def run_WN(photoreceptor, I):
Z_dictionary = {}
V_dictionary = {}
Vl_dictionary = {}
I_dictionary = {}
for i, V in enumerate(Vr):
DepolarisePhotoreceptor.WithLight(photoreceptor, V)
## Filtering signal
print("Processing V=", V, " mV")
## Run HH
print("Running HH...")
Vm, g = Experiment.inject_current(photoreceptor, I, dt)
Vl = Linearise.inject_current(photoreceptor, I, dt)
print("Variance of voltage is ", var(Vm), "mV2")
## Calculate impedance
Vmm = (Vm - mean(Vm)) #without DC
CPSD = zeros(round(len(time) / 2 + 1), dtype=complex_)
PSD = zeros(round(len(time) / 2 + 1))
window = hamming(len(time))
print("len(window)", len(window))
for ii in range(repetitions):
I_cut = I[ii * len(time):(ii + 1) * len(time)]
V_cut = Vmm[ii * len(time):(ii + 1) * len(time)]
PSD += power(absolute(rfft(I_cut * window)), 2)
CPSD += rfft(V_cut * window) * rfft(I_cut * window).conjugate()
Z = CPSD / PSD #MOhm
Z_dictionary[V] = Z
I_dictionary[V] = I[sample * len(time):(sample + 1) * len(time)]
V_dictionary[V] = Vm[sample * len(time):(sample + 1) * len(time)]
Vl_dictionary[V] = Vl[sample * len(time):(sample + 1) * len(time)]
return (Z_dictionary, V_dictionary, Vl_dictionary, I_dictionary)
for ii, condition in enumerate(conditions):
photoreceptor = FlyFactory.DrosophilaR16(shift="none")
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V)
if condition == 'PIP2':
ShiftConductances.WithLight(photoreceptor,
change_LIC_to_keep_depolarisation=
change_LIC_to_keep_depolarisation)
elif condition == 'Serotonin':
ShiftConductances.WithSerotonin(photoreceptor,
change_LIC_to_keep_depolarisation=
change_LIC_to_keep_depolarisation)
elif condition == 'Shab-50':
Experiment.modify_conductance(photoreceptor,
"Shab",
.5,
change_LIC_to_keep_depolarisation=
change_LIC_to_keep_depolarisation)
elif condition == 'Shab+50':
Experiment.modify_conductance(photoreceptor,
"Shab",
1.5,
change_LIC_to_keep_depolarisation=
change_LIC_to_keep_depolarisation)
else:
print("Warning, option not recognised")
Vr_new_r[ii, i] = photoreceptor.body.V_m
Z_cut = photoreceptor.body.impedance(
f_from_medium
gain_bandwidth_product_fixed = zeros_like(Vr)
HH_RC = []
for i, V in enumerate(Vr):
label_str = str(V) + ' mV'
DepolarisePhotoreceptor.WithLight(HH, V)
gain_max[i], Bandwidth[i] = Gain_Bandwidth(HH.body.voltage_contrast_gain,
f_min=f_medium)
gain = abs(HH.body.voltage_contrast_gain(f))
gain_bandwidth_product[i] = gain_max[i] * Bandwidth[i]
Experiment.freeze_conductances(HH)
gain_max_fixed[i], Bandwidth_fixed[i] = Gain_Bandwidth(
HH.body.voltage_contrast_gain, f_min=f_medium)
gain_fixed = abs(HH.body.voltage_contrast_gain(f))
gain_bandwidth_product_fixed[i] = gain_max_fixed[i] * Bandwidth_fixed[i]
Experiment.unfreeze_conductances(HH)
ax_bwprod.plot(V,
gain_bandwidth_product[i],
colour_graph[i] + '.',
markersize=15)
ax_bwprod.plot(V,
gain_bandwidth_product_fixed[i],
colour_graph[i] + '.',
photoreceptor = Drone.Vallet92()
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V_membrane)
fig1.text(0.06,
0.5,
'Membrane potential deflection (mV)',
ha='center',
va='center',
rotation='vertical')
for ii in range(5):
for i, t in enumerate(time_array):
if 10 <= t <= 110: I[i] = 1e-3 * (-0.02 + 0.01 * ii) # nA->uA
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V_membrane)
V_array, g_Ch = Experiment.inject_current(photoreceptor, I, dt)
ax_curr.plot(time_array, I, 'k')
ax.plot(time_array, V_array - V_membrane, color='black') #mV
ax.set_xticklabels([])
V_array = Linearise.inject_current(photoreceptor, I, dt)
ax.plot(time_array, V_array, 'k--') #mV
ax.set_xticklabels([])
V_membrane = -38 #mV
photoreceptor = Drone.Vallet92(k_h=1)
DepolarisePhotoreceptor.WithLight(photoreceptor, V=V_membrane)
for ii in range(5):
for i, t in enumerate(time_array):
if 10 <= t <= 110: I[i] = 1e-3 * (-0.02 + 0.01 * ii) # nA->uA
V_membrane = -60 # mV
else:
N_rep = 8
a = -0.7
b = 0.2
V_membrane = -40 #mV
photoreceptor = FlyFactory.CalliphoraR16(channel_choice = "Anderson")
for ii in range(N_rep) :
for i, t in enumerate(time_array):
if 10 <= t <= 110: I[i] = 1e-3*(a+b*ii) # nA->uA --- Fig S1b
DepolarisePhotoreceptor.WithLight(photoreceptor, V = V_membrane)
V_array, g_Ch = Experiment.inject_current(photoreceptor,I,dt)
plt.ylabel_set = False
ax = plt.subplot(2,1,1)
ax.plot(time_array, V_array,color='black') #mV
ax.set_title('Hodgkin-Huxley voltage (top) and conductances (bottom)')
plt.ylabel('Potential (mV)')
ax.set_xticklabels([])
ax = plt.subplot(2,1,2)
ax.plot(time_array, g_Ch[0]*1e6,color='blue') #Fast conductance, nS
ax.plot(time_array, g_Ch[1]*1e6,color='red') #Slow conductance, nS
plt.xlabel('Time (msec)')
plt.ylabel('Conductances (nS)')
Experiment.freeze_conductances(photoreceptor)
V_array, g_Ch = Experiment.inject_current(photoreceptor,I,dt)
ha='right')
Vr = np.arange(-68.0, -30.0, 8)
deltaV = 0.5
Vr_continuous = np.arange(-68, -36 + deltaV, deltaV)
colour_graph = list('ybgrc')
GBWP_continuous_ = np.zeros_like(Vr_continuous)
GBWP_RC_continuous_ = np.zeros_like(Vr_continuous)
GBWP_selective_continuous_ = np.zeros((3, len(Vr_continuous)))
for i, V in enumerate(Vr_continuous):
DepolarisePhotoreceptor.WithLight(HH, V)
GBWP_continuous_[i] = GBWP(HH.body.impedance, f_min=f_medium)
Experiment.freeze_conductances(HH)
GBWP_RC_continuous_[i] = GBWP(HH.body.impedance, f_min=f_medium)
Experiment.unfreeze_conductances(HH)
for ii in range(3):
for iii in range(3):
if ii != iii:
Experiment.freeze_conductances(HH, index=iii)
GBWP_selective_continuous_[ii, i] = GBWP(HH.body.impedance,
f_min=f_medium)
Experiment.unfreeze_conductances(HH)
for ii in range(3):
ax_GBWP[ii].plot(Vr_continuous,
GBWP_continuous_ / 1e3,
'k',
V_membrane_ = [-68,-59,-41] #mV
plot_window = array([-.5,3.5])
drosophila = FlyFactory.DrosophilaR16()
fig1 = figure(1)
T=200 #ms
dt=0.5 #ms
time_array = arange(0,T+dt,dt)
I = zeros_like(time_array)
for ii,V_membrane in enumerate(V_membrane_) :
for i, t in enumerate(time_array):
if 10 <= t <= 160: I[i] = 1e-3*(0.01) # nA->uA
DepolarisePhotoreceptor.WithLight(drosophila, V = V_membrane)
V_array, g_Ch = Experiment.inject_current(drosophila,I,dt)
ax = fig1.add_subplot(3,1,ii+1)
ax.plot(time_array, V_array,color='black') #mV
#Experiment.unfreeze_conductances(drosophila)
DepolarisePhotoreceptor.WithLight(drosophila, V = V_membrane) #To make sure that all channels are back at rest
Experiment.freeze_inactivations(drosophila)
V_array, g_Ch = Experiment.inject_current(drosophila,I,dt)
Experiment.unfreeze_inactivations(drosophila)
ax.plot(time_array, V_array,'k:') #mV
DepolarisePhotoreceptor.WithLight(drosophila, V = V_membrane) #To make sure that all channels are back at rest
Experiment.freeze_conductances(drosophila)
DepolarisePhotoreceptor.WithLight(HH,V)
passive_gbwp = 1/2/pi/HH.body.C
tau_fast_original = HH.body.voltage_channels[0].m_time(V)
print("Passive GBWP is ", passive_gbwp, " MOhm Hz")
print("Original time constant for FDR is ", tau_fast_original, "ms")
low_pass_found = False
for i,tau in enumerate(tau_fast):
HH.body.voltage_channels[0].time_multiplier = tau_fast[i]/tau_fast_original
GBWP_a[i]= GBWP(HH.body.impedance)/passive_gbwp
GDV_a[i] = GDV(HH.body.impedance, f_down=f_down)
if (Is_Band_Pass(HH.body.impedance) and low_pass_found==False):
print ("First low pass when tau = ", tau)
low_pass_found = True
Experiment.freeze_conductances(HH,index=1) #freeze SDR
low_pass_found = False
for i,tau in enumerate(tau_fast):
HH.body.voltage_channels[0].time_multiplier = tau_fast[i]/tau_fast_original
GBWPf_a[i]= GBWP(HH.body.impedance)/passive_gbwp
GDVf_a[i] = GDV(HH.body.impedance, f_down=f_down)
if (Is_Band_Pass(HH.body.impedance) and low_pass_found==False):
print ("First low pass when tau = ", tau)
low_pass_found = True
Experiment.freeze_conductances(HH,index=0) #freeze FDR and SDR
passive_gdv = GDV(HH.body.impedance)
ax_gbwp1.plot(tau_fast,GBWP_a,'k')
deltaV = 0.5
Vr_continuous = np.arange(-68, -36 + deltaV, deltaV)
colour_graph=['y','b','g','r','c']
##Continuous across depolarisations
GBWP_continuous_ = np.zeros_like(Vr_continuous)
GBWP_RC_continuous_ = np.zeros_like(Vr_continuous)
GBWP_shift_continuous_ = np.zeros((3,len(Vr_continuous)))
Vr_shift_continuous = np.zeros((3,len(Vr_continuous)))
for i,V in enumerate(Vr_continuous):
DepolarisePhotoreceptor.WithLight(HH,V)
GBWP_continuous_[i] = GBWP(HH.body.impedance, f_min = f_medium)
Experiment.freeze_conductances(HH)
GBWP_RC_continuous_[i] = GBWP(HH.body.impedance, f_min = f_medium)
Experiment.unfreeze_conductances(HH)
for ii in range(3):
HH_shifted = copy.deepcopy(HH)
if ii==0:
ShiftConductances.WithLight(HH_shifted, change_LIC_to_keep_depolarisation = change_LIC_to_keep_depolarisation)
elif ii==2:
ShiftConductances.WithSerotonin(HH_shifted, change_LIC_to_keep_depolarisation = change_LIC_to_keep_depolarisation)
elif ii==1:
Experiment.modify_conductance(HH_shifted, "Shab", .5, change_LIC_to_keep_depolarisation = change_LIC_to_keep_depolarisation)
else:
raise Exception
GBWP_shift_continuous_[ii,i] = GBWP(HH_shifted.body.impedance, f_min = f_medium)
Vr_shift_continuous[ii,i] = HH_shifted.body.V_m
