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MSN_builder.py
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#
'''
The MSN class defining the cell
'''
from neuron import h
from math import exp
import json
# Distributions:
'''
T-type Ca: g = 1.0/( 1 +np.exp{(x-70)/-4.5} )
naf (den): (0.1 + 0.9/(1 + np.exp((x-60.0)/10.0)))
'''
def calculate_distribution(d3, dist, a4, a5, a6, a7, g8):
'''
Used for setting the maximal conductance of a segment.
Scales the maximal conductance based on somatic distance and distribution type.
Parameters:
d3 = distribution type:
0 linear,
1 sigmoidal,
2 exponential
3 step function
dist = somatic distance of segment
a4-7 = distribution parameters
g8 = base conductance (similar to maximal conductance)
'''
if d3 == 0:
value = a4 + a5*dist
elif d3 == 1:
value = a4 + a5/(1 + exp((dist-a6)/a7) )
elif d3 == 2:
value = a4 + a5*exp((dist-a6)/a7)
elif d3 == 3:
if (dist > a6) and (dist < a7):
value = a4
else:
value = a5
if value < 0:
value = 0
value = value*g8
return value
# ======================= the MSN class ==================================================
class MSN:
def __init__(self, params=None, \
morphology='latest_WT-P270-20-14ak.swc' ):
Import = h.Import3d_SWC_read()
Import.input(morphology)
imprt = h.Import3d_GUI(Import, 0)
imprt.instantiate(None)
h.define_shape()
# h.cao0_ca_ion = 2 # default in nrn
h.celsius = 35
self._create_sectionlists()
self._set_nsegs()
self.v_init = -80
for sec in self.somalist:
for mech in [
"naf",
"kaf",
"kas",
"kdr",
"kir",
"cal12",
"cal13",
"can",
"car",
"cadyn",
"caldyn",
"sk",
"bk"
]:
sec.insert(mech)
for sec in self.axonlist:
for mech in [
"naf",
"kas"
]:
sec.insert(mech)
for sec in self.dendlist:
for mech in [
"naf",
"kaf",
"kas",
"kdr",
"kir",
"cal12",
"cal13",
"car",
"cat32",
"cat33",
"cadyn",
"caldyn",
"sk",
"bk"
]:
sec.insert(mech)
for sec in self.allseclist:
sec.Ra = 150
sec.cm = 1.0
sec.insert('pas')
#sec.g_pas = 1e-5 # set using json file
sec.e_pas = -70 # -73
sec.ena = 50
sec.ek = -85 # -90
with open(params) as file:
par = json.load(file)
self.distribute_channels("soma", "g_pas", 0, 1, 0, 0, 0, float(par['g_pas_all']['Value']))
self.distribute_channels("axon", "g_pas", 0, 1, 0, 0, 0, float(par['g_pas_all']['Value']))
self.distribute_channels("dend", "g_pas", 0, 1, 0, 0, 0, float(par['g_pas_all']['Value']))
self.distribute_channels("soma", "gbar_naf", 0, 1, 0, 0, 0, float(par['gbar_naf_somatic']['Value']))
self.distribute_channels("soma", "gbar_kaf", 0, 1, 0, 0, 0, float(par['gbar_kaf_somatic']['Value']))
self.distribute_channels("soma", "gbar_kas", 0, 1, 0, 0, 0, float(par['gbar_kas_somatic']['Value']))
self.distribute_channels("soma", "gbar_kdr", 0, 1, 0, 0, 0, float(par['gbar_kdr_somatic']['Value']))
self.distribute_channels("soma", "gbar_kir", 0, 1, 0, 0, 0, float(par['gbar_kir_somatic']['Value']))
self.distribute_channels("soma", "gbar_sk", 0, 1, 0, 0, 0, float(par['gbar_sk_somatic']['Value']))
self.distribute_channels("soma", "gbar_bk", 0, 1, 0, 0, 0, float(par['gbar_bk_somatic']['Value']))
self.distribute_channels("axon", "gbar_naf", 3, 1, 1.1, 30, 500, float(par['gbar_naf_axonal']['Value']))
self.distribute_channels("axon", "gbar_kas", 0, 1, 0, 0, 0, float(par['gbar_kas_axonal']['Value']))
self.distribute_channels("dend", "gbar_naf", 1, 0.1, 0.9, 60.0, 10.0, float(par['gbar_naf_basal']['Value']))
self.distribute_channels("dend", "gbar_kaf", 1, 1, 0.5, 120.0, -30.0, float(par['gbar_kaf_basal']['Value']))
self.distribute_channels("dend", "gbar_kas", 2, 1, 9.0, 0.0, -5.0, float(par['gbar_kas_basal']['Value']))
self.distribute_channels("dend", "gbar_kdr", 0, 1, 0, 0, 0, float(par['gbar_kdr_basal']['Value']))
self.distribute_channels("dend", "gbar_kir", 0, 1, 0, 0, 0, float(par['gbar_kir_basal']['Value']))
self.distribute_channels("dend", "gbar_sk", 0, 1, 0, 0, 0, float(par['gbar_sk_basal']['Value']))
self.distribute_channels("dend", "gbar_bk", 0, 1, 0, 0, 0, float(par['gbar_bk_basal']['Value']))
self.distribute_channels("soma", "pbar_cal12", 0, 1, 0, 0, 0, 1e-5)
self.distribute_channels("soma", "pbar_cal13", 0, 1, 0, 0, 0, 1e-6)
self.distribute_channels("soma", "pbar_car", 0, 1, 0, 0, 0, 1e-4)
self.distribute_channels("soma", "pbar_can", 0, 1, 0, 0, 0, 3e-5)
self.distribute_channels("dend", "pbar_cal12", 0, 1, 0, 0, 0, 1e-5)
self.distribute_channels("dend", "pbar_cal13", 0, 1, 0, 0, 0, 1e-6)
self.distribute_channels("dend", "pbar_car", 0, 1, 0, 0, 0, 1e-4)
self.distribute_channels("dend", "pbar_cat32", 1, 0, 1.0, 120.0, -30.0, 1e-7)
self.distribute_channels("dend", "pbar_cat33", 1, 0, 1.0, 120.0, -30.0, 1e-8)
def _create_sectionlists(self):
self.allsecnames = []
self.allseclist = h.SectionList()
for sec in h.allsec():
self.allsecnames.append(sec.name())
self.allseclist.append(sec=sec)
self.nsomasec = 0
self.somalist = h.SectionList()
for sec in h.allsec():
if sec.name().find('soma') >= 0:
self.somalist.append(sec=sec)
if self.nsomasec == 0:
self.soma = sec
self.nsomasec += 1
self.axonlist = h.SectionList()
for sec in h.allsec():
if sec.name().find('axon') >= 0:
self.axonlist.append(sec=sec)
self.dendlist = h.SectionList()
for sec in h.allsec():
if sec.name().find('dend') >= 0:
self.dendlist.append(sec=sec)
def _set_nsegs(self):
for sec in self.allseclist:
sec.nseg = 2*int(sec.L/40.0)+1
for sec in self.axonlist:
sec.nseg = 2 # two segments in axon initial segment
def distribute_channels(self, as1, as2, d3, a4, a5, a6, a7, g8):
h.distance(sec=self.soma)
for sec in self.allseclist:
# if right cellular compartment (axon, soma or dend)
if sec.name().find(as1) >= 0:
for seg in sec:
dist = h.distance(seg.x, sec=sec) - 7.06 + 5.6
val = calculate_distribution(d3, dist, a4, a5, a6, a7, g8)
cmd = 'seg.%s = %g' % (as2, val)
exec(cmd)