# 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) """