decor = arbor.decor()
# Set the default properties.
decor.set_property(Vm=-55)
# Override the defaults.
decor.paint('"custom"', tempK=270)
decor.paint('"soma"', Vm=-50)
# Paint density mechanisms.
decor.paint('"all"', 'pas')
decor.paint('"custom"', 'hh')
decor.paint('"dend"', mech('Ih', {'gbar': 0.001}))
# Place stimuli and spike detectors.
decor.place('"root"', arbor.iclamp(10, 1, current=2), "iclamp0")
decor.place('"root"', arbor.iclamp(30, 1, current=2), "iclamp1")
decor.place('"root"', arbor.iclamp(50, 1, current=2), "iclamp2")
decor.place('"axon_terminal"', arbor.spike_detector(-10), "detector")
# Set cv_policy
soma_policy = arbor.cv_policy_single('"soma"')
dflt_policy = arbor.cv_policy_max_extent(1.0)
policy = dflt_policy | soma_policy
decor.discretization(policy)
'axon': '(tag 2)', # axon has tag 2 in swc files.
'dend': '(tag 3)', # dendrites have tag 3 in swc files.
'root':
'(root)', # the start of the soma in this morphology is at the root of the cell.
'stim_site':
'(location 0 0.5)', # site for the stimulus, in the middle of branch 0.
'axon_end': '(restrict (terminal) (region "axon"))'
} # end of the axon.
labels = arbor.label_dict(defs)
decor = arbor.decor()
# Set initial membrane potential to -55 mV
decor.set_property(Vm=-55)
# Use Nernst to calculate reversal potential for calcium.
decor.set_ion('ca', method=mech('nernst/x=ca'))
#decor.set_ion('ca', method='nernst/x=ca')
# hh mechanism on the soma and axon.
decor.paint('"soma"', 'hh')
decor.paint('"axon"', 'hh')
# pas mechanism the dendrites.
decor.paint('"dend"', 'pas')
# Increase resistivity on dendrites.
decor.paint('"dend"', rL=500)
# Attach stimuli that inject 4 nA current for 1 ms, starting at 3 and 8 ms.
decor.place('"root"', arbor.iclamp(10, 1, current=5), "iclamp0")
decor.place('"stim_site"', arbor.iclamp(3, 1, current=0.5), "iclamp1")
decor.place('"stim_site"', arbor.iclamp(10, 1, current=0.5), "iclamp2")
decor.place('"stim_site"', arbor.iclamp(8, 1, current=4), "iclamp3")
# Detect spikes at the soma with a voltage threshold of -10 mV.
decor.place('"axon_end"', arbor.spike_detector(-10), "detector")
