-
Notifications
You must be signed in to change notification settings - Fork 0
/
AVAL_simulation_vclamp.py
164 lines (111 loc) · 3.91 KB
/
AVAL_simulation_vclamp.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
# "Biophysical modeling of the whole-cell dynamics of C. elegans motor and interneurons families"
# M. Nicoletti et al. PloS ONE, 19(3): e0298105.
# https://doi.org/10.1371/journal.pone.0298105
def AVA_simulation_vc(gAVA_scaled,vstart,vstop,ns):
from neuron import h,gui
import numpy
import math
surf=1123.84e-8 # surface in cm^2 form neuromorpho AVAL
vol=129.6e-12 # total volume
L=math.sqrt(surf/math.pi)
rsoma=L*1e4
cm_uFcm2=gAVA_scaled[5]
cm_pF=cm_uFcm2*1e6/surf
soma=h.Section(name="soma")
soma.L=rsoma
soma.diam=rsoma
soma.Ra=100
soma.cm=cm_uFcm2
h.psection(sec=soma)
soma.insert('irk')
soma.insert('leak')
soma.insert('egl19')
soma.insert('nca')
for seg in soma:
seg.egl19.gbar=gAVA_scaled[0]
seg.leak.gbar=gAVA_scaled[1]
seg.irk.gbar=gAVA_scaled[2]
seg.nca.gbar=gAVA_scaled[3]
seg.leak.e=gAVA_scaled[4]
seg.eca=60
seg.ek=-80
stim=h.VClamp(soma(0.5))
dir(stim)
simdur = 1500
stim.amp[0]=-30
stim.amp[1]=-110
stim.amp[2]=-30
stim.dur[0]=1007.8
stim.dur[1]=250
stim.dur[2]=242.2
ik_vec = h.Vector()
ica_vec=h.Vector()
inca_vec=h.Vector()
ileakAVA_vec=h.Vector()
t_vec = h.Vector()
ik_vec.record(soma(0.5)._ref_ik)
ica_vec.record(soma(0.5)._ref_ica)
inca_vec.record(soma(0.5)._ref_i_nca)
ileakAVA_vec.record(soma(0.5)._ref_i_leak)
t_vec.record(h._ref_t)
ref_ik=[]
ref_ica=[]
ref_t=[]
ref_inca=[]
ref_ileakAVA=[]
for i in numpy.linspace(start=vstart, stop=vstop, num=ns):
stim.amp[1]=i
h.tstop=simdur
h.dt=0.01
h.finitialize(-30)
h.run()
#time
ref_t_vec=numpy.zeros_like(t_vec)
t_vec.to_python(ref_t_vec)
ref_t.append(ref_t_vec)
# potassium current
ref_ik_vec=numpy.zeros_like(ik_vec)
ik_vec.to_python(ref_ik_vec)
ref_ik.append(ref_ik_vec)
#calcium currents
ref_ica_vec=numpy.zeros_like(ica_vec)
ica_vec.to_python(ref_ica_vec)
ref_ica.append(ref_ica_vec)
# NCA currents
ref_inca_vec=numpy.zeros_like(inca_vec)
inca_vec.to_python(ref_inca_vec)
ref_inca.append(ref_inca_vec)
# LEAKAGE current
ref_ileakAVA_vec=numpy.zeros_like(ileakAVA_vec)
ileakAVA_vec.to_python(ref_ileakAVA_vec)
ref_ileakAVA.append(ref_ileakAVA_vec)
# total current calculation
itot=[]
itot=map(sum, zip(ref_ik,ref_ica,ref_inca,ref_ileakAVA))
current=numpy.array(list(itot))
inorm=current*1e9*surf #total current in pA
#time array
time1=numpy.array(ref_t)
resc_ind=numpy.where(time1[1,:]>=1000)
resc_min=numpy.amin(resc_ind)
resc_max=numpy.amax(resc_ind)
itot_normalized=inorm[:,resc_min:resc_max]
time=time1[:,resc_min:resc_max]-1000
## SS I-V
ind=numpy.where(numpy.logical_and(time[0]>=247, time[0]<=257))
ind_max=numpy.amax(ind)
ind_min=numpy.amin(ind)
iv=numpy.mean(itot_normalized[:,ind_min:ind_max],axis=1)
# PEAKS I-V
ind2=numpy.where(numpy.logical_and(time[0]>=7.8, time[0]<=17.8))
ind2_max=numpy.amax(ind2)
ind2_min=numpy.amin(ind2)
iv_peak=numpy.amax(itot_normalized[:,ind2_min:ind2_max])
iv_peak=[]
for j in range(ns):
if j<=6:
peak=numpy.amin(itot_normalized[j,ind2_min:ind2_max])
else:
peak=numpy.amax(itot_normalized[j,ind2_min:ind2_max])
iv_peak.append(peak)
return itot_normalized, time, iv_peak, iv