

In [1]:

    
%pylab inline









    



Populating the interactive namespace from numpy and matplotlib

Example 2: Extracellular response of synaptic input

This is an example of LFPy running in an IPython notebook. To run through this example code and produce output, press <shift-Enter> in each code block below.

First step is to import LFPy and other packages for analysis and plotting:



In [2]:

    
import LFPy

Create some dictionarys with parameters for cell, synapse and extracellular electrode:



In [3]:

    
cellParameters = {
    'morphology' : 'morphologies/L5_Mainen96_LFPy.hoc',
    'tstart' : -50,
    'tstop' : 100,
    'dt' : 2**-4,
    'passive' : True,
}

synapseParameters = {
    'syntype' : 'Exp2Syn',
    'e' : 0.,
    'tau1' : 0.5,
    'tau2' : 2.0,
    'weight' : 0.005,
    'record_current' : True,
}

z = mgrid[-400:1201:100]
electrodeParameters = {
    'x' : zeros(z.size),
    'y' : zeros(z.size),
    'z' : z,
    'sigma' : 0.3,
}

Then, create the cell, synapse and electrode objects using LFPy.Cell, LFPy.Synapse, LFPy.RecExtElectrode.



In [4]:

    
cell = LFPy.Cell(**cellParameters)
cell.set_pos(x=-10, y=0, z=0)
cell.set_rotation(z=np.pi)

synapse = LFPy.Synapse(cell,
                       idx = cell.get_closest_idx(z=800),
                       **synapseParameters)
synapse.set_spike_times(array([10, 30, 50]))
                        
electrode = LFPy.RecExtElectrode(**electrodeParameters)

Run the simulation with electrode as input to cell.simulate()



In [5]:

    
cell.simulate(electrode = electrode)

Then plot the somatic potential and the LFP from electrode object:



In [6]:

    
figure(figsize=(12, 6))
subplot(133)
pcolormesh(cell.tvec, electrode.z, electrode.LFP,
           vmin=-abs(electrode.LFP).max(), vmax=abs(electrode.LFP).max())
colorbar()
title('LFP (mV)')

subplot(232)
plot(cell.tvec, synapse.i, 'r'), title('synaptic current (pA)')

subplot(235)
plot(cell.tvec, cell.somav, 'k'), title('somatic voltage (mV)')

subplot(131)
for sec in LFPy.cell.neuron.h.allsec():
    idx = cell.get_idx(sec.name())
    plot(np.r_[cell.xstart[idx], cell.xend[idx][-1]],
            np.r_[cell.zstart[idx], cell.zend[idx][-1]],
            color='k')
plot([cell.synapses[0].x], [cell.synapses[0].z], 
     color='r', marker='o', markersize=10)
plot(electrode.x, electrode.z, '.', marker='o', color='g')
axis([-500, 500, -400, 1200])

#savefig('LFPy-example-2.pdf', dpi=300)









    Out[6]:





[-500, 500, -400, 1200]



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