dt = 0.025
tstop=50
# Parameters
dist = 2.5 #mm
rho = 3.5 #conductivity, Ohm.m
alpha = 0. #angle, rad
cutoff = 800. #high-pass cutoff, Hz
order = 401 #filter order
# Electrode position and filter
pos = (dist*np.sin(alpha)*1000, dist*np.cos(alpha)*1000, 0)
fir = field.hp_fir(order, cutoff, dt)
# Simulation
cell.load_model('models/Mainen/demo_ext.hoc',
'models/Mainen/%s/.libs/libnrnmech.so' % ARCH)
cell.initialize(dt=dt)
t, I = cell.integrate(tstop)
coords = cell.get_seg_coords()
# Select segments
dend = field.select_sections(coords, "dend")
soma = field.select_sections(coords, "soma")
axon = field.select_sections(coords, "(node)|(myelin)")
iseg = field.select_sections(coords, "iseg")
hill = field.select_sections(coords, "hill")
all = field.select_sections(coords, ".*")
colors = {"dend": "r",
"soma": "c",
"axon": "b",
import platform
ARCH = platform.uname()[4]
dt = 0.025
tstop=50
# Parameters
rho = 3.5 #conductivity, Ohm.m
cutoff = 800. #high-pass cutoff, Hz
order = 401 #filter order
Nsamp = 30
filter = None
# Simulation
cell.load_model('models/Mainen/demo_ext.hoc',
'models/Mainen/%s/.libs/libnrnmech.so' % ARCH)
cell.initialize(dt=dt)
t, I = cell.integrate(tstop)
coords = cell.get_seg_coords()
# Plots
fig = plt.figure(figsize=(6,6), facecolor=(0.7, 0.7, 0.7))
fig.subplots_adjust(left=0.05, right=0.95)
ax = plt.subplot(111, frameon=False)
S = np.pi*coords['diam']*coords['L'] #segment surface
p2p = np.abs(I).max(0)-np.abs(I).min(0)
norm = colors.LogNorm(vmin=p2p.min(), vmax=p2p.max())
col = graph.plot_neuron(coords, p2p, norm=norm)
plt.xticks([])
plt.yticks([])
plt.ylim((-200, 610))
rho = 3.5 #conductivity, Ohm.m
cutoff = 800. #high-pass cutoff, Hz
order = 401 #filter order
Nsamp = 30
filter = None
y_range = (-200, 610)
x_range = (-550, 250)
bg_color = (0.7, 0.7, 0.7)
cmap = cm.viridis
simulation_filename = "data/neuron_simulation_data.npz"
# Simulation
if not os.path.exists(simulation_filename):
from eap import cell
cell.load_model('models/Mainen/demo_ext.hoc',
'models/Mainen/{}/.libs/libnrnmech.so'.format(ARCH))
cell.initialize(dt=dt)
t, I = cell.integrate(tstop)
coords = cell.get_seg_coords()
I = I[(t > t0) & (t < t1)]
t = t[(t > t0) & (t < t1)]
np.savez(simulation_filename, coords=coords, I=I, t=t)
else:
data = np.load(simulation_filename)
coords = data['coords']
t = data['t']
I = data['I']
# Plots
fig = plt.figure(figsize=(6,6), facecolor=bg_color)
fig.subplots_adjust(left=0.05, right=0.95)
import matplotlib.pyplot as plt
from eap import field, cell, graph
from matplotlib import transforms
dt = 0.025
tstop=35
win = [25, 33]
# Parameters
rho = 3.5 #conductivity, Ohm.m
cutoff = 800. #high-pass cutoff, Hz
order = 51 #filter order
Nsamp = 20
filter = None
# Simulation
cell.load_model('models/Mainen/demo_ext.hoc',
'models/Mainen/i686/.libs/libnrnmech.so')
cell.initialize(dt=dt)
t, I = cell.integrate(tstop)
tmin, tmax = win
I = I[(t>tmin) & (t<tmax), :]
t = t[(t>tmin) & (t<tmax)]
# Calculation of field
xrange = [-3000, 3000]
yrange = [-3000, 3000]
coords = cell.get_seg_coords()
xx, yy = field.calc_grid(xrange, yrange, n_samp=Nsamp)
v_ext = field.estimate_on_grid(coords, I, xx, yy)
#Filter
dt = 0.025
tstop = 50
xyz_cell1 = [0, 0, 0] #microm
xyz_cell2 = [200, 0, 0]
cell_list = []
syn_e = -72.0
con_weight = .45e-3
tau1 = 0.25
tau2 = 8
t_length = 5
time_to_plot = 4
# SETUP CELLS
# load your model cell
cell.load_model('models/amaral.hoc')
cells = cell.h.List()
cells.append(cell.h.AmaralCell(xyz_cell1[0], xyz_cell1[1], xyz_cell1[2], 0))
cells.append(cell.h.AmaralCell(xyz_cell2[0], xyz_cell2[1], xyz_cell2[2], 0))
nclist = []
stimlist = []
# init synapses
def init_synapse(cell_no, syn_start):
syn = cell.h.Exp2Syn(0.5, sec=cells[cell_no].soma[0])
syn.e = syn_e
syn.tau1 = tau1 #.1
syn.tau2 = tau2 #5
import matplotlib.pyplot as plt
from eap import field, cell, graph
from matplotlib import transforms
dt = 0.025
tstop = 35
win = [25, 33]
# Parameters
rho = 3.5 #conductivity, Ohm.m
cutoff = 800. #high-pass cutoff, Hz
order = 51 #filter order
Nsamp = 20
filter = None
# Simulation
cell.load_model('models/Mainen/demo_ext.hoc',
'models/Mainen/i686/.libs/libnrnmech.so')
cell.initialize(dt=dt)
t, I = cell.integrate(tstop)
tmin, tmax = win
I = I[(t > tmin) & (t < tmax), :]
t = t[(t > tmin) & (t < tmax)]
# Calculation of field
xrange = [-3000, 3000]
yrange = [-3000, 3000]
coords = cell.get_seg_coords()
xx, yy = field.calc_grid(xrange, yrange, n_samp=Nsamp)
v_ext = field.estimate_on_grid(coords, I, xx, yy)
#Filter