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Purkinje_py3.py
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Purkinje_py3.py
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#Template of the Purkinje cell model, Masoli et al.,2015
#The code is compliant with the latest python indentation scheme - "11 October 2019"
from neuron import h
import numpy as np
import random
import math
from Syntype_py3 import Synapse_py3
#import of the dictionary with the conductance
from PC_param import pc_param
class Purkinje_py3:
def __init__(self):
self.zebrinnegative = 0 #0 for Zebrin positive. 1 for Zebrin negative
#Soma
self.soma = h.Section(name='soma')
self.soma.nseg = 1
self.soma.diam = 29.8
self.soma.cm = 0.77
self.soma.L = 29.8
self.soma.Ra = 122
self.soma.insert('Leak')
self.soma.e_Leak = pc_param['eleak']
self.soma.gmax_Leak = pc_param['LeakSoma']
self.soma.insert('Cav3_1')
self.soma.pcabar_Cav3_1 = pc_param['Cav3.1Soma']
self.soma.insert('Cav2_1')
self.soma.pcabar_Cav2_1 = pc_param['Cav2.1Soma']
self.soma.insert('HCN1')
self.soma.gbar_HCN1 = pc_param['HCNSoma']
self.soma.eh = -34.4
self.soma.insert('Nav1_6')
self.soma.gbar_Nav1_6 = pc_param['Nav1.6Soma']
self.soma.ena = 60
self.soma.insert('Kv3_4')
self.soma.gkbar_Kv3_4 = pc_param['Kv3.4Soma']
self.soma.ek = -88
self.soma.insert('Kv1_1')
self.soma.gbar_Kv1_1 = pc_param['Kv1.1Soma']
self.soma.insert('Cav3_2')
self.soma.gcabar_Cav3_2 = pc_param['Cav3.2Soma']
self.soma.insert('Kca3_1')
self.soma.gkbar_Kca3_1 = pc_param['Kca3.1Soma']
self.soma.insert('Cav3_3')
self.soma.pcabar_Cav3_3 = pc_param['Cav3.3Soma']
self.soma.insert('Kir2_3')
self.soma.gkbar_Kir2_3 = pc_param['PC_KirSoma']
self.soma.insert('Kca1_1')
self.soma.gbar_Kca1_1 = pc_param['Kca1.1Soma']
self.soma.insert('Kca2_2')
self.soma.gkbar_Kca2_2 = pc_param['Kca2.2Soma']
self.soma.insert('cdp5')
self.soma.Nannuli_cdp5 = 0.326 + (1.94 * (self.soma.diam)) + (0.289*(self.soma.diam)*(self.soma.diam)) - ((3.33e-2)*(self.soma.diam)*(self.soma.diam)*(self.soma.diam)) + ((1.55e-3)*(self.soma.diam)*(self.soma.diam)*(self.soma.diam)*(self.soma.diam)) - (2.55e-5*(self.soma.diam)*(self.soma.diam)*(self.soma.diam)*(self.soma.diam)*(self.soma.diam))
self.soma.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.soma.diam)/1.4)
self.soma.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.soma.diam)/2.29)
self.soma.rf4_cdp5 = 0.000267 + 0.0167* math.exp(-(self.soma.diam)/0.722) + 0.0028* math.exp(-(self.soma.diam)/4)
self.soma.TotalPump_cdp5 = 5e-8
self.soma.push()
h.pt3dclear()
h.pt3dadd(0.0, 0, 0.0, 29.8)
h.pt3dadd(0.0, 29.8, 0.0, 29.8)
h.pop_section()
self.soma.push()
h.ion_style("ca_ion", 1, 1, 0, 1, 0)
self.soma.eca = 137.52625
self.soma.cai = h.cai0_ca_ion
self.soma.cao = h.cao0_ca_ion
h.pop_section()
self.whatami = "prk"
#Dend coordinate
self.sectioncoordinate = np.genfromtxt("coordinate.csv")
fh = open("PC_dendnames.dlist")
self.dendnames = [line[:-1] for line in fh.readlines()]
self.dend = []
for i_idx,i in enumerate(self.sectioncoordinate):
self.dend.append(h.Section(name=self.dendnames[i_idx]))
self.dend[-1].push()
h.pt3dclear()
h.pt3dadd(i.item(1), i.item(2), i.item(3), i.item(4))
h.pt3dadd(i.item(5), i.item(6), i.item(7), i.item(8))
self.dend[-1].diam = i.item(4)
self.dend[-1].insert('cdp5')
self.dend[-1].Nannuli_cdp5 = 0.326 + (1.94 * (i.item(8))) + (0.289*(i.item(8))*(i.item(8))) - ((3.33e-2)*(i.item(8))*(i.item(8))*(i.item(8))) + ((1.55e-3)*(i.item(8))*(i.item(8))*(i.item(8))*(i.item(8))) - (2.55e-5*(i.item(8))*(i.item(8))*(i.item(8))*(i.item(8))*(i.item(8)))
self.dend[-1].Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(i.item(8))/1.4)
self.dend[-1].rf3_cdp5 = 0.162 - 0.106* math.exp(-(i.item(8))/2.29)
if ((i.item(8))>=2):
self.dend[-1].rf4_cdp5 = 0.000267 + 0.0167* math.exp(-(i.item(8))/0.722) + 0.0028* math.exp(-(i.item(8))/4)
else:
self.dend[-1].rf4_cdp5 = 0.003
h.pop_section()
#Connection between dend and soma
self.dend[0].connect(self.soma,1,0)
#Connection between each dend
for c in np.genfromtxt("connections.csv"):
self.dend[int(c[0])].connect(self.dend[int(c[2])],int(c[3]),int(c[1]))
self.subsets = np.genfromtxt("ModelViewParmSubset.txt", dtype = int)
self.ModelViewParmSubset = [[self.dend[int(i)] for i in self.subsets[np.where(self.subsets[...,1]==M),0][0]] for M in range(88) ]
for d in self.dend:
d.Ra = 122
d.insert('Leak')
d.e_Leak = pc_param['eleak']
d.insert('Cav2_1')
d.pcabar_Cav2_1 = pc_param['Cav2.1Dend']
d.insert('Kca1_1')
d.gbar_Kca1_1 = pc_param['Kca1.1Dend']
d.insert('Kv4_3')
d.gkbar_Kv4_3 = pc_param['Kv4.3Dend']
d.insert('Kv1_1')
d.gbar_Kv1_1 = pc_param['Kv1.1Dend']
d.insert('Kv1_5')
d.gKur_Kv1_5 = pc_param['Kv1.5Dend']
d.insert('Kv3_3')
d.gbar_Kv3_3 = pc_param['Kv3.3Dend']
d.insert('Cav3_3')
d.pcabar_Cav3_3 = pc_param['Cav3.3Dend']
d.insert('HCN1')
d.gbar_HCN1 = pc_param['HCNDend']
d.eh = -34.4
if d.diam >= 3.5 and d.diam <= 12:
d.insert('Cav3_2')
d.gcabar_Cav3_2 = pc_param['Cav3.2Dend']
d.insert('Kca3_1')
d.gkbar_Kca3_1 = pc_param['Kca3.1Dend']
d.insert('Cav3_1')
d.pcabar_Cav3_1 = pc_param['Cav3.1Dend']
d.insert('Kca2_2')
d.gkbar_Kca2_2 = pc_param['Kca2.2Dend']
d.insert('Kir2_3')
d.gkbar_Kir2_3 = pc_param['PC_KirDend']
if d.diam >=8 and d.diam <=12:
d.insert('Nav1_6')
d.gbar_Nav1_6 = pc_param['Nav1.6Dend']
d.ena = 60
elif self.zebrinnegative == 1:
if d.diam <= 3.5:
d.insert('Ubc_TRP')
d.gtrp_Ubc_TRP = 4.18e-6
print("zebrin negative")
d.TotalPump_cdp5 = 2e-8
d.ek = -88
d.push()
d.eca = 137.52625
d.cai = h.cai0_ca_ion
d.cao = h.cao0_ca_ion
h.ion_style("ca_ion", 1, 1, 0, 1, 0)
h.pop_section()
self.subsets_cm = np.genfromtxt("ModelViewParmSubset_cm.txt")
for cm in self.subsets_cm:
for d in self.ModelViewParmSubset[int(cm[0])]:
d.cm = cm[1] * 0.77/1.64
self.dend[138].cm = 8.58298 * 0.77/1.64
self.subsets_paraextra = np.genfromtxt("modelsubsetextra.txt", dtype=[('modelviewsubset','f8'),('channel','U4'),('channel2','U4'),('value','f8')], delimiter=" ")
for para in self.subsets_paraextra:
for d in self.ModelViewParmSubset[int(para[0])]:
d.insert(para[1])
exec('d.gmax_'+para[2]+' = '+str(para[3]))
listgmax = []
for d in self.ModelViewParmSubset[2]:
d.gmax_Leak = d.gmax_Leak/2
self.dend[138].insert('Leak')
self.dend[138].gmax_Leak = 1.74451E-4 / 2
#Axon AIS. First section after the soma
self.axonAIS = h.Section(name='axonAIS')
self.axonAIS.nseg = 1
self.axonAIS.diam = 0.97
self.axonAIS.cm = 0.77
self.axonAIS.L = 17
self.axonAIS.Ra = 122
self.axonAIS.insert('Leak')
self.axonAIS.e_Leak = pc_param['eleak']
self.axonAIS.gmax_Leak = 0.0003
self.axonAIS.insert('Nav1_6')
self.axonAIS.gbar_Nav1_6 = pc_param['Nav1.6AIS']
self.axonAIS.ena = 75
self.axonAIS.insert('Cav3_1')
self.axonAIS.pcabar_Cav3_1 = pc_param['Cav3.1Ais']
self.axonAIS.insert('Cav2_1')
self.axonAIS.pcabar_Cav2_1 = pc_param['Cav2.1AIS']
self.axonAIS.insert('Kv3_4')
self.axonAIS.gkbar_Kv3_4 = pc_param['Kv3.4AIS']
self.axonAIS.ek = -88
self.axonAIS.insert('cdp5')
self.axonAIS.Nannuli_cdp5 = 0.326 + (1.94 * (self.axonAIS.diam)) + (0.289*(self.axonAIS.diam)*(self.axonAIS.diam)) - ((3.33e-2)*(self.axonAIS.diam)*(self.axonAIS.diam)*(self.axonAIS.diam)) + ((1.55e-3)*(self.axonAIS.diam)*(self.axonAIS.diam)*(self.axonAIS.diam)*(self.axonAIS.diam)) - (2.55e-5*(self.axonAIS.diam)*(self.axonAIS.diam)*(self.axonAIS.diam)*(self.axonAIS.diam)*(self.axonAIS.diam))
self.axonAIS.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.axonAIS.diam)/1.4)
self.axonAIS.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.axonAIS.diam)/2.29)
self.axonAIS.rf4_cdp5 = 0.003
self.axonAIS.TotalPump_cdp5 = 5e-8
self.axonAIS.push()
h.ion_style("ca_ion", 1, 1, 0, 1, 0)
self.axonAIS.eca = 137.52625
self.axonAIS.cai = h.cai0_ca_ion
self.axonAIS.cao = h.cao0_ca_ion
h.pop_section()
#AISK
self.axonAISK = h.Section(name='axonAISK')
self.axonAISK.nseg = 1
self.axonAISK.diam = 0.97
self.axonAISK.cm = 0.77
self.axonAISK.L = 4
self.axonAISK.Ra = 122
self.axonAISK.insert('Leak')
self.axonAISK.e_Leak = pc_param['eleak']
self.axonAISK.gmax_Leak = 0.0003
self.axonAISK.insert('Kv1_1')
self.axonAISK.gbar_Kv1_1 = pc_param['Kv1.1AisK']
self.axonAISK.ek = -88
#First Myelination
self.axonmyelin = h.Section(name='axonmyelin')
self.axonmyelin.nseg = 1
self.axonmyelin.diam = 0.73
self.axonmyelin.L = 100
self.axonmyelin.insert('pas')
self.axonmyelin.e_pas = -63
self.axonmyelin.g_pas = 5.60e-9
self.axonmyelin.cm = 1.87e-11
self.axonmyelin.Ra = 122
#First Node of Ranvier
self.axonNOR = h.Section(name='axonNOR')
self.axonNOR.nseg = 1
self.axonNOR.diam = 0.73
self.axonNOR.cm = 0.77
self.axonNOR.L = 4
self.axonNOR.Ra = 122
self.axonNOR.insert('Leak')
self.axonNOR.e_Leak = pc_param['eleak']
self.axonNOR.gmax_Leak = 0.0003
self.axonNOR.insert('Nav1_6')
self.axonNOR.gbar_Nav1_6 = pc_param['Nav1.6Nor']
self.axonNOR.ena = 60
self.axonNOR.insert('Kv3_4')
self.axonNOR.gkbar_Kv3_4 = pc_param['Kv3.4Nor']
self.axonNOR.ek = -88
self.axonNOR.insert('cdp5')
self.axonNOR.Nannuli_cdp5 = 0.326 + (1.94 * (self.axonNOR.diam)) + (0.289*(self.axonNOR.diam)*(self.axonNOR.diam)) - ((3.33e-2)*(self.axonNOR.diam)*(self.axonNOR.diam)*(self.axonNOR.diam)) + ((1.55e-3)*(self.axonNOR.diam)*(self.axonNOR.diam)*(self.axonNOR.diam)*(self.axonNOR.diam)) - (2.55e-5*(self.axonNOR.diam)*(self.axonNOR.diam)*(self.axonNOR.diam)*(self.axonNOR.diam)*(self.axonNOR.diam))
self.axonNOR.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.axonNOR.diam)/1.4)
self.axonNOR.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.axonNOR.diam)/2.29)
self.axonNOR.rf4_cdp5 = 0.003
self.axonNOR.insert('Cav3_1')
self.axonNOR.pcabar_Cav3_1 = pc_param['Cav3.1Nor']
self.axonNOR.insert('Cav2_1')
self.axonNOR.pcabar_Cav2_1 = pc_param['Cav2.1Nor']
self.axonNOR.TotalPump_cdp5 = 5e-7
#second part of the axon
self.axonmyelin2 = h.Section(name='axonmyelin2')
self.axonmyelin2.nseg = 1
self.axonmyelin2.diam = 0.73
self.axonmyelin2.L = 100
self.axonmyelin2.insert('pas')
self.axonmyelin2.e_pas = -63
self.axonmyelin2.g_pas = 5.60e-9
self.axonmyelin2.cm = 1.87e-11
self.axonmyelin2.Ra = 122
#Second Node of Ranvier
self.axonNOR2 = h.Section(name='axonNOR2')
self.axonNOR2.nseg = 1
self.axonNOR2.diam = 0.73
self.axonNOR2.cm = 0.77
self.axonNOR2.L = 4
self.axonNOR2.Ra = 122
self.axonNOR2.insert('Leak')
self.axonNOR2.e_Leak = pc_param['eleak']
self.axonNOR2.gmax_Leak = 0.0003
self.axonNOR2.insert('Nav1_6')
self.axonNOR2.gbar_Nav1_6 = pc_param['Nav1.6Nor2']
self.axonNOR2.ena = 60
self.axonNOR2.insert('Kv3_4')
self.axonNOR2.gkbar_Kv3_4 = pc_param['Kv3.4Nor2']
self.axonNOR2.ek = -88
self.axonNOR2.insert('cdp5')
self.axonNOR2.Nannuli_cdp5 = 0.326 + (1.94 * (self.axonNOR2.diam)) + (0.289*(self.axonNOR2.diam)*(self.axonNOR2.diam)) - ((3.33e-2)*(self.axonNOR2.diam)*(self.axonNOR2.diam)*(self.axonNOR2.diam)) + ((1.55e-3)*(self.axonNOR2.diam)*(self.axonNOR2.diam)*(self.axonNOR2.diam)*(self.axonNOR2.diam)) - (2.55e-5*(self.axonNOR2.diam)*(self.axonNOR2.diam)*(self.axonNOR2.diam)*(self.axonNOR2.diam)*(self.axonNOR2.diam))
self.axonNOR2.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.axonNOR2.diam)/1.4)
self.axonNOR2.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.axonNOR2.diam)/2.29)
self.axonNOR2.rf4_cdp5 = 0.003
self.axonNOR2.insert('Cav3_1')
self.axonNOR2.pcabar_Cav3_1 = pc_param['Cav3.1Nor2']
self.axonNOR2.insert('Cav2_1')
self.axonNOR2.pcabar_Cav2_1 = pc_param['Cav2.1Nor2']
self.axonNOR2.TotalPump_cdp5 = 5e-7
#Third part of the axon
self.axonmyelin3 = h.Section(name='axonmyelin3')
self.axonmyelin3.nseg = 1
self.axonmyelin3.diam = 0.73
self.axonmyelin3.L = 100
self.axonmyelin3.insert('pas')
self.axonmyelin3.e_pas = -63
self.axonmyelin3.g_pas = 5.60e-9
self.axonmyelin3.cm = 1.87e-11
self.axonmyelin3.Ra = 122
#Third Node of Ranvier
self.axonNOR3 = h.Section(name='axonNOR3')
self.axonNOR3.nseg = 1
self.axonNOR3.diam = 0.73
self.axonNOR3.cm = 0.77
self.axonNOR3.L = 4
self.axonNOR3.Ra = 122
self.axonNOR3.insert('Leak')
self.axonNOR3.e_Leak = pc_param['eleak']
self.axonNOR3.gmax_Leak = 0.0003
self.axonNOR3.insert('Nav1_6')
self.axonNOR3.gbar_Nav1_6 = pc_param['Nav1.6Nor3']
self.axonNOR3.ena = 60
self.axonNOR3.insert('Kv3_4')
self.axonNOR3.gkbar_Kv3_4 = pc_param['Kv3.4Nor3']
self.axonNOR3.ek = -88
self.axonNOR3.insert('cdp5')
self.axonNOR3.Nannuli_cdp5 = 0.326 + (1.94 * (self.axonNOR3.diam)) + (0.289*(self.axonNOR3.diam)*(self.axonNOR3.diam)) - ((3.33e-2)*(self.axonNOR3.diam)*(self.axonNOR3.diam)*(self.axonNOR3.diam)) + ((1.55e-3)*(self.axonNOR3.diam)*(self.axonNOR3.diam)*(self.axonNOR3.diam)*(self.axonNOR3.diam)) - (2.55e-5*(self.axonNOR3.diam)*(self.axonNOR3.diam)*(self.axonNOR3.diam)*(self.axonNOR3.diam)*(self.axonNOR3.diam))
self.axonNOR3.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.axonNOR3.diam)/1.4)
self.axonNOR3.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.axonNOR3.diam)/2.29)
self.axonNOR3.rf4_cdp5 = 0.003
self.axonNOR3.insert('Cav3_1')
self.axonNOR3.pcabar_Cav3_1 = pc_param['Cav3.1Nor3']
self.axonNOR3.insert('Cav2_1')
self.axonNOR3.pcabar_Cav2_1 = pc_param['Cav2.1Nor3']
self.axonNOR3.TotalPump_cdp5 = 5e-7
#Third part of the axon
self.axonmyelin4 = h.Section(name='axonmyelin4')
self.axonmyelin4.nseg = 1
self.axonmyelin4.diam = 0.73
self.axonmyelin4.L = 100
self.axonmyelin4.insert('pas')
self.axonmyelin4.e_pas = -63
self.axonmyelin4.g_pas = 5.60e-9
self.axonmyelin4.cm = 1.87e-11
self.axonmyelin4.Ra = 122
#Collateral.
self.axoncoll = h.Section(name='axoncoll')
self.axoncoll.nseg = 1
self.axoncoll.diam = 0.6
self.axoncoll.L = 100
self.axoncoll.Ra = 122
self.axoncoll.insert('Leak')
self.axoncoll.e_Leak = pc_param['eleak']
self.axoncoll.gmax_Leak = 0.0003
self.axoncoll.insert('Nav1_6')
self.axoncoll.gbar_Nav1_6 = pc_param['Nav1.6Axoncoll']
self.axoncoll.ena = 60
self.axoncoll.insert('Kv3_4')
self.axoncoll.gkbar_Kv3_4 = pc_param['Kv3.4Axoncoll']
self.axoncoll.ek = -88
self.axoncoll.insert('Cav3_1')
self.axoncoll.pcabar_Cav3_1 = pc_param['Cav3.1Axoncoll']
self.axoncoll.insert('Cav2_1')
self.axoncoll.pcabar_Cav2_1 = pc_param['Cav2.1Axoncoll']
self.axoncoll.insert('cdp5')
self.axoncoll.Nannuli_cdp5 = 0.326 + (1.94 * (self.axoncoll.diam)) + (0.289*(self.axoncoll.diam)*(self.axoncoll.diam)) - ((3.33e-2)*(self.axoncoll.diam)*(self.axoncoll.diam)*(self.axoncoll.diam)) + ((1.55e-3)*(self.axoncoll.diam)*(self.axoncoll.diam)*(self.axoncoll.diam)*(self.axoncoll.diam)) - (2.55e-5*(self.axoncoll.diam)*(self.axoncoll.diam)*(self.axoncoll.diam)*(self.axoncoll.diam)*(self.axoncoll.diam))
self.axoncoll.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.axoncoll.diam)/1.4)
self.axoncoll.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.axoncoll.diam)/2.29)
self.axoncoll.rf4_cdp5 = 0.003
self.axoncoll.TotalPump_cdp5 = 5e-7
self.axoncoll.push()
h.ion_style("ca_ion", 1, 1, 0, 1, 0)
self.axoncoll.eca = 137.52625
self.axoncoll.cai = h.cai0_ca_ion
self.axoncoll.cao = h.cao0_ca_ion
h.pop_section()
#Collateral second part
self.axoncoll2 = h.Section(name='axoncoll2')
self.axoncoll2.nseg = 1
self.axoncoll2.diam = 0.6
self.axoncoll2.L = 100
self.axoncoll2.Ra = 122
self.axoncoll2.insert('Leak')
self.axoncoll2.e_Leak = pc_param['eleak']
self.axoncoll2.gmax_Leak = 0.0003
self.axoncoll2.insert('Nav1_6')
self.axoncoll2.gbar_Nav1_6 = pc_param['Nav1.6Axoncoll']
self.axoncoll2.ena = 60
self.axoncoll2.insert('Kv3_4')
self.axoncoll2.gkbar_Kv3_4 = pc_param['Kv3.4Axoncoll']
self.axoncoll2.ek = -88
self.axoncoll2.insert('cdp5')
self.axoncoll2.Nannuli_cdp5 = 0.326 + (1.94 * (self.axoncoll2.diam)) + (0.289*(self.axoncoll2.diam)*(self.axoncoll2.diam)) - ((3.33e-2)*(self.axoncoll2.diam)*(self.axoncoll2.diam)*(self.axoncoll2.diam)) + ((1.55e-3)*(self.axoncoll2.diam)*(self.axoncoll2.diam)*(self.axoncoll2.diam)*(self.axoncoll2.diam)) - (2.55e-5*(self.axoncoll2.diam)*(self.axoncoll2.diam)*(self.axoncoll2.diam)*(self.axoncoll2.diam)*(self.axoncoll2.diam))
self.axoncoll2.Buffnull2_cdp5 = 64.2 - 57.3* math.exp(-(self.axoncoll2.diam)/1.4)
self.axoncoll2.rf3_cdp5 = 0.162 - 0.106* math.exp(-(self.axoncoll2.diam)/2.29)
self.axoncoll2.rf4_cdp5 = 0.003
self.axoncoll2.insert('Cav3_1')
self.axoncoll2.pcabar_Cav3_1 = pc_param['Cav3.1Axoncoll']
self.axoncoll2.insert('Cav2_1')
self.axoncoll2.pcabar_Cav2_1 = pc_param['Cav2.1Axoncoll']
self.axoncoll2.TotalPump_cdp5 = 5e-7
self.axoncoll2.push()
h.ion_style("ca_ion", 1, 1, 0, 1, 0)
self.axoncoll2.eca = 137.52625
self.axoncoll2.cai = h.cai0_ca_ion
self.axoncoll2.cao = h.cao0_ca_ion
h.pop_section()
#Connections of the axon
self.axonAIS.connect(self.soma,1,0)
self.axonAISK.connect(self.axonAIS,1,0)
self.axonmyelin.connect(self.axonAISK,1,0)
self.axonNOR.connect(self.axonmyelin,1,0)
self.axonmyelin2.connect(self.axonNOR,1,0)
self.axonNOR2.connect(self.axonmyelin2,1,0)
self.axonmyelin3.connect(self.axonNOR2,1,0)
self.axonNOR3.connect(self.axonmyelin3,1,0)
self.axonmyelin4.connect(self.axonNOR3,1,0)
self.axoncoll.connect(self.axonNOR2,1,0)
self.axoncoll2.connect(self.axoncoll,1,0)
#vectors for the time and voltage in the soma and axon.
self.rec_t = h.Vector()
self.rec_t.record(h._ref_t)
self.vm_soma = h.Vector()
self.vm_soma.record(self.soma(0.5)._ref_v)
self.vm_NOR3 = h.Vector()
self.vm_NOR3.record(self.axonNOR3(0.5)._ref_v)
#Synapses
self.dend_pf = []
self.dend_aa = []
self.dend_stl = []
for i in self.dend:
#Parallel fibers
if i.diam > 1.2 and i.diam < 3.5:
self.dend_pf.append(i)
#Ascending axon
if i.diam <= 1.2: #Ascending axon
self.dend_aa.append(i)
#Stellate cell
if i.diam > 1 and i.diam < 3.5:
self.dend_stl.append(i)
def createsyn(self, npf=0, naa=0, numstl=0):
pf_random = len(self.dend_pf)
aa_random = len(self.dend_aa)
stl_random = len(self.dend_stl)
self.pfrand = []
self.aarand = []
self.stlrand = []
self.PF_syn = []
self.AA_syn = []
self.stl_syn = []
for j in range(npf):
pf_random -= 1
i = random.randint(0, pf_random)
self.dend_pf[i], self.dend_pf[pf_random] = self.dend_pf[pf_random], self.dend_pf[i]
self.pfrand.append(self.dend_pf[pf_random])
self.PF_syn.append(Synapse_py3('pf',self,self.pfrand[j]))
#aa random
for m in range(naa):
aa_random -= 1
i = random.randint(0, aa_random)
self.dend_aa[i], self.dend_aa[aa_random] = self.dend_aa[aa_random], self.dend_aa[i]
self.aarand.append(self.dend_aa[aa_random])
self.AA_syn.append(Synapse_py3('aa',self,self.aarand[m]))
#aa random
for n in range(numstl):
stl_random -= 1
i = random.randint(0, stl_random)
self.dend_stl[i], self.dend_stl[stl_random] = self.dend_stl[stl_random], self.dend_stl[i]
self.stlrand.append(self.dend_stl[stl_random])
self.stl_syn.append(Synapse_py3('stl',self,self.stlrand[n]))