Example: compensation_ex1 (electrophysiology)ΒΆ
Example of L^p electrode compensation method. Requires binary files “current.npy” and “rawtrace.npy”.
Rossant et al., “A calibration-free electrode compensation method” J. Neurophysiol 2012
import os
from brian import *
import numpy as np
from brian.library.electrophysiology import *
working_dir = os.path.dirname(__file__)
# load data
dt = 0.1*ms
current = np.load(os.path.join(working_dir, "current.npy")) # 10000-long vector, 1s duration
rawtrace = np.load(os.path.join(working_dir, "trace.npy")) # 10000-long vector, 1s duration
t = linspace(0., 1., len(current))
# launch compensation
r = Lp_compensate(current, rawtrace, dt, p=1.0, full=True)
# print best parameters
print "Best parameters: R, tau, Vr, Re, taue:"
print r["params"]
# plot traces
subplot(211)
plot(t, current, 'k')
subplot(212)
plot(t, rawtrace, 'k') # raw trace
plot(t, r["Vfull"], 'b') # full model trace (neuron and electrode)
plot(t, r["Vcompensated"], 'g') # compensated trace
show()