.Adend3(0.5).pas.g = 0.0000714
self.Adend3(0.5).nacurrent.ki = 0.5
self.Adend3(0.5).kacurrent.g = 0
self.Adend3(0.5).kacurrent.gd = 0.200
self.Adend3(0.5).hcurrent.v50 = -90
self.Adend3(0.5).hcurrent.gbar = 0.0007 * hCurrent_g_pyr_scaling
self.Bdend(0.5).nacurrent.ki = 1
self.Bdend(0.5).hcurrent.gbar = 0.0001 * hCurrent_g_pyr_scaling # default from CA1ih.mod file is 0.0001
def set_synapses(self):
self.somaGABAf = Synapse( sect=self.soma, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
self.somaAMPAf = Synapse( sect=self.soma, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.BdendAMPA = Synapse( sect=self.Bdend, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.BdendNMDA = SynapseNMDA(sect=self.Bdend, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
# insert synapses into the middle segment of apical dendrites which will be targeted by recurrent collateral fibres - added by mohdsh on 2016Jan26 (molpsychistb@gmail.com)
self.Adend2AMPA = Synapse( sect=self.Adend2, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.Adend2NMDA = SynapseNMDA(sect=self.Adend2, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
self.Adend2GABAf = Synapse( sect=self.Adend1, loc=0.5, tau1=0.07, tau2=9.1, e=-80) # for CCK_Adend2Pyr cells
self.Adend2GABAs = Synapse( sect=self.Adend2, loc=0.5, tau1=0.2, tau2=20, e=-80) # was used for OLM cells - now OLM cells will target Adend3 # either Adend2GABAs or Adend3GABAs are used
self.Adend3GABAs = Synapse( sect=self.Adend3, loc=0.5, tau1=0.2, tau2=20, e=-80) # added by mohdsh 2016jan22 - for olm to target distal dendrites
self.Adend3GABAf = Synapse( sect=self.Adend3, loc=0.5, tau1=0.07, tau2=9.1, e=-80)
self.Adend3AMPAf = Synapse( sect=self.Adend3, loc=0.5, tau1=0.05, tau2=5.3, e=0)
self.Adend3NMDA = SynapseNMDA(sect=self.Adend3, loc=0.5, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
self.Adend3AMPASTDP = SynapseSTDP(sect=self.Adend3,loc=0.5,tau=5.35,e=0,dtau=34,ptau=17,d=0.5,p=0.5)
