def create_ca_rxd(self):
cainf = 100e-6
taur = self.p_all['L5Pyr_dend_taur_cad'] # temporary
# drive_channel = -(10000) * self.ica_soma / (.2)
# [sec for sec in h.allsec() if 'soma' in sec.name()]
ca_reg = rxd.Region(h.allsec(),
nrn_region='i',
name='ca_reg',
geometry=rxd.Shell(0.9848, 1))
ca = rxd.Species(ca_reg, d=0.3, name='ca', charge=2, initial=cainf)
ca_pump = rxd.Rate(ca, (cainf - ca) / taur)
self.ca = ca
self.ca_reg = ca_reg
self.ca_pump = ca_pump
cell1.pt3dclear()
cell1.pt3dadd(-20, 0, 0, 10)
cell1.pt3dadd(-10, 0, 0, 10)
cell1.nseg = 11
# create cell2 where `x` will be pumped in and accumulate
cell2 = h.Section("cell2")
cell2.pt3dclear()
cell2.pt3dadd(10, 0, 0, 10)
cell2.pt3dadd(20, 0, 0, 10)
cell2.nseg = 11
# Where?
# the intracellular spaces
cyt = rxd.Region(
h.allsec(),
name="cyt",
nrn_region="i",
geometry=rxd.FractionalVolume(0.9, surface_fraction=1.0),
)
org = rxd.Region(h.allsec(), name="org", geometry=rxd.FractionalVolume(0.1))
cyt_org_membrane = rxd.Region(h.allsec(),
name="mem",
geometry=rxd.ScalableBorder(
pi / 2.0, on_cell_surface=False))
cyt_ecs_membrane = rxd.Region(h.allsec(),
name="cell_mem",
geometry=rxd.membrane())
# the extracellular space
ecs = rxd.Extracellular(-55,
ip3Diff = 0.283 #ip3Diff = 0 cac_init = 1.e-4 ip3_init = 0.1 gip3r = 12040 gserca = 0.3913 gleak = 6.020 kserca = 0.1 kip3 = 0.15 kact = 0.4 ip3rtau = 2000 h.CVode().active(1) h.cvode.atol(1e-10) # define the regions for the rxd cyt = rxd.Region(h.allsec(), nrn_region='i', geometry=rxd.FractionalVolume(fc, surface_fraction=1)) er = rxd.Region(h.allsec(), geometry=rxd.FractionalVolume(fe)) cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.FixedPerimeter(1)) # the species and other states ca = rxd.Species([cyt, er], d=caDiff, name='ca', charge=2, initial=cac_init) ip3 = rxd.Species(cyt, d=ip3Diff, initial=ip3_init) ip3r_gate_state = rxd.State(cyt_er_membrane, initial=0.8) h_gate = ip3r_gate_state[cyt_er_membrane] # pumps and channels between ER and Cytosol serca = rxd.MultiCompartmentReaction(ca[cyt]>ca[er], gserca/((kserca / (1000. * ca[cyt])) ** 2 + 1), membrane=cyt_er_membrane, custom_dynamics=True) leak = rxd.MultiCompartmentReaction(ca[er]!=ca[cyt], gleak, gleak, membrane=cyt_er_membrane)
results['species'] = set(my_species)
results['name'] = sec.hname()
results['hoc_internal_name'] = sec.hoc_internal_name()
results['cell'] = sec.cell()
#all_active_reactions = [r() for r in rxd_module._all_reactions if r() is not None]
return results
if __name__ == '__main__':
from pprint import pprint
from neuron import h, rxd
soma = h.Section(name='soma')
soma.insert('hh')
soma.insert('pas')
soma.nseg = 3
iclamp = h.IClamp(soma(0.3))
gaba = h.ExpSyn(soma(0.7))
dend = h.Section(name='dend')
dend.connect(soma)
cyt = rxd.Region([dend], name='cyt', nrn_region='i')
er = rxd.Region([dend], name='er')
na = rxd.Species(cyt, name='na', charge=1)
ca = rxd.Species([cyt, er], name='ca', charge=2)
h.finitialize(-65)
pprint(psection(soma))
print('\n')
pprint(psection(dend))
somaA.nseg = 11
somaB = h.Section('somaB')
somaB.pt3dclear()
somaB.pt3dadd(60, 0, 0, 1)
somaB.pt3dadd(90, 0, 0, 1)
somaB.nseg = 11
# mod version
somaB.insert('hh')
# rxd version
# Where?
# intracellular
cyt = rxd.Region(h.allsec(), name='cyt', nrn_region='i')
# membrane
mem = rxd.Region(h.allsec(), name='cell_mem', geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=100)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
import __main__
name = __main__.__file__
if name[-3 :] == '.py':
name = name[: -3]
h.load_file('stdrun.hoc')
dend = h.Section()
dend.diam = 2
dend.nseg = 101
dend.L = 100
rxd.set_solve_type(dimension=3)
diff_constant = 1
r = rxd.Region(h.allsec(),dx=0.5)
ca = rxd.Species(r, d=diff_constant, initial=lambda node:
1 if 0.4 < node.x < 0.6 else 0)
h.finitialize()
initial_amount = (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
for t in [25, 50, 75, 100, 125]:
h.continuerun(t)
pyplot.plot([nd.x for nd in ca.nodes], ca.nodes.concentration)
final_amount = (numpy.array(ca.nodes.concentration) * numpy.array(ca.nodes.volume)).sum()
print("initial {}\tfinal {}\tdiff {}".format(initial_amount, final_amount, initial_amount - final_amount))
pyplot.tight_layout()
gleak = 6.020
kserca = 0.1
kip3 = 0.15
kact = 0.4
ip3rtau = 2000.0
rescale_v = 1000 / -65.0
#These parameters where missing in the tutorial so arbitrary values were chosen
#any resemblance to experimental values is purely coincidental.
fc = 0.7
fe = 0.3
caCYT_init = 0.1
cyt = rxd.Region(h.allsec(),
name='cyt',
nrn_region='i',
geometry=rxd.FractionalVolume(fc, surface_fraction=1))
er = rxd.Region(h.allsec(), name='er', geometry=rxd.FractionalVolume(fe / 2.))
cyt_er_membrane = rxd.Region(h.allsec(),
name='mem',
geometry=rxd.ScalableBorder(
1, on_cell_surface=False))
ca = rxd.Species([cyt, er], d=caDiff, name="ca", charge=2, initial=caCYT_init)
ip3 = rxd.Species(cyt, d=ip3Diff, name="ip3", initial=ip3_init)
ip3r_gate_state = rxd.Species(cyt_er_membrane, name="gate", initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
minf = ip3[cyt] * rescale_v * v * ca[cyt] / (ip3[cyt] + kip3) / (
def _addRegions(self, params):
from .. import sim
for label, param in params.items():
if 'extracellular' in param and param['extracellular'] == True:
self._addExtracellularRegion(label, param)
continue
# cells
if 'cells' not in param:
param['cells'] = ['all']
# secs
if 'secs' not in param:
param['secs'] = ['all']
if not isinstance(param['secs'], list):
param['secs'] = [param['secs']]
# nrn_region
if 'nrn_region' not in param:
param['nrn_region'] = None
# geomery
if 'geometry' not in param:
param['geometry'] = None
geometry = param['geometry']
# import IPython; IPython.embed()
if isinstance(geometry, dict):
try:
if 'args' in geometry:
geometry['hObj'] = getattr(rxd, param['geometry']['class'])(**param['geometry']['args'])
geometry = geometry['hObj']
except:
print(' Error creating %s Region geometry using %s class'%(label, param['geometry']['class']))
elif isinstance(param['geometry'], str):
geometry = getattr(rxd, param['geometry'])()
# List of allowed geometry classes:
# class neuron.rxd.geometry.FixedCrossSection(cross_area, surface_area=0)
# class neuron.rxd.geometry.FractionalVolume(volume_fraction=1, surface_fraction=0, neighbor_areas_fraction=None)
# class neuron.rxd.geometry.FixedPerimeter(perimeter, on_cell_surface=False)
# class neuron.rxd.geometry.Shell(lo=None, hi=None)
# geomery
if 'dimension' not in param:
param['dimension'] = None
# geomery
if 'dx' not in param:
param['dx'] = None
# get list of h.Sections() based on cells and secs
if 'all' in param['cells'] and 'all' in param['secs']:
nrnSecs = list(sim.h.allsec())
else:
cells = sim.getCellsList(param['cells'])
nrnSecs = []
for cell in cells:
for secName,sec in cell.secs.items():
if 'all' in param['secs'] or secName in param['secs']:
nrnSecs.append(sec['hObj'])
# call rxd method to create Region
if nrnSecs: self.rxd['regions'][label]['hObj'] = rxd.Region(secs=nrnSecs,
nrn_region=param['nrn_region'],
geometry=geometry,
dimension=param['dimension'],
dx=param['dx'],
name=label)
else: self.rxd['regions'][label]['hObj'] = None
print(' Created Region %s'%(label))
somaA.nseg = 11
somaB = h.Section("somaB")
somaB.pt3dclear()
somaB.pt3dadd(60, 0, 0, 1)
somaB.pt3dadd(90, 0, 0, 1)
somaB.nseg = 11
# mod version
somaB.insert("hh")
# rxd version
# Where?
# intracellular
cyt = rxd.Region(h.allsec(), name="cyt", nrn_region="i")
# membrane
mem = rxd.Region(h.allsec(), name="cell_mem", geometry=rxd.membrane())
# extracellular
ecs = rxd.Extracellular(-100, -100, -100, 100, 100, 100, dx=100)
# Who?
def init(ics, ecs):
return lambda nd: ecs if isinstance(nd, rxd.node.NodeExtracellular
) else ics
# ions
from neuron import h, crxd as rxd
h.load_file("stdrun.hoc")
cell = h.Section(name="cell")
r = rxd.Region([cell])
def Declare_Parameters(**kwargs):
"""helper function enabling clean declaration of parameters in top namespace"""
for key, value in kwargs.items():
globals()[key] = rxd.Parameter(r, name=key, initial=value)
def Declare_Species(**kwargs):
"""helper function enabling clean declaration of species in top namespace"""
for key, value in kwargs.items():
globals()[key] = rxd.Species(r, name=key, initial=value)
k3 = rxd.Parameter(r, name="k3", initial=1.2)
k4 = rxd.Parameter(r, name="k4", initial=0.6)
P2 = rxd.Species(r, name="P2", initial=0.0614368)
T2 = rxd.Species(r, name="T2", initial=0.0145428)
C = rxd.Species(r, name="C", initial=0.207614)
h.finitialize(-65)
h.continuerun(72)
from matplotlib import pyplot
import numpy
import __main__
name = __main__.__file__
if name[-3:] == '.py':
name = name[:-3]
h.load_file('stdrun.hoc')
dend = h.Section()
dend.diam = 2
dend.nseg = 101
dend.L = 100
diff_constant = 1
r = rxd.Region(h.allsec())
ca = rxd.Species(r,
d=diff_constant,
initial=lambda node: 1 if 0.4 < node.x < 0.6 else 0)
h.finitialize()
for t in [25, 50, 75, 100, 125]:
h.continuerun(t)
pyplot.plot([seg.x for seg in dend], ca.states)
pyplot.tight_layout()
pyplot.savefig('{0}.png'.format(name))
from neuron import h, crxd as rxd
h.load_file('stdrun.hoc')
soma = h.Section(name='soma')
r = rxd.Region([soma])
soma.nseg = 5
c = rxd.Species(r, initial=1.0)
assert (len(c.nodes) == 5)
soma.nseg = 3
assert (len(c.nodes) == 3)
soma.nseg = 7
assert (len(c[r].nodes) == 7)
h.tstop = 100
h.run()
kserca = 0.1
kip3 = 0.15
kact = 0.4
ip3rtau = 2000.0
rescale_v = 1000 / -65.0
# These parameters where missing in the tutorial so arbitrary values were chosen
# any resemblance to experimental values is purely coincidental.
fc = 0.7
fe = 0.3
caCYT_init = 0.1
cyt = rxd.Region(
h.allsec(),
name="cyt",
nrn_region="i",
geometry=rxd.FractionalVolume(fc, surface_fraction=1),
)
er = rxd.Region(h.allsec(), name="er", geometry=rxd.FractionalVolume(fe / 2.0))
cyt_er_membrane = rxd.Region(h.allsec(),
name="mem",
geometry=rxd.ScalableBorder(
1, on_cell_surface=False))
ca = rxd.Species([cyt, er], d=caDiff, name="ca", charge=2, initial=caCYT_init)
ip3 = rxd.Species(cyt, d=ip3Diff, name="ip3", initial=ip3_init)
ip3r_gate_state = rxd.Species(cyt_er_membrane, name="gate", initial=0.8)
h_gate = ip3r_gate_state[cyt_er_membrane]
cell1 = h.Section('cell1')
cell1.pt3dclear()
cell1.pt3dadd(-20, 0, 0, 10)
cell1.pt3dadd(-10, 0, 0, 10)
cell1.nseg = 11
# create cell2 where `x` will be pumped in and accumulate
cell2 = h.Section('cell2')
cell2.pt3dclear()
cell2.pt3dadd(10, 0, 0, 10)
cell2.pt3dadd(20, 0, 0, 10)
cell2.nseg = 11
# Where?
# the intracellular spaces
cyt = rxd.Region(h.allsec(),
name='cyt',
nrn_region='i',
geometry=rxd.FractionalVolume(0.9, surface_fraction=1.0))
org = rxd.Region(h.allsec(), name='org', geometry=rxd.FractionalVolume(0.1))
cyt_org_membrane = rxd.Region(h.allsec(),
name='mem',
geometry=rxd.ScalableBorder(
pi / 2.0, on_cell_surface=False))
cyt_ecs_membrane = rxd.Region(h.allsec(),
name='cell_mem',
geometry=rxd.membrane())
# the extracellular space
ecs = rxd.Extracellular(-55,
-55,
from neuron import h, crxd as rxd, gui from neuron.crxd import initializer h.CVode().active(1) rxdsec = [h.Section(), h.Section()] cyt = rxd.Region(rxdsec) er = rxd.Region(rxdsec) ca = rxd.Species([cyt, er]) caextrude = rxd.Rate(ca, 1) # test for forced initialization before model fully described initializer._do_init() ip3 = rxd.Species(cyt) h.tstop = 1000 h.run()
def __init__(self):
self.soma = h.Section(name='soma', cell=self)
self.soma.pt3dclear()
self.soma.pt3dadd(x, y, z + somaR, 2.0 * somaR)
self.soma.pt3dadd(x, y, z - somaR, 2.0 * somaR)
self.dend = h.Section(name='dend', cell=self)
self.dend.pt3dclear()
self.dend.pt3dadd(x, y, z - somaR, 2.0 * dendR)
self.dend.pt3dadd(x, y, z - somaR - dendL, 2.0 * dendR)
self.dend.nseg = 10
self.dend.connect(self.soma, 1, 0)
self.all = [self.soma, self.dend]
#---------------soma----------------
# for mechanism_s in ['h','hNa','hha2', 'IA','kadcr','borgka','Ih','Ihvip', 'kap', 'km' ,'pas', 'Nafcr', 'kdrcr', 'IKscr', 'iCcr', 'kadcr']:
# self.soma.insert(mechanism_s)
for mechanism_s in [
'extracellular', 'h', 'hNa', 'hha2', 'IA', 'Ih', 'Nasoma',
'km', 'Ksoma', 'pas', 'k_ion', 'na_ion', 'kap', 'nap', 'kdrcr',
'Nafcr', 'IKscr'
]:
self.soma.insert(mechanism_s)
self.soma(0.5).IA.gkAbar = 0.0165
self.soma(0.5).Ih.gkhbar = 0.00035 * 0.1
self.soma(0.5).Nasoma.gnasoma = 0.0107 * 1.2
self.soma(0.5).Nasoma.gl = 1 / Rm
self.soma(0.5).Nasoma.el = -67
self.soma(0.5).Ksoma.gksoma = 0.0319 * 1.5
#print(self.soma.psection())
self.n_Ksoma = h.Vector().record(self.soma(0.5).Ksoma._ref_n)
self.h_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_h)
self.m_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_m)
self.soma(0.5).h.ghdbar = 0.00005
self.soma(0.5).h.vhalfl = -73
self.soma(0.5).Ih.gkhbar = 0.00035 * 0.1
self.soma(0.5).km.gbar = 0.06
#self.soma(0.5).borgka.gkabar = 0.00015*4*0.5
#self.soma(0.5).kadcr.gkabar = 0.003
self.soma(0.5).hha2.gnabar = 0.007
self.soma(0.5).hha2.gkbar = 0.007 / 10
self.soma(0.5).hha2.gl = 0
self.soma(0.5).hha2.el = -70
#self.soma(0.5).pas.g = 1/Rm
#self.soma(0.5).pas.e = -70
self.soma(0.5).Nafcr.gnafbar = 0.015
self.soma(0.5).kdrcr.gkdrbar = 0.018
self.soma(0.5).IKscr.gKsbar = 0.000725
#self.soma(0.5).iCcr.gkcbar = 0.00003
#self.soma(0.5).kadcr.gkabar = 0.003
#print(self.soma.psection())
#self.n_Ksoma = h.Vector().record(self.soma(0.5).Ksoma._ref_n)
#self.h_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_h)
#self.m_Nasoma = h.Vector().record(self.soma(0.5).Nasoma._ref_m)
self.somaV = h.Vector()
self.somaV.record(self.soma(0.5)._ref_v)
#---------------dend----------------
for mechanism_d in [
'Nadend', 'Kdend', 'hha_old', 'h', 'hNa', 'IA', 'kap', 'pas',
'Nafcr', 'kdrcr', 'nap', 'k_ion', 'na_ion', 'Ihvip', 'kad'
]:
self.dend.insert(mechanism_d)
self.dend(0.5).IA.gkAbar = 0.004 * 1.2
#self.dend1(0.5).Ih.gkhbar = 0.00035*0.1
self.dend(0.5).Nadend.gnadend = 2 * 0.0117
self.dend(0.5).Nadend.gl = 1 / Rm
self.dend(0.5).Nadend.el = -65
self.dend(0.5).Kdend.gkdend = 20 * 0.023
self.dend(0.5).h.ghdbar = 0.00005 * 4
self.dend(0.5).h.vhalfl = -81
self.dend(0.5).IA.gkAbar = 0.004 * 1.2
self.dend(0.5).kad.gkabar = 0
#self.dend(0.5).km.gbar = 0.06
#self.dend(0.5).borgka.gkabar = 0.00015*4*0.5
self.dend(0.5).hha_old.gnabar = 0.007
self.dend(0.5).hha_old.gkbar = 0.007 / 8.065
self.dend(0.5).hha_old.el = -70
self.dend(0.5).hha_old.gl = 0
#self.dend(0.5).pas.g = 1/20000
#self.dend(0.5).pas.e = -70
self.dend(0.5).Nafcr.gnafbar = 0.018 * 5
self.dend(0.5).kdrcr.gkdrbar = 0.018 * 0.5
#self.Dn_Kdend = h.Vector().record(self.dend(0.5).Kdend._ref_n)
#self.Dh_Nadend = h.Vector().record(self.dend(0.5).Nadend._ref_h)
#self.Dm_Nadend = h.Vector().record(self.dend(0.5).Nadend._ref_m)
self.dendV = h.Vector()
self.dendV.record(self.dend(0.5)._ref_v)
self.k_vec = h.Vector().record(self.soma(0.5)._ref_ik)
self.na_vec = h.Vector().record(self.soma(0.5)._ref_ina)
self.na_concentration = h.Vector().record(self.soma(0.5)._ref_nai)
self.k_concentration = h.Vector().record(self.soma(0.5)._ref_ki)
self.v_vec = h.Vector().record(self.soma(0.5)._ref_vext[0])
for sec in self.all:
Ra = 150
cm = 1.2
self.cyt = rxd.Region(self.all,
name='cyt',
nrn_region='i',
dx=1.0,
geometry=rxd.FractionalVolume(
0.9, surface_fraction=1.0))
self.na = rxd.Species([self.cyt],
name='na',
charge=1,
d=1.0,
initial=14)
self.k = rxd.Species([self.cyt],
name='k',
charge=1,
d=1.0,
initial=120)
self.k_i = self.k[self.cyt]
