#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Feb 5 09:19:08 2022
@author: spiros
"""
from neuron import h
from neuron.units import um
h.load_file("stdrun.hoc")
class PyramidalCell:
def __init__(self, gid):
self._gid = gid
self._setup_morphology()
self._setup_topology()
self._create_lists()
self._setup_geometry()
self._setup_passive()
self._setup_segments()
self._setup_biophysics()
def _setup_morphology(self):
self.soma = h.Section(name='soma', cell=self)
self.radTprox = h.Section(name='radTprox', cell=self)
self.radTmed = h.Section(name='radTmed', cell=self)
self.radTdist1 = h.Section(name='radTdist1', cell=self)
self.radTdist2 = h.Section(name='radTdist2', cell=self)
self.radTdist3 = h.Section(name='radTdist3', cell=self)
self.lm_thick1 = h.Section(name='lm_thick1', cell=self)
self.lm_medium1 = h.Section(name='lm_medium1', cell=self)
self.lm_thin1a = h.Section(name='lm_thin1a', cell=self)
self.lm_thin1b = h.Section(name='lm_thin1b', cell=self)
self.lm_thick2 = h.Section(name='lm_thick2', cell=self)
self.lm_medium2 = h.Section(name='lm_medium2', cell=self)
self.lm_thin2a = h.Section(name='lm_thin2a', cell=self)
self.lm_thin2b = h.Section(name='lm_thin2b', cell=self)
self.rad_thick1 = h.Section(name='rad_thick1', cell=self)
self.rad_medium1 = h.Section(name='rad_medium1', cell=self)
self.rad_thin1a = h.Section(name='rad_thin1a', cell=self)
self.rad_thin1b = h.Section(name='rad_thin1b', cell=self)
self.rad_thick2 = h.Section(name='rad_thick2', cell=self)
self.rad_medium2 = h.Section(name='rad_medium2', cell=self)
self.rad_thin2a = h.Section(name='rad_thin2a', cell=self)
self.rad_thin2b = h.Section(name='rad_thin2b', cell=self)
self.oriprox1 = h.Section(name='oriprox1', cell=self)
self.oridist1a = h.Section(name='oridist1a', cell=self)
self.oridist1b = h.Section(name='oridist1b', cell=self)
self.oriprox2 = h.Section(name='oriprox2', cell=self)
self.oridist2a = h.Section(name='oridist2a', cell=self)
self.oridist2b = h.Section(name='oridist2b', cell=self)
self.axon = h.Section(name='axon', cell=self)
def _create_lists(self):
self.all = self.soma.wholetree()
self.ori = [sec for sec in self.all if sec.name().__contains__('ori')]
self.rad = [sec for sec in self.all if sec.name().__contains__('rad_')]
self.slm = [sec for sec in self.all if sec.name().__contains__('lm_')]
self.trunk = [sec for sec in self.all if sec.name().__contains__('radT')]
def _setup_topology(self):
# Connect sections
# Apical trunk
self.radTprox.connect(self.soma(1))
self.radTmed.connect(self.radTprox(1))
self.radTdist1.connect(self.radTmed(1))
self.radTdist2.connect(self.radTdist1(1))
self.radTdist3.connect(self.radTdist2(1))
# Apical oblique tree
# Right
self.rad_thick1.connect(self.radTmed(1))
self.rad_medium1.connect(self.rad_thick1(1))
self.rad_thin1a.connect(self.rad_medium1(1))
self.rad_thin1b.connect(self.rad_medium1(1))
# Left
self.rad_thick2.connect(self.radTmed(1))
self.rad_medium2.connect(self.rad_thick2(1))
self.rad_thin2a.connect(self.rad_medium2(1))
self.rad_thin2b.connect(self.rad_medium2(1))
# Apical tuft tree
# Right
self.lm_thick1.connect(self.radTdist3(1))
self.lm_medium1.connect(self.lm_thick1(1))
self.lm_thin1a.connect(self.lm_medium1(1))
self.lm_thin1b.connect(self.lm_medium1(1))
# Left
self.lm_thick2.connect(self.radTdist3(1))
self.lm_medium2.connect(self.lm_thick2(1))
self.lm_thin2a.connect(self.lm_medium2(1))
self.lm_thin2b.connect(self.lm_medium2(1))
# Basal tree
# Right
self.oriprox1.connect(self.soma(0))
self.oridist1a.connect(self.oriprox1(1))
self.oridist1b.connect(self.oriprox1(1))
# Left
self.oriprox2.connect(self.soma(0))
self.oridist2a.connect(self.oriprox2(1))
self.oridist2b.connect(self.oriprox2(1))
# Axon
self.axon.connect(self.soma(0))
def _setup_geometry(self):
self.soma.L = self.soma.diam = 10 * um
self.radTprox.L, self.radTprox.diam = 80 * um, 3 * um
self.radTmed.L, self.radTmed.diam = 70 * um, 2.5 * um
self.radTdist1.L, self.radTdist1.diam = 50 * um, 2 * um
self.radTdist2.L, self.radTdist2.diam = 50 * um, 1.75 * um
self.radTdist3.L, self.radTdist3.diam = 50 * um, 1.5 * um
self.lm_thick1.L, self.lm_thick1.diam = 50 * um, 0.95 * um
self.lm_medium1.L, self.lm_medium1.diam = 50 * um, 0.9 * um
self.lm_thin1a.L, self.lm_thin1a.diam = 75 * um, 0.6 * um
self.lm_thin1b.L, self.lm_thin1b.diam = 75 * um, 0.6 * um
self.lm_thick2.L, self.lm_thick2.diam = 50 * um, 0.95 * um
self.lm_medium2.L, self.lm_medium2.diam = 50 * um, 0.90 * um
self.lm_thin2a.L, self.lm_thin2a.diam = 75 * um, 0.6 * um
self.lm_thin2b.L, self.lm_thin2b.diam = 75 * um, 0.6 * um
self.rad_thick1.L, self.rad_thick1.diam = 50 * um, 1.9 * um
self.rad_medium1.L, self.rad_medium1.diam = 50 * um, 1.5 * um
self.rad_thin1a.L, self.rad_thin1a.diam = 75 * um, 0.95 * um
self.rad_thin1b.L, self.rad_thin1b.diam = 75 * um, 0.95 * um
self.rad_thick2.L, self.rad_thick2.diam = 50 * um, 1.9 * um
self.rad_medium2.L, self.rad_medium2.diam = 50 * um, 1.5 * um
self.rad_thin2a.L, self.rad_thin2a.diam = 75 * um, 0.95 * um
self.rad_thin2b.L, self.rad_thin2b.diam = 75 * um, 0.95 * um
self.oriprox1.L, self.oriprox1.diam = 75 * um, 1.6 * um
self.oridist1a.L, self.oridist1a.diam = 75 * um, 1.1 * um
self.oridist1b.L, self.oridist1b.diam = 75 * um, 1.1 * um
self.oriprox2.L, self.oriprox2.diam = 75 * um, 1.6 * um
self.oridist2a.L, self.oridist2a.diam = 75 * um, 1.1 * um
self.oridist2b.L, self.oridist2b.diam = 75 * um, 1.1 * um
self.axon.L, self.axon.diam = 150 * um, 1 * um
def _setup_passive(self):
Ra_soma = 300.0 # Axial resistance in Ohm * cm
# Soma
self.soma.Ra = Ra_soma
self.soma.cm = 1 # Membrane capacitance in uF/cm2
# Axon
self.axon.Ra = Ra_soma
self.axon.cm = 1 # Membrane capacitance in uF/cm2
# Apical trunk
Ra_trunk = [j*Ra_soma for j in [0.95, 0.90, 0.85, 0.75, 0.72]]
for i, sec in enumerate(self.trunk):
sec.Ra = Ra_trunk[i]
sec.cm = 2.2 # Membrane capacitance in uF/cm2
# Apical tuft
for i, sec in enumerate(self.slm):
sec.Ra = 0.5*Ra_soma
sec.cm = 3.0 # Membrane capacitance in uF/cm2
# Oblique dendrtites
for i, sec in enumerate(self.rad):
sec.Ra = 0.5*Ra_soma
sec.cm = 3.0 # Membrane capacitance in uF/cm2
# Basal dendrites
for i, sec in enumerate(self.ori):
sec.Ra = Ra_soma
sec.cm = 3.0 # Membrane capacitance in uF/cm2
def _setup_segments(self):
# Create segments based on `lambda_f`
d_lambda = 0.1
frequency = 100
for sec in self.all:
sec.nseg = int((sec.L/(d_lambda*h.lambda_f(frequency, sec=sec)) + 0.9) / 2)*2 + 1
def _setup_biophysics(self):
# =====================================================================
# General Parameters
gna_hh_dend = 0.007 # sodium (Na+) dend channel
gk_hh_dend = 0.007/8.065 # Delayed rectified potassium (K+) channel
gka_soma = 0.0075 # A-type K @ soma
gka_dend = 0.048672 # A-type @ dends
gh_soma = 0.000015 # for sag ratio
gkm_trunk = 0.0006 # K m-type @ trunk
gCaL_trunk = .1*0.000316 # Ca L-type @ trunk
gkca_trunk = 0.0005 # slow AHP K+ current
Rm_soma = 200000 # ohm cm2
Ra_soma = 300.0 # ohm cm
# =====================================================================
# =====================================================================
# Somatic compartment
self.soma.Ra = Ra_soma
self.soma.cm = 1
# Na+, Kdr, and leak channels
self.soma.insert('hha2')
for seg in self.soma:
seg.hha2.gnabar = 0.035
seg.hha2.gkbar = 0.0014
seg.hha2.gl = 0.01*1/Rm_soma
seg.hha2.el = -70
# h channels
self.soma.insert('h')
for seg in self.soma:
seg.h.ghbar = gh_soma
seg.h.vhalf = -90
seg.h.eh = -10
# A-type K+ channels
self.soma.insert('kap')
for seg in self.soma:
seg.kap.gkabar = gka_soma
# m-type K+ channels
self.soma.insert('km')
for seg in self.soma:
seg.km.gbar = 0.0166
# medium Ca2+-dependent K+ channels (mAHP)
self.soma.insert('mykca')
for seg in self.soma:
seg.mykca.gkbar = 0.09075
# slow Ca2+-dependent K+ channels (sAHP)
self.soma.insert('kca')
for seg in self.soma:
seg.kca.gbar = gkca_trunk
# T-type Ca2+ channels
self.soma.insert('cat')
for seg in self.soma:
seg.cat.gcatbar = 0.00005
# R-type Ca2+ channels
self.soma.insert('somacar')
for seg in self.soma:
seg.somacar.gcabar = 0.003
# L-type Ca2+ channels
self.soma.insert('cal')
for seg in self.soma:
seg.cal.gcalbar = 0.007
# Constant current for Vrest calibration
self.soma.insert('constant')
for seg in self.soma:
seg.constant.ic = 0.008
# =====================================================================
# =====================================================================
# Axonal compartment(s)
Rm_axon = 200000
# Na+, Kdr, and leak channels
self.axon.insert('hha2')
for seg in self.axon:
seg.hha2.gnabar = 1.5
seg.hha2.gkbar = 0.1
seg.hha2.gl = 0.01*1/Rm_axon
seg.hha2.el = -70
# m-type K+ channels
self.axon.insert('km')
for seg in self.axon:
seg.km.gbar = 0.000003
# Constant current for Vrest calibration
self.axon.insert('constant')
for seg in self.axon:
seg.constant.ic = -0.001
# =====================================================================
# =====================================================================
# Apical trunk -- all compartments
Rm_trunk = [190000, 150000, 35000, 35000, 35000]
Ra_trunk = [j*Ra_soma for j in [0.95, 0.9, 0.85, 0.75, 0.72]]
gka_trunk = [2.4*gka_soma] + [j*gka_dend for j in [200/350, 270/350, 340/350, 1]]
gCaL_scale = [0.1, 0.2, 0.4, 0.6, 0.8]
gh_trunk = [j*gh_soma for j in [1.2, 4, 6, 6.5, 7]]
gkca_ = [j*gkca_trunk for j in [1, 1, 0.1, 0.1, 0.1]]
gcagk = [0.066, 0.066, 0.004125, 0.004125, 0.004125]
ic_ = [-0.0016, -0.0022, -0.0028, -0.0034, -0.004]
for i, sec in enumerate(self.trunk):
sec.Ra = Ra_trunk[i]
sec.cm = 2.2
# Na+ and Kdr channels
sec.insert('hha_old')
for seg in sec:
seg.hha_old.gl = 0.01*1/Rm_trunk[i]
seg.hha_old.gnabar = 2.0*gna_hh_dend
seg.hha_old.gkbar = 2.0*gk_hh_dend
seg.hha_old.el = -70
seg.hha_old.ar2 = 0.9
# h channels
sec.insert('h')
for seg in sec:
seg.h.ghbar = gh_trunk[i]
seg.h.vhalf = -90
seg.h.eh = -10
# A-type K+ channels
if sec.name().__contains__('radTprox'):
sec.insert('kap')
for seg in sec:
seg.kap.gkabar = gka_trunk[i]
else:
sec.insert('kad')
for seg in sec:
seg.kad.gkabar = gka_trunk[i]
# m-type K+ channels
sec.insert('km')
for seg in sec:
seg.km.gbar = gkm_trunk
# L-type Ca2+ channels
sec.insert('calH')
for seg in sec:
seg.calH.gcalbar = gCaL_scale[i]*gCaL_trunk
# slow Ca2+-dependent K+ channels (sAHP)
sec.insert('kca')
for seg in sec:
seg.kca.gbar = gkca_[i]
# medium Ca2+-dependent K+ channels (mAHP)
sec.insert('mykca')
for seg in sec:
seg.mykca.gkbar = gcagk[i]
# T-type Ca2+ channel
sec.insert('cat')
for seg in sec:
seg.cat.gcatbar = 0.0004
# R-type Ca2+ channel
sec.insert('car')
for seg in sec:
seg.car.gcabar = 0.1*0.003
# Constant current for Vrest calibration
sec.insert('constant')
for seg in sec:
seg.constant.ic = ic_[i]
# =====================================================================
# =====================================================================
# Apical tuft (s.lm.) -- all compartments
Rm_slm = [12000]*8
for i, sec in enumerate(self.slm):
sec.Ra = 0.5*Ra_soma
sec.cm = 3.0
# Na+ and Kdr channels
sec.insert('hha_old')
for seg in sec:
seg.hha_old.gl = 0.01*1/Rm_slm[i]
seg.hha_old.gnabar = 2.2*gna_hh_dend
seg.hha_old.gkbar = 2.2*gk_hh_dend
seg.hha_old.el = -70
seg.hha_old.ar2 = 0.95
# h channels
sec.insert('h')
for seg in sec:
seg.h.ghbar = 8*gh_soma
seg.h.vhalf = -90
seg.h.eh = -10
# A-type K+ channels
sec.insert('kad')
for seg in sec:
# K channels
seg.kad.gkabar = gka_dend
# m-type K+ channel
sec.insert('km')
for seg in sec:
seg.km.gbar = 2*gkm_trunk
# L-type Ca2+ channels
sec.insert('calH')
for seg in sec:
seg.calH.gcalbar = 0.1*gCaL_trunk
# medium Ca2+-dependent K+ channel (mAHP)
sec.insert('mykca')
for seg in sec:
seg.mykca.gkbar = 0.004125
# slow Ca2+-dependent K+ channel (sAHP)
sec.insert('kca')
for seg in sec:
seg.kca.gbar = 0.1*gkca_trunk
# Constant current for Vrest calibration
sec.insert('constant')
for seg in sec:
seg.constant.ic = -0.004
# =====================================================================
# =====================================================================
# Apical oblique (s.rad.) -- all compartments
Rm_rad = [13000, 12000, 12000, 12000]*2
for i, sec in enumerate(self.rad):
sec.Ra = 0.5*Ra_soma
sec.cm = 3.0
# Na+, Kdr, and leak channels
sec.insert('hha_old')
for seg in sec:
seg.hha_old.gl = 0.01*1/Rm_rad[i]
seg.hha_old.gnabar = 1.2*gna_hh_dend
seg.hha_old.gkbar = 1.2*gk_hh_dend
seg.hha_old.el = -70
# h channels
sec.insert('h')
for seg in sec:
seg.h.ghbar = 4*gh_soma
seg.h.vhalf = -80
seg.h.eh = -10
# A-type K+ channels
sec.insert('kad')
for seg in sec:
seg.kad.gkabar = gka_dend * 300/350
# m-type K+ channels
sec.insert('km')
for seg in sec:
seg.km.gbar = 2*gkm_trunk
# L-type Ca2+ channels
sec.insert('calH')
for seg in sec:
seg.calH.gcalbar = 0.4*gCaL_trunk
# medium Ca2+-dependent K+ channel (mAHP)
sec.insert('mykca')
for seg in sec:
seg.mykca.gkbar = 0.004125
# slow Ca2+-dependent K+ channel (sAHP)
sec.insert('kca')
for seg in sec:
seg.kca.gbar = 0.1*gkca_trunk
# Constant current for Vrest calibration
sec.insert('constant')
for seg in sec:
seg.constant.ic = -0.0024
# =====================================================================
# =====================================================================
# Basal dendrites (s.o.) -- all compartments
Rm_ori = [18000]*6
for i, sec in enumerate(self.ori):
sec.Ra = Ra_soma
sec.cm = 3.0
# Na+, Kdr, and leak channels
sec.insert('hha_old')
for seg in sec:
seg.hha_old.gl = 0.01*1/Rm_ori[i]
seg.hha_old.gnabar = gna_hh_dend
seg.hha_old.gkbar = gk_hh_dend
seg.hha_old.el = -70
# h channels
gh_basal = [j*gh_soma for j in [1, 1.5, 1.5]*2]
sec.insert('h')
for seg in sec:
seg.h.ghbar = gh_basal[i]
seg.h.vhalf = -81
seg.h.eh = -10
# A-type K+ channels
sec.insert('kap')
for seg in sec:
seg.kap.gkabar = gka_soma
# m-type K+ channels
sec.insert('km')
for seg in sec:
seg.km.gbar = gkm_trunk
# slow Ca2+-dependent K+ channel (sAHP)
sec.insert('kca')
for seg in sec:
seg.kca.gbar = gkca_trunk
# medium Ca2+-dependent K+ channel (mAHP)
sec.insert('mykca')
for seg in sec:
seg.mykca.gkbar = 0.0165
# Constant current for Vrest calibration
sec.insert('constant')
for seg in sec:
seg.constant.ic = -0.001
# =====================================================================
# =====================================================================
# All compartments
for sec in self.all:
sec.insert('cad')
sec.ena = 50 # Na reversal potential in mV
sec.ek = -80 # K reversal potential in mV
sec.eca = 140 # Ca reversal potential in mV
# =====================================================================
def __repr__(self):
return 'PyramidalCell[{}]'.format(self._gid)
class CCKCell:
def __init__(self, gid):
self._gid = gid
self._setup_morphology()
self._setup_topology()
self._create_lists()
self._setup_geometry()
self._setup_passive()
self._setup_segments()
self._setup_biophysics()
def _setup_morphology(self):
self.soma = h.Section(name='soma', cell=self)
self.radProx1 = h.Section(name='radProx1', cell=self)
self.radMed1 = h.Section(name='radMed1', cell=self)
self.radDist1 = h.Section(name='radDist1', cell=self)
self.lmM1 = h.Section(name='lmM1', cell=self)
self.lmt1 = h.Section(name='lmt1', cell=self)
self.radProx2 = h.Section(name='radProx2', cell=self)
self.radMed2 = h.Section(name='radMed2', cell=self)
self.radDist2 = h.Section(name='radDist2', cell=self)
self.lmM2 = h.Section(name='lmM2', cell=self)
self.lmt2 = h.Section(name='lmt2', cell=self)
self.oriProx1 = h.Section(name='oriProx1', cell=self)
self.oriMed1 = h.Section(name='oriMed1', cell=self)
self.oriDist1 = h.Section(name='oriDist1', cell=self)
self.oriProx2 = h.Section(name='oriProx2', cell=self)
self.oriMed2 = h.Section(name='oriMed2', cell=self)
self.oriDist2 = h.Section(name='oriDist2', cell=self)
def _create_lists(self):
self.all = self.soma.wholetree()
self.dends = [sec for sec in self.all if not sec.name().__contains__('soma')]
def _setup_topology(self):
# Connect sections
self.radProx1.connect(self.soma(0))
self.radMed1.connect(self.radProx1(1))
self.radDist1.connect(self.radMed1(1))
self.lmM1.connect(self.radDist1(1))
self.lmt1.connect(self.lmM1(1))
self.radProx2.connect(self.soma(1))
self.radMed2.connect(self.radProx2(1))
self.radDist2.connect(self.radMed2(1))
self.lmM2.connect(self.radDist2(1))
self.lmt2.connect(self.lmM2(1))
self.oriProx1.connect(self.soma(0))
self.oriMed1.connect(self.oriProx1(1))
self.oriDist1.connect(self.oriMed1(1))
self.oriProx2.connect(self.soma(1))
self.oriMed2.connect(self.oriProx2(1))
self.oriDist2.connect(self.oriMed2(1))
def _setup_geometry(self):
self.soma.L, self.soma.diam = 20 * um, 10 * um
self.radProx1.L, self.radProx1.diam = 100 * um, 4 * um
self.radMed1.L, self.radMed1.diam = 100 * um, 3 * um
self.radDist1.L, self.radDist1.diam = 200 * um, 2 * um
self.lmM1.L, self.lmM1.diam = 100 * um, 1.5 * um
self.lmt1.L, self.lmt1.diam = 100 * um, 1 * um
self.radProx2.L, self.radProx2.diam = 100 * um, 4 * um
self.radMed2.L, self.radMed2.diam = 100 * um, 3 * um
self.radDist2.L, self.radDist2.diam = 200 * um, 2 * um
self.lmM2.L, self.lmM2.diam = 100 * um, 1.5 * um
self.lmt2.L, self.lmt2.diam = 100 * um, 1 * um
self.oriProx1.L, self.oriProx1.diam = 100 * um, 2 * um
self.oriMed1.L, self.oriMed1.diam = 100 * um, 1.5 * um
self.oriDist1.L, self.oriDist1.diam = 100 * um, 1 * um
self.oriProx2.L, self.oriProx2.diam = 100 * um, 2 * um
self.oriMed2.L, self.oriMed2.diam = 100 * um, 1.5 * um
self.oriDist2.L, self.oriDist2.diam = 100 * um, 1 * um
def _setup_passive(self):
for sec in self.all:
sec.Ra = 100 # Axial resistance
sec.cm = 1.1 # membrane capacitance
def _setup_segments(self):
# Create segments based on `lambda_f`
d_lambda = 0.1
frequency = 100
for sec in self.all:
sec.nseg = int((sec.L/(d_lambda*h.lambda_f(frequency, sec=sec)) + 0.9) / 2)*2 + 1
def _setup_biophysics(self):
# =====================================================================
# All compartments
for sec in self.all:
# HH channels (Na, Kdr, and leak)
sec.insert('ichan2cck')
for seg in sec:
seg.ichan2cck.gnabar = 0.188*0.9*1.2
seg.ichan2cck.gkbar = 0.013*0.85*1.2
seg.ichan2cck.gl = 0.00006*0.61
seg.ichan2cck.el = -70
# Ca buffering mechanism
sec.insert('ccanl')
# A-type K+ channel
sec.insert('borgka')
for seg in sec:
seg.borgka.gkabar = 0.0006
# N-type Ca2+ channel
sec.insert('nca')
for seg in sec:
seg.nca.gncabar = 0.0000016
# L-type Ca2+ channel
sec.insert('lca')
for seg in sec:
seg.lca.glcabar = 0.000025
# Ca2+-dependent K+ (SK) channel
sec.insert('gskch')
for seg in sec:
seg.gskch.gskbar = 0.0004
# Ca2+ and Voltage-dependent K+ (BK) channel
sec.insert('mykca')
for seg in sec:
seg.mykca.gkbar = 0.072
# Ih
sec.insert('Ih')
for seg in sec:
seg.Ih.gkhbar = 0.000025
seg.Ih.alpha = 100
seg.Ih.slope = 10
seg.Ih.amp = 0.01
seg.Ih.taumin = 20
# Properties
sec.eca = 130 # Ca reversal potential in mV
sec.ena = 55 # Na reversal potential in mV
sec.ek = -85 # K reversal potential in mV
sec.eh = -40 # h-channel reversal potential in mV
# =====================================================================
# =====================================================================
self.soma.insert('constant')
for seg in self.soma:
seg.constant.ic = -0.00455
# =====================================================================
def __repr__(self):
return 'CCKCell[{}]'.format(self._gid)
class OLMCell:
def __init__(self, gid):
self._gid = gid
self._setup_morphology()
self._setup_topology()
self._create_lists()
self._setup_geometry()
self._setup_passive()
self._setup_segments()
self._setup_biophysics()
def _setup_morphology(self):
self.soma = h.Section(name='soma', cell=self)
self.dend1 = h.Section(name='dend1', cell=self)
self.dend2 = h.Section(name='dend2', cell=self)
self.axon = h.Section(name='axon', cell=self)
def _create_lists(self):
self.all = self.soma.wholetree()
self.dends = [sec for sec in self.all if sec.name().__contains__('dend')]
def _setup_topology(self):
# Connect sections
self.dend1.connect(self.soma(0))
self.dend2.connect(self.soma(1))
self.axon.connect(self.soma(0.5))
def _setup_geometry(self):
self.soma.L, self.soma.diam = 25 * um, 10 * um
self.dend1.L, self.dend1.diam = 250 * um, 3 * um
self.dend2.L, self.dend2.diam = 250 * um, 3 * um
self.axon.L, self.axon.diam = 150 * um, 1.5 * um
def _setup_passive(self):
for sec in self.all:
sec.Ra = 150 # Axial resistance
sec.cm = 1.6 # membrane capacitance
def _setup_segments(self):
# Create segments based on `lambda_f`
d_lambda = 0.1
frequency = 100
for sec in self.all:
sec.nseg = int((sec.L/(d_lambda*h.lambda_f(frequency, sec=sec)) + 0.9) / 2)*2 + 1
def _setup_biophysics(self):
Rm = 20000*2
# =====================================================================
# Soma
self.soma.insert('IA')
for seg in self.soma:
seg.IA.gkAbar = 0.008*1.5
self.soma.insert('Ih')
for seg in self.soma:
seg.Ih.gkhbar = 0.00035*0.1*0.6*0.025*26
seg.Ih.alpha = 125
seg.Ih.slope = 12
self.soma.insert('k_olm')
for seg in self.soma:
seg.k_olm.gkbar = 0.0319*1.5
self.soma.insert('na_olm')
for seg in self.soma:
seg.na_olm.gnabar = 0.0107*1.2*2
seg.na_olm.gl = 1/Rm*2
seg.na_olm.el = -67
self.soma.insert('constant')
for seg in self.soma:
seg.constant.ic = -0.012
# =====================================================================
# =====================================================================
# Dendrites
for sec in self.dends:
sec.insert('IA')
for seg in sec:
seg.IA.gkAbar = 0.008*0.9
sec.insert('Ih')
for seg in sec:
seg.Ih.gkhbar = 0.00035*0.06*0.025*26
seg.Ih.alpha = 125
seg.Ih.slope = 12
sec.insert('k_olm')
for seg in sec:
seg.k_olm.gkbar = 20*0.023
seg.k_olm.vhalf_a = 20
seg.k_olm.qa = 21
seg.k_olm.vhalf_b = 30
seg.k_olm.qb = 12
sec.insert('na_olm')
for seg in sec:
seg.na_olm.gnabar = 2*0.0117*2
seg.na_olm.gl = 1/Rm
seg.na_olm.el = -65
seg.na_olm.vhalfa_m = 39
seg.na_olm.vhalfb_m = 64
seg.na_olm.vhalfa_h = 65
seg.na_olm.vhalfb_h = 35
# =====================================================================
# =====================================================================
# Axon
self.axon.insert('k_olm')
for seg in self.axon:
seg.k_olm.gkbar = 0.05104
self.axon.insert('na_olm')
for seg in self.axon:
seg.na_olm.gnabar = 0.01712*2
seg.na_olm.gl = 1/Rm
seg.na_olm.el = -67
# =====================================================================
def __repr__(self):
return 'OLMCell[{}]'.format(self._gid)
class VIPCCKCell:
def __init__(self, gid):
self._gid = gid
self._setup_morphology()
self._setup_topology()
self._create_lists()
self._setup_geometry()
self._setup_passive()
self._setup_segments()
self._setup_biophysics()
def _setup_morphology(self):
self.soma = h.Section(name='soma', cell=self)
self.radProx1 = h.Section(name='radProx1', cell=self)
self.radMed1 = h.Section(name='radMed1', cell=self)
self.radDist1 = h.Section(name='radDist1', cell=self)
self.lmM1 = h.Section(name='lmM1', cell=self)
self.lmt1 = h.Section(name='lmt1', cell=self)
self.radProx2 = h.Section(name='radProx2', cell=self)
self.radMed2 = h.Section(name='radMed2', cell=self)
self.radDist2 = h.Section(name='radDist2', cell=self)
self.lmM2 = h.Section(name='lmM2', cell=self)
self.lmt2 = h.Section(name='lmt2', cell=self)
self.oriProx1 = h.Section(name='oriProx1', cell=self)
self.oriMed1 = h.Section(name='oriMed1', cell=self)
self.oriDist1 = h.Section(name='oriDist1', cell=self)
self.oriProx2 = h.Section(name='oriProx2', cell=self)
self.oriMed2 = h.Section(name='oriMed2', cell=self)
self.oriDist2 = h.Section(name='oriDist2', cell=self)
def _create_lists(self):
self.all = self.soma.wholetree()
self.dends = [sec for sec in self.all if not sec.name().__contains__('soma')]
def _setup_topology(self):
# Connect sections
self.radProx1.connect(self.soma(0))
self.radMed1.connect(self.radProx1(1))
self.radDist1.connect(self.radMed1(1))
self.lmM1.connect(self.radDist1(1))
self.lmt1.connect(self.lmM1(1))
self.radProx2.connect(self.soma(1))
self.radMed2.connect(self.radProx2(1))
self.radDist2.connect(self.radMed2(1))
self.lmM2.connect(self.radDist2(1))
self.lmt2.connect(self.lmM2(1))
self.oriProx1.connect(self.soma(0))
self.oriMed1.connect(self.oriProx1(1))
self.oriDist1.connect(self.oriMed1(1))
self.oriProx2.connect(self.soma(1))
self.oriMed2.connect(self.oriProx2(1))
self.oriDist2.connect(self.oriMed2(1))
def _setup_geometry(self):
self.soma.L, self.soma.diam = 20 * um, 10 * um
self.radProx1.L, self.radProx1.diam = 50 * um, 4 * um
self.radMed1.L, self.radMed1.diam = 50 * um, 3 * um
self.radDist1.L, self.radDist1.diam = 100 * um, 2 * um
self.lmM1.L, self.lmM1.diam = 50 * um, 1.5 * um
self.lmt1.L, self.lmt1.diam = 50 * um, 1 * um
self.radProx2.L, self.radProx2.diam = 50 * um, 4 * um
self.radMed2.L, self.radMed2.diam = 50 * um, 3 * um
self.radDist2.L, self.radDist2.diam = 100 * um, 2 * um
self.lmM2.L, self.lmM2.diam = 50 * um, 1.5 * um
self.lmt2.L, self.lmt2.diam = 50 * um, 1 * um
self.oriProx1.L, self.oriProx1.diam = 50 * um, 2 * um
self.oriMed1.L, self.oriMed1.diam = 50 * um, 1.5 * um
self.oriDist1.L, self.oriDist1.diam = 50 * um, 1 * um
self.oriProx2.L, self.oriProx2.diam = 50 * um, 2 * um
self.oriMed2.L, self.oriMed2.diam = 50 * um, 1.5 * um
self.oriDist2.L, self.oriDist2.diam = 50 * um, 1 * um
def _setup_passive(self):
for sec in self.all:
sec.Ra = 100 # Axial resistance
sec.cm = 1.3 # membrane capacitance
def _setup_segments(self):
# Create segments based on `lambda_f`
d_lambda = 0.1
frequency = 100
for sec in self.all:
sec.nseg = int((sec.L/(d_lambda*h.lambda_f(frequency, sec=sec)) + 0.9) / 2)*2 + 1
def _setup_biophysics(self):
# =====================================================================
# All compartments
for sec in self.all:
# HH channels (Na, Kdr, and leak)
sec.insert('ichan2vip')
for seg in sec:
seg.ichan2vip.gnabar = 0.18/0.1*2
seg.ichan2vip.gkbar = 0.013/0.1*2
seg.ichan2vip.gl = 0.00018/2*0.1*2
seg.ichan2vip.el = -65
# Ca buffering mechanism
sec.insert('ccanl')
for seg in sec:
seg.ccanl.catau = 70
# A-type K+ channel
sec.insert('borgka')
for seg in sec:
seg.borgka.gkabar = 0.00015
# N-type Ca2+ channel
sec.insert('nca')
for seg in sec:
seg.nca.gncabar = 0.0008*0.15
# L-type Ca2+ channel
sec.insert('lca')
for seg in sec:
seg.lca.glcabar = 0.005*0.15
# Ca2+-dependent K+ (SK) channel
sec.insert('gskch')
for seg in sec:
seg.gskch.gskbar = 0.000002*2*10000
seg.gskch.beta = 0.00025*0.5
# Ca2+ and Voltage-dependent K+ (BK) channel
sec.insert('mykca')
for seg in sec:
seg.mykca.gkbar = 0.0002*10
# Ih
sec.insert('Ih')
for seg in sec:
seg.Ih.gkhbar = 0.000025*1.1
seg.Ih.alpha = 100
seg.Ih.slope = 8
seg.Ih.amp = 0.001
seg.Ih.taumin = 30
sec.ena = 55 # Na reversal potential in mV
sec.ek = -85 # K reversal potential in mV
sec.eca = 130 # Ca reversal potential in mV
sec.eh = -40 # h-channel reversal potential in mV
# =====================================================================
# =====================================================================
self.soma.insert('constant')
for seg in self.soma:
seg.constant.ic = -0.0003
# =====================================================================
def __repr__(self):
return 'VIPCCKCell[{}]'.format(self._gid)
class VIPCRCell:
def __init__(self, gid):
self._gid = gid
self._setup_morphology()
self._setup_topology()
self._create_lists()
self._setup_geometry()
self._setup_passive()
self._setup_segments()
self._setup_biophysics()
def _setup_morphology(self):
self.soma = h.Section(name='soma', cell=self)
self.radProx1 = h.Section(name='radProx1', cell=self)
self.radMed1 = h.Section(name='radMed1', cell=self)
self.radDist1 = h.Section(name='radDist1', cell=self)
self.lmM1 = h.Section(name='lmM1', cell=self)
self.lmt1 = h.Section(name='lmt1', cell=self)
self.radProx2 = h.Section(name='radProx2', cell=self)
self.radMed2 = h.Section(name='radMed2', cell=self)
self.radDist2 = h.Section(name='radDist2', cell=self)
self.lmM2 = h.Section(name='lmM2', cell=self)
self.lmt2 = h.Section(name='lmt2', cell=self)
self.oriProx1 = h.Section(name='oriProx1', cell=self)
self.oriMed1 = h.Section(name='oriMed1', cell=self)
self.oriDist1 = h.Section(name='oriDist1', cell=self)
self.oriProx2 = h.Section(name='oriProx2', cell=self)
self.oriMed2 = h.Section(name='oriMed2', cell=self)
self.oriDist2 = h.Section(name='oriDist2', cell=self)
def _create_lists(self):
self.all = self.soma.wholetree()
self.dends = [sec for sec in self.all if not sec.name().__contains__('soma')]
def _setup_topology(self):
# Connect sections
self.radProx1.connect(self.soma(0))
self.radMed1.connect(self.radProx1(1))
self.radDist1.connect(self.radMed1(1))
self.lmM1.connect(self.radDist1(1))
self.lmt1.connect(self.lmM1(1))
self.radProx2.connect(self.soma(1))
self.radMed2.connect(self.radProx2(1))
self.radDist2.connect(self.radMed2(1))
self.lmM2.connect(self.radDist2(1))
self.lmt2.connect(self.lmM2(1))
self.oriProx1.connect(self.soma(0))
self.oriMed1.connect(self.oriProx1(1))
self.oriDist1.connect(self.oriMed1(1))
self.oriProx2.connect(self.soma(1))
self.oriMed2.connect(self.oriProx2(1))
self.oriDist2.connect(self.oriMed2(1))
def _setup_passive(self):
for sec in self.all:
sec.Ra = 150 # Axial resistance
sec.cm = 1.4 # membrane capacitance
def _setup_segments(self):
# Create segments based on `lambda_f`
d_lambda = 0.1
frequency = 100
for sec in self.all:
sec.nseg = int((sec.L/(d_lambda*h.lambda_f(frequency, sec=sec)) + 0.9) / 2)*2 + 1
def _setup_geometry(self):
self.soma.L, self.soma.diam = 20 * um, 10 * um
self.radProx1.L, self.radProx1.diam = 100 * um, 4 * um
self.radMed1.L, self.radMed1.diam = 100 * um, 3 * um
self.radDist1.L, self.radDist1.diam = 200 * um, 2 * um
self.lmM1.L, self.lmM1.diam = 100 * um, 1.5 * um
self.lmt1.L, self.lmt1.diam = 100 * um, 1 * um
self.radProx2.L, self.radProx2.diam = 100 * um, 4 * um
self.radMed2.L, self.radMed2.diam = 100 * um, 3 * um
self.radDist2.L, self.radDist2.diam = 200 * um, 2 * um
self.lmM2.L, self.lmM2.diam = 100 * um, 1.5 * um
self.lmt2.L, self.lmt2.diam = 100 * um, 1 * um
self.oriProx1.L, self.oriProx1.diam = 100 * um, 2 * um
self.oriMed1.L, self.oriMed1.diam = 100 * um, 1.5 * um
self.oriDist1.L, self.oriDist1.diam = 100 * um, 1 * um
self.oriProx2.L, self.oriProx2.diam = 100 * um, 2 * um
self.oriMed2.L, self.oriMed2.diam = 100 * um, 1.5 * um
self.oriDist2.L, self.oriDist2.diam = 100 * um, 1 * um
def _setup_biophysics(self):
# =====================================================================
Rm = 20000*1.6
# Somatic compartment
self.soma.insert('pas')
for seg in self.soma:
seg.pas.g = 1/Rm
seg.pas.e = -70
# Na channels
self.soma.insert('Nafcr')
for seg in self.soma:
seg.Nafcr.gnafbar = 0.015*2
# Kdr channels
self.soma.insert('kdrcr')
for seg in self.soma:
seg.kdrcr.gkdrbar = 0.0018*2
# IKscr
self.soma.insert('IKscr')
for seg in self.soma:
seg.IKscr.gKsbar = 0.000725*5*1.8
# iCcr
self.soma.insert('iCcr')
for seg in self.soma:
seg.iCcr.gkcbar = 0.00003*10*1.5
# cancr
self.soma.insert('cancr')
for seg in self.soma:
seg.cancr.gcabar = 0.001*0.1*10
# gskch
self.soma.insert('gskch')
for seg in self.soma:
seg.gskch.gskbar = 0.000002*1000*2
# Constant current for Vrest calibration
self.soma.insert('constant')
for seg in self.soma:
seg.constant.ic = -0.003
# ccanl
self.soma.insert('ccanl')
for seg in self.soma:
seg.ccanl.catau = 20
# Ih
self.soma.insert('Ih')
for seg in self.soma:
seg.Ih.gkhbar = 0.000025*8
seg.Ih.alpha = 100
seg.Ih.slope = 10
seg.Ih.amp = 0.001
seg.Ih.taumin = 5
self.soma.eca = 130
self.soma.eh = -40
# =====================================================================
# =====================================================================
# Dendritic compartments
for sec in self.dends:
sec.insert('pas')
for seg in sec:
seg.pas.g = 1/Rm
seg.pas.e = -70
sec.insert('Nafcr')
for seg in sec:
seg.Nafcr.gnafbar = 0.018*5
sec.insert('kdrcr')
for seg in sec:
seg.kdrcr.gkdrbar = 0.018*0.5
sec.insert('Ih')
for seg in sec:
seg.Ih.gkhbar = 0.000025*1.1
seg.Ih.alpha = 100
seg.Ih.slope = 8
seg.Ih.amp = 0.001
seg.Ih.taumin = 30
# =====================================================================
# =====================================================================
# All compartments
for sec in self.all:
sec.ena = 55 # Na reversal potential in mV
sec.ek = -85 # K reversal potential in mV
# =====================================================================
def __repr__(self):
return 'VIPCRCell[{}]'.format(self._gid)