# $Id: geom.py,v 1.30 2011/01/02 19:56:14 samn Exp $
from pyinit import *
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
###############################################################################
#
# General Cell
#
###############################################################################
class Cell:
"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 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, fig=1):
figure(fig)
volt = self.__dict__[name+"_volt"].to_python()
plot(arange(len(volt))*h.dt, volt)
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
###############################################################################
#
# Basket Cell -- Bwb
#
###############################################################################
class Bwb(Cell):
"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 # S/cm2
self.soma.insert('Nafbwb')
self.soma.insert('Kdrbwb')
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)
###############################################################################
#
# 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.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)
###############################################################################
#
# 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 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(0.5).pas.e = -70 # mV
sect.cm = 1
sect.Ra = 150
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.g = 0.0002
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.g = 0.0004
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.g = 0.0007
self.Bdend(0.5).nacurrent.ki = 1
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=1.0, tau1=0.05, tau2=5.3, e=0)
self.BdendNMDA = SynapseNMDA(sect=self.Bdend, loc=1.0, tau1=0.05, tau2=5.3, tau1NMDA=15, tau2NMDA=150, r=1, e=0)
self.Adend2GABAs = Synapse( sect=self.Adend2, loc=0.5, tau1=0.2, tau2=20, e=-80)
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)
