# global variables
tstop = 10
Vrest = -70
jonas = jonas1993()
# create VClamps on cells
jonas_vclamp = h.SEClamp(0.5, sec = jonas.soma)
# fill same VClamp parameters for both
jonas_vclamp.rs = 0.1
jonas_vclamp.amp1 = Vrest
jonas_vclamp.dur1 = tstop
# set one synapse originally at the soma
jonas_syn = h.synapse(0.5, sec = jonas.soma)
jonas_syn.tonset = 0
jonas_syn.tau0 = 0.2 # in ms (tau onset in Jonas et al., 1993)
jonas_syn.tau1 = 2.5 # in ms (tau decay in Jonas et al., 1993)
jonas_syn.gmax = 300e-6 # 300 pS in Jonas et al., 1993
# run simulation
# init
h.load_file('stdrun.hoc')
h.v_init = Vrest
h.tstop = tstop
jonas.set_Vrest(Vrest)
current, time = h.Vector(), h.Vector()
#------------------------------------------------------------------------- # global variables for simulation #------------------------------------------------------------------------- tstop = 50 # in ms v_init = -70 # in mV #------------------------------------------------------------------------- # create a CA3-15 morphology cell # with a synapse at the soma # # Cm = 1 uF/cm^2 # Ra = 194 Ohms*cm # Rm = 164 kOhms*cm^2 #------------------------------------------------------------------------- mycell = christoph2007() mysyn = h.synapse(0.5, sec = mycell.soma) mysyn.tonset = 0.5 # ms mysyn.tau0 = 0.2 # ms mysyn.tau1 = 2.5 # ms mysyn.gmax = 300e-6 # in uS #------------------------------------------------------------------------- # Voltage-clamp at the soma # set soma as zero distance # insert a synapse at the soma #------------------------------------------------------------------------- VClamp = h.SEClamp(0.5, sec= mycell.soma) VClamp.rs = 0.1 # MegaOhms VClamp.amp1 = v_init # see global variables VClamp.dur1 = tstop # see global variables
import matplotlib.pyplot as plt
from CA3.library import jonas1993
from neuron import h
cell = jonas1993()
# initial parameters
# voltage-clamp at the soma
VC_patch = h.SEClamp(0.5, sec = cell.soma)
VC_patch.rs = 0.1
VC_patch.amp1 = -70
# set one synapse originally at the soma
# for parameters check page 624 and 649
syn = h.synapse(0.5, sec = cell.soma)
syn.tonset = 0
syn.tau0 = 0.2 # in ms (tau onset in Jonas et al., 1993)
syn.tau1 = 2.5 # in ms (tau decay in Jonas et al., 1993)
syn.gmax = 300e-6 # 300 pS in Jonas et al., 1993
def simulation(tstop, with_time = False):
"""
runs the simulation and returns the current and
time vectors as Numpy arrays
"""
h.load_file('stdrun.hoc')
h.v_init = -70
h.tstop = tstop
"""
show_soma.py
Show somatic epsc
"""
import matplotlib.pyplot as plt
import numpy as np
from neuron import h
from CA3.library import jonas1993
cell = jonas1993()
# prepare synapse at the soma (see Jonas et al., 1993, page 624)
mysyn = h.synapse(0.5, cell.soma)
mysyn.tonset = 0.5 # in ms
mysyn.tau0 = .2 # in ms (tau onset in Jonas et al., 1993)
mysyn.tau1 = 2.5 # in ms (tau decay in Jonas et al., 1993)
mysyn.gmax = 300e-6 # (300 pS, see Jonast et al., page 649)
# voltage clamp mechanism
VC_patch = h.SEClamp(0.5)
VC_patch.rs = 0.1 # series resistance
VC_patch.amp1 = -70 # holding potential (in mV)
def simulate(tstop):
"""
simulate the somatic EPSC and
returns the time (in ms) and current (in pA)
"""
