You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
897 lines
33 KiB
897 lines
33 KiB
from __future__ import print_function |
|
from neuron import h |
|
from ..util import nstomho |
|
from .cell import Cell |
|
from ..util import Params |
|
from .. import synapses |
|
from .. import data |
|
|
|
__all__ = ["DStellate", "DStellateRothman", "DStellateEager"] |
|
|
|
|
|
class DStellate(Cell): |
|
|
|
type = "dstellate" |
|
|
|
@classmethod |
|
def create(cls, model="RM03", **kwds): |
|
if model == "RM03": |
|
return DStellateRothman(**kwds) |
|
elif model == "Eager": |
|
return DStellateEager(**kwds) |
|
elif model == "dummy": |
|
return DummyDStellate(**kwds) |
|
else: |
|
raise ValueError("DStellate type %s is unknown", type) |
|
|
|
def __init__(self): |
|
Cell.__init__(self) |
|
self.spike_source = ( |
|
None |
|
) # used by DummyDStellate to connect VecStim to terminal |
|
|
|
def make_psd(self, terminal, psd_type, **kwds): |
|
""" |
|
Connect a presynaptic terminal to one post section at the specified location, with the fraction |
|
of the "standard" conductance determined by gbar. |
|
The default condition is designed to pass the unit test (loc=0.5) |
|
|
|
Parameters |
|
---------- |
|
terminal : Presynaptic terminal (NEURON object) |
|
|
|
psd_type : either simple or multisite PSD for bushy cell |
|
|
|
kwds: dictionary of options. |
|
Two are currently handled: |
|
postsize : expect a list consisting of [sectionno, location (float)] |
|
AMPAScale : float to scale the ampa currents |
|
|
|
""" |
|
if ( |
|
"postsite" in kwds |
|
): # use a defined location instead of the default (soma(0.5) |
|
postsite = kwds["postsite"] |
|
loc = postsite[1] # where on the section? |
|
uname = ( |
|
"sections[%d]" % postsite[0] |
|
) # make a name to look up the neuron section object |
|
post_sec = self.hr.get_section(uname) # Tell us where to put the synapse. |
|
else: |
|
loc = 0.5 |
|
post_sec = self.soma |
|
|
|
if psd_type == "simple": |
|
if terminal.cell.type in ["sgc", "dstellate", "tuberculoventral"]: |
|
weight = data.get( |
|
"%s_synapse" % terminal.cell.type, |
|
species=self.species, |
|
post_type=self.type, |
|
field="weight", |
|
) |
|
tau1 = data.get( |
|
"%s_synapse" % terminal.cell.type, |
|
species=self.species, |
|
post_type=self.type, |
|
field="tau1", |
|
) |
|
tau2 = data.get( |
|
"%s_synapse" % terminal.cell.type, |
|
species=self.species, |
|
post_type=self.type, |
|
field="tau2", |
|
) |
|
erev = data.get( |
|
"%s_synapse" % terminal.cell.type, |
|
species=self.species, |
|
post_type=self.type, |
|
field="erev", |
|
) |
|
return self.make_exp2_psd( |
|
post_sec, |
|
terminal, |
|
weight=weight, |
|
loc=loc, |
|
tau1=tau1, |
|
tau2=tau2, |
|
erev=erev, |
|
) |
|
else: |
|
raise TypeError( |
|
"Cannot make simple PSD for %s => %s" |
|
% (terminal.cell.type, self.type) |
|
) |
|
|
|
elif psd_type == "multisite": |
|
if terminal.cell.type == "sgc": |
|
# Max conductances for the glu mechanisms are calibrated by |
|
# running `synapses/tests/test_psd.py`. The test should fail |
|
# if these values are incorrect |
|
self.AMPAR_gmax = ( |
|
data.get( |
|
"sgc_synapse", |
|
species=self.species, |
|
post_type=self.type, |
|
field="AMPAR_gmax", |
|
) |
|
* 1e3 |
|
) |
|
self.NMDAR_gmax = ( |
|
data.get( |
|
"sgc_synapse", |
|
species=self.species, |
|
post_type=self.type, |
|
field="NMDAR_gmax", |
|
) |
|
* 1e3 |
|
) |
|
self.Pr = data.get( |
|
"sgc_synapse", species=self.species, post_type=self.type, field="Pr" |
|
) |
|
# adjust gmax to correct for initial Pr |
|
self.AMPAR_gmax = self.AMPAR_gmax / self.Pr |
|
self.NMDAR_gmax = self.NMDAR_gmax / self.Pr |
|
# old values: |
|
# AMPA_gmax = 0.22479596944138733*1e3 # factor of 1e3 scales to pS (.mod mechanisms) from nS. |
|
# NMDA_gmax = 0.12281291946623739*1e3 |
|
if "AMPAScale" in kwds: |
|
self.AMPAR_gmax = ( |
|
self.AMPAR_gmax * kwds["AMPAScale"] |
|
) # allow scaling of AMPA conductances |
|
if "NMDAScale" in kwds: |
|
self.NMDAR_gmax = self.NMDAR_gmax * kwds["NMDAScale"] |
|
return self.make_glu_psd( |
|
post_sec, terminal, self.AMPAR_gmax, self.NMDAR_gmax, loc=loc |
|
) |
|
|
|
elif terminal.cell.type == "dstellate": |
|
# Get GLY kinetic constants from database |
|
return self.make_gly_psd(post_sec, terminal, psdtype="glyfast", loc=loc) |
|
elif terminal.cell.type == "tuberculoventral": |
|
# Get GLY kinetic constants from database |
|
return self.make_gly_psd(post_sec, terminal, psdtype="glyfast", loc=loc) |
|
else: |
|
raise TypeError( |
|
"Cannot make PSD for %s => %s" % (terminal.cell.type, self.type) |
|
) |
|
else: |
|
raise ValueError("Unsupported psd type %s" % psd_type) |
|
|
|
def make_terminal(self, post_cell, term_type, **kwds): |
|
if term_type == "simple": |
|
return synapses.SimpleTerminal( |
|
self.soma, post_cell, spike_source=self.spike_source, **kwds |
|
) |
|
elif term_type == "multisite": |
|
if post_cell.type in [ |
|
"dstellate", |
|
"tuberculoventral", |
|
"pyramidal", |
|
"bushy", |
|
"tstellate", |
|
]: |
|
nzones = data.get( |
|
"dstellate_synapse", |
|
species=self.species, |
|
post_type=post_cell.type, |
|
field="n_rsites", |
|
) |
|
delay = data.get( |
|
"dstellate_synapse", |
|
species=self.species, |
|
post_type=post_cell.type, |
|
field="delay", |
|
) |
|
else: |
|
raise NotImplementedError( |
|
"No knowledge as to how to connect D stellate cell to cell type %s" |
|
% type(post_cell) |
|
) |
|
pre_sec = self.soma |
|
return synapses.StochasticTerminal( |
|
pre_sec, |
|
post_cell, |
|
nzones=nzones, |
|
spike_source=self.spike_source, |
|
delay=delay, |
|
**kwds |
|
) |
|
else: |
|
raise ValueError("Unsupported terminal type %s" % term_type) |
|
|
|
|
|
class DStellateRothman(DStellate): |
|
""" |
|
VCN D-stellate model: |
|
as a type I-II from Rothman and Manis, 2003 |
|
""" |
|
|
|
def __init__( |
|
self, |
|
morphology=None, |
|
decorator=None, |
|
nach=None, |
|
ttx=False, |
|
species="guineapig", |
|
modelType=None, |
|
modelName=None, |
|
debug=False, |
|
): |
|
""" |
|
initialize a radial stellate (D-stellate) cell, using the default parameters for guinea pig from |
|
R&M2003, as a type I-II cell. |
|
Modifications to the cell can be made by calling methods below. These include: |
|
|
|
* changing the sodium channel |
|
* Changing "species" to mouse or cat (scales conductances) |
|
* Shifting model type |
|
|
|
Parameters |
|
---------- |
|
morphology : string (default: None) |
|
Name of a .hoc file representing the morphology. This file is used to constructe |
|
an electrotonic (cable) model. |
|
If None (default), then a "point" (really, single cylinder) model is made, exactly according to RM03. |
|
|
|
decorator : Python function (default: None) |
|
decorator is a function that "decorates" the morphology with ion channels according |
|
to a set of rules. |
|
If None, a default set of channels is inserted into the first soma section, and the |
|
rest of the structure is "bare". |
|
|
|
nach : string (default: None) |
|
nach selects the type of sodium channel that will be used in the model. A channel mechanism |
|
by that name must exist. A value of None will set the channel to a default for the model (nacn). |
|
|
|
ttx : Boolean (default: False) |
|
If ttx is True, then the sodium channel conductance is set to 0 everywhere in the cell. |
|
This flag duplicates the effects of tetrodotoxin in the model. Currently, the flag is not implemented. |
|
|
|
species: string (default 'guineapig') |
|
species defines the pattern of ion channel densities that will be inserted, according to |
|
prior measurements in various species. Note that |
|
if a decorator function is specified, this argument is ignored as the decorator will |
|
specify the channel density. |
|
|
|
modelType: string (default: None) |
|
modelType specifies the subtype of the cell model that will be used (e.g., "II", "II-I", etc). |
|
modelType is passed to the decorator, or to species_scaling to adjust point (single cylinder) models. |
|
|
|
debug: boolean (default: False) |
|
When True, there will be multiple printouts of progress and parameters. |
|
|
|
|
|
Returns |
|
------- |
|
Nothing |
|
""" |
|
|
|
super(DStellateRothman, self).__init__() |
|
if modelType == None: |
|
modelType = "I-II" |
|
if species == "guineapig": |
|
modelName = "RM03" |
|
temp = 22.0 |
|
if nach == None: |
|
nach = "nacn" |
|
if species == "mouse": |
|
temp = 34.0 |
|
if modelName is None: |
|
modelName = "XM13" |
|
if nach is None: |
|
nach = "na" |
|
self.debug = debug |
|
# if modelType == None: # allow us to pass None to get the default |
|
# modelType = 'I-II' |
|
# if nach == None: |
|
# nach = 'na' |
|
self.status = { |
|
"soma": True, |
|
"axon": False, |
|
"dendrites": False, |
|
"pumps": False, |
|
"na": nach, |
|
"species": species, |
|
"modelType": modelType, |
|
"modelName": modelName, |
|
"ttx": ttx, |
|
"name": "DStellate", |
|
"morphology": morphology, |
|
"decorator": decorator, |
|
"temperature": None, |
|
} |
|
self.i_test_range = { |
|
"pulse": [(-0.3, 0.3, 0.03), (-0.05, 0.0, 0.005)] |
|
} # set range for ic command test |
|
self.vrange = [-75.0, -55.0] |
|
self.spike_threshold = ( |
|
-40.0 |
|
) # matches threshold in released CNModel (set in base cell class) |
|
|
|
if morphology is None: |
|
""" |
|
instantiate a basic soma-only ("point") model |
|
""" |
|
soma = h.Section( |
|
name="DStellate_Soma_%x" % id(self) |
|
) # one compartment of about 29000 um2 |
|
soma.nseg = 1 |
|
self.add_section(soma, "soma") |
|
else: |
|
""" |
|
instantiate a structured model with the morphology as specified by |
|
the morphology file |
|
""" |
|
self.set_morphology(morphology_file=morphology) |
|
|
|
# decorate the morphology with ion channels |
|
if decorator is None: # basic model, only on the soma |
|
self.mechanisms = ["klt", "kht", "ihvcn", "leak", nach] |
|
for mech in self.mechanisms: |
|
self.soma.insert(mech) |
|
self.soma.ena = self.e_na |
|
self.soma.ek = self.e_k |
|
self.soma().leak.erev = self.e_leak |
|
self.c_m = 0.9 |
|
self.set_soma_size_from_Cm(12.0) |
|
self.species_scaling( |
|
silent=True, species=species, modelType=modelType |
|
) # set the default type II cell parameters |
|
else: # decorate according to a defined set of rules on all cell compartments |
|
self.decorate() |
|
self.save_all_mechs() # save all mechanisms inserted, location and gbar values... |
|
self.get_mechs(self.soma) |
|
|
|
if self.debug: |
|
print("<< D-stellate: JSR Stellate Type I-II cell model created >>") |
|
|
|
def get_cellpars(self, dataset, species="guineapig", modelType="I-II"): |
|
cellcap = data.get( |
|
dataset, species=species, model_type=modelType, field="soma_Cap" |
|
) |
|
chtype = data.get( |
|
dataset, species=species, model_type=modelType, field="na_type" |
|
) |
|
pars = Params(cap=cellcap, natype=chtype) |
|
# pars.show() |
|
|
|
if self.status["modelName"] == "RM03": |
|
for g in [ |
|
"%s_gbar" % pars.natype, |
|
"kht_gbar", |
|
"klt_gbar", |
|
"ka_gbar", |
|
"ih_gbar", |
|
"leak_gbar", |
|
"leak_erev", |
|
"ih_eh", |
|
"e_k", |
|
"e_na", |
|
]: |
|
pars.additem( |
|
g, data.get(dataset, species=species, model_type=modelType, field=g) |
|
) |
|
if self.status["modelName"] == "XM13": |
|
for g in [ |
|
"%s_gbar" % pars.natype, |
|
"kht_gbar", |
|
"klt_gbar", |
|
"ka_gbar", |
|
"ihvcn_gbar", |
|
"leak_gbar", |
|
"leak_erev", |
|
"ih_eh", |
|
"e_k", |
|
"e_na", |
|
]: |
|
pars.additem( |
|
g, data.get(dataset, species=species, model_type=modelType, field=g) |
|
) |
|
if self.status["modelName"] == "mGBC": |
|
for g in [ |
|
"%s_gbar" % pars.natype, |
|
"kht_gbar", |
|
"klt_gbar", |
|
"ka_gbar", |
|
"ihvcn_gbar", |
|
"leak_gbar", |
|
"leak_erev", |
|
]: |
|
pars.additem( |
|
g, data.get(dataset, species=species, model_type=modelType, field=g) |
|
) |
|
return pars |
|
|
|
def species_scaling(self, species="guineapig", modelType="I-II", silent=True): |
|
""" |
|
Adjust all of the conductances and the cell size according to the species requested. |
|
|
|
Parameters |
|
---------- |
|
species : string (default: 'guineapig') |
|
A string specifying the species used for scaling. Recognized values are |
|
'mouse', 'guineapig', and 'cat' (cat is just a larger version of the guineapig) |
|
|
|
modelType : string (default: 'I-II') |
|
A string specifying the version of the model to use. |
|
Current choices are 'I-II' (others need to be implemented) |
|
|
|
silent : boolean (default: True) |
|
Flag for printing debugging information. |
|
|
|
""" |
|
soma = self.soma |
|
celltype = modelType |
|
if species == "mouse": |
|
# use conductance levels from Cao et al., J. Neurophys., 2007. |
|
dataset = "XM13_channels" |
|
self._valid_temperatures = (34.0,) |
|
if self.status["temperature"] is None: |
|
self.set_temperature(34.0) |
|
self.c_m = 0.9 |
|
pars = self.get_cellpars(dataset, species=species, modelType=modelType) |
|
self.set_soma_size_from_Cm(pars.cap) |
|
self.status["na"] = pars.natype |
|
# pars.show() |
|
self.adjust_na_chans(soma, gbar=pars.na_gbar, sf=1.0) |
|
soma().kht.gbar = nstomho(pars.kht_gbar, self.somaarea) |
|
soma().klt.gbar = nstomho(pars.klt_gbar, self.somaarea) |
|
# soma().ka.gbar = nstomho(pars.ka_gbar, self.somaarea) |
|
soma().ihvcn.gbar = nstomho(pars.ihvcn_gbar, self.somaarea) |
|
soma().ihvcn.eh = pars.ih_eh # Rodrigues and Oertel, 2006 |
|
soma().leak.gbar = nstomho(pars.leak_gbar, self.somaarea) |
|
soma().leak.erev = pars.leak_erev |
|
self.e_k = pars.e_k |
|
self.e_na = pars.e_na |
|
soma.ena = self.e_na |
|
soma.ek = self.e_k |
|
# soma().leak.erev = pars.leak_erev |
|
self.axonsf = 0.5 |
|
|
|
elif species == "guineapig": # values from R&M 2003, Type II-I |
|
dataset = "RM03_channels" |
|
self.c_m = 0.9 |
|
self._valid_temperatures = (22.0, 38.0) |
|
if self.status["temperature"] is None: |
|
self.set_temperature(22.0) |
|
sf = 1.0 |
|
if ( |
|
self.status["temperature"] == 38.0 |
|
): # adjust for 2003 model conductance levels at 38 |
|
sf = 3.03 # Q10 of 2, 22->38C. (p3106, R&M2003c) |
|
self.i_test_range = {"pulse": (-0.3, 0.3, 0.03)} |
|
self.vrange = [-75.0, -55.0] |
|
pars = self.get_cellpars(dataset, species=species, modelType=modelType) |
|
self.set_soma_size_from_Cm(pars.cap) |
|
self.status["na"] = pars.natype |
|
# pars.show() |
|
self.adjust_na_chans(soma, gbar=pars.nacn_gbar, sf=sf) |
|
soma().kht.gbar = nstomho(pars.kht_gbar, self.somaarea) |
|
soma().klt.gbar = nstomho(pars.klt_gbar, self.somaarea) |
|
# soma().ka.gbar = nstomho(pars.ka_gbar, self.somaarea) |
|
soma().ihvcn.gbar = nstomho(pars.ih_gbar, self.somaarea) |
|
soma().leak.gbar = nstomho(pars.leak_gbar, self.somaarea) |
|
soma().leak.erev = pars.leak_erev |
|
self.axonsf = 0.5 |
|
|
|
else: |
|
raise ValueError( |
|
"Species %s or species-modelType %s is not recognized for D-Stellate cells" |
|
% (species, modelType) |
|
) |
|
self.status["species"] = species |
|
self.status["modelType"] = modelType |
|
self.check_temperature() |
|
# self.cell_initialize(showinfo=False) |
|
if not silent: |
|
print("set cell as: ", species) |
|
print(" with Vm rest = %6.3f" % self.vm0) |
|
|
|
def adjust_na_chans(self, soma, sf=1.0, gbar=1000.0): |
|
""" |
|
adjust the sodium channel conductance |
|
|
|
Parameters |
|
---------- |
|
soma : soma object (no default) |
|
soma object whose sodium channel complement will have it's |
|
conductances adjusted depending on the channel type |
|
|
|
gbar : float (default: 1000.) |
|
The conductance to be set for the sodium channel |
|
|
|
debug : boolean (default: False) |
|
Flag for printing the conductance value and Na channel model |
|
|
|
Returns |
|
------- |
|
Nothing |
|
""" |
|
if self.status["ttx"]: |
|
gnabar = 0.0 |
|
else: |
|
gnabar = nstomho(gbar, self.somaarea) * sf |
|
nach = self.status["na"] |
|
if nach == "jsrna": |
|
soma().jsrna.gbar = gnabar |
|
soma.ena = self.e_na |
|
if self.debug: |
|
print("jsrna gbar: ", soma().jsrna.gbar) |
|
elif nach == "nav11": |
|
soma().nav11.gbar = gnabar * 0.5 |
|
soma.ena = self.e_na |
|
soma().nav11.vsna = 4.3 |
|
if self.debug: |
|
print("bushy using inva11") |
|
print("nav11 gbar: ", soma().nav11.gbar) |
|
elif nach == "na": |
|
soma().na.gbar = gnabar |
|
soma.ena = self.e_na |
|
if self.debug: |
|
print("na gbar: ", soma().na.gbar) |
|
elif nach == "nacn": |
|
soma().nacn.gbar = gnabar |
|
soma.ena = self.e_na |
|
if self.debug: |
|
print("nacn gbar: ", soma().nacn.gbar) |
|
else: |
|
raise ValueError( |
|
"Dstellate setting Na channels: channel %s not known" % nach |
|
) |
|
|
|
def add_axon(self): |
|
""" |
|
Add a default axon from the generic cell class to the bushy cell (see cell class). |
|
""" |
|
Cell.add_axon(self, self.soma, self.somaarea, self.c_m, self.R_a, self.axonsf) |
|
|
|
def add_dendrites(self): |
|
""" |
|
Add simple unbranched dendrites to basic Rothman Type I-II model. |
|
The dendrites have some kht and ih current |
|
""" |
|
cs = False # not implemented outside here - internal Cesium. |
|
nDend = range(4) # these will be simple, unbranced, N=4 dendrites |
|
dendrites = [] |
|
for i in nDend: |
|
dendrites.append(h.Section(cell=self.soma)) |
|
for i in nDend: |
|
dendrites[i].connect(self.soma) |
|
dendrites[i].L = 300 # length of the dendrite (not tapered) |
|
dendrites[i].diam = 1.25 # dendrite diameter |
|
dendrites[i].nseg = 21 # # segments in dendrites |
|
dendrites[i].Ra = 150 # ohm.cm |
|
dendrites[i].insert("kht") |
|
if cs is False: |
|
dendrites[i]().kht.gbar = 0.005 # a little Ht |
|
else: |
|
dendrites[i]().kht.gbar = 0.0 |
|
dendrites[i].insert("leak") # leak |
|
dendrites[i]().leak.gbar = 0.0001 |
|
dendrites[i].insert("ihvcn") # some H current |
|
dendrites[i]().ihvcn.gbar = 0.0 # 0.001 |
|
dendrites[i]().ihvcn.eh = -43.0 |
|
self.maindend = dendrites |
|
self.status["dendrites"] = True |
|
self.add_section(self.maindend, "maindend") |
|
|
|
|
|
class DummyDStellate(DStellate): |
|
""" DStellate class with no cell body; this cell only replays a predetermined |
|
spike train. Useful for testing, or replacing spike trains to determine |
|
the importance of spike structures within a network. |
|
""" |
|
|
|
def __init__(self, cf=None, species="mouse"): |
|
""" |
|
Parameters |
|
---------- |
|
cf : float (default: None) |
|
Required: the characteristic frequency for the DStellate |
|
Really just for reference. |
|
|
|
""" |
|
|
|
DStellate.__init__(self) |
|
self.vecstim = h.VecStim() |
|
|
|
# this causes the terminal to receive events from the VecStim: |
|
self.spike_source = self.vecstim |
|
|
|
# just an empty section for holding the terminal |
|
self.add_section(h.Section(), "soma") |
|
self.status = { |
|
"soma": True, |
|
"axon": False, |
|
"dendrites": False, |
|
"pumps": False, |
|
"na": None, |
|
"species": species, |
|
"modelType": "Dummy", |
|
"modelName": "DummyDStellate", |
|
"ttx": None, |
|
"name": "DummyDStellate", |
|
"morphology": None, |
|
"decorator": None, |
|
"temperature": None, |
|
} |
|
print("<< DStellate: Dummy DStellate Cell created >>") |
|
|
|
def set_spiketrain(self, times): |
|
""" Set the times of spikes (in seconds) to be replayed by the cell. |
|
""" |
|
self._spiketrain = times |
|
self._stvec = h.Vector(times) |
|
self.vecstim.play(self._stvec) |
|
|
|
|
|
class DStellateEager(DStellate): |
|
""" |
|
This is a model of the VCN D-Stellate cells as proposed by |
|
Eager, M.A., Grayden, D.B., Burkitt, A.N., and Meffin, H., |
|
"A neural circuit model of the ventral cochlear nucleus", |
|
Internet: |
|
http://citeseerx.ist.pus.edu/viewdoc/download?doi=10.1.79.9620.pdf&rep |
|
=rep&type=pdf |
|
also cited as: |
|
Proceedings of the 10th Australian International Conference on |
|
Speech Science and Technology, pp. 539-544, 2004. |
|
It is based on the Rothman and Manis (2003c) model, |
|
with small modifications. |
|
Their model includes dendrites and an axon, which are added in this version |
|
""" |
|
|
|
def __init__( |
|
self, nach="na", ttx=False, species="guineapig", modelType="I-II", debug=False |
|
): |
|
""" |
|
Initialize the VCN D-stellate model of Eager et al. Some model parameters may be modified. |
|
|
|
Parameters |
|
---------- |
|
nach : string (default: 'na') |
|
Set the sodium channel model. Choices are 'na', 'nav11', 'jsrna' |
|
|
|
ttx : boolean (default: False) |
|
ttx sets the sodium channel conductance to 0 |
|
|
|
species : string (default: 'guineapig') |
|
species to use for conductance scaling |
|
|
|
modelType : string (default: 'I-II') |
|
RM03 model type to use for conductances. |
|
|
|
debug : boolean (default: False) |
|
Flag to use to enable print statements for debugging purposes. |
|
|
|
""" |
|
super(DStellateEager, self).__init__() |
|
|
|
self.status = { |
|
"soma": True, |
|
"axon": False, |
|
"dendrites": False, |
|
"pumps": False, |
|
"na": nach, |
|
"species": species, |
|
"modelType": modelType, |
|
"ttx": ttx, |
|
"name": "DStellateEager", |
|
} |
|
self.i_test_range = (-0.25, 0.25, 0.025) # set range for ic command test |
|
|
|
soma = h.Section(name="DStellateEager_Soma_%x" % id(self)) # one compartment |
|
|
|
soma.nseg = 1 |
|
|
|
if nach in ["nacn", "na"]: |
|
soma.insert("na") |
|
elif nach == "nav11": |
|
soma.insert("nav11") |
|
elif nach == "jsrna": |
|
soma.insert("jsrna") |
|
else: |
|
raise ValueError("Sodium channel %s in type 1 cell not known" % nach) |
|
self.debug = debug |
|
soma.insert("kht") |
|
soma.insert("klt") |
|
soma.insert("ihvcn") |
|
soma.insert("leak") |
|
soma.ek = self.e_k |
|
soma().leak.erev = self.e_leak |
|
self.mechanisms = ["kht", "klt", "ihvcn", "leak", nach] |
|
self.add_section(soma, "soma") |
|
self.species_scaling( |
|
silent=False, species=species, modelType=modelType |
|
) # set the default type II cell parameters |
|
self.add_axon() # must follow species scaling so that area parameters are available |
|
self.add_dendrites() # similar for dendrites |
|
self.save_all_mechs() # save all mechanisms inserted, location and gbar values... |
|
self.get_mechs(soma) |
|
|
|
if self.debug: |
|
print("<< D-stellateEager: Eager DStellate Type I-II cell model created >>") |
|
|
|
def species_scaling(self, species="guineapig", modelType="I-II", silent=True): |
|
""" |
|
Adjust all of the conductances and the cell size according to the species requested. |
|
|
|
Parameters |
|
---------- |
|
species : string (default: 'guineapig') |
|
A string specifying the species used for scaling. Recognized values are |
|
'mouse', 'guineapig', and 'cat' (cat is just a larger version of the guineapig) |
|
|
|
modelType : string (default: 'I-II') |
|
A string specifying the version of the model to use. |
|
Current choices are 'I-II' (others need to be implemented) |
|
|
|
silent : boolean (default: True) |
|
Flag for printing debugging information. |
|
|
|
""" |
|
soma = self.soma |
|
if species == "mouse" and modelType == "I-II": |
|
# use conductance levels from Cao et al., J. Neurophys., 2007. |
|
self.set_soma_size_from_Cm(25.0) |
|
self.adjust_na_chans(soma, gbar=800.0) |
|
soma().kht.gbar = nstomho(150.0, self.somaarea) |
|
soma().klt.gbar = nstomho(20.0, self.somaarea) |
|
soma().ihvcn.gbar = nstomho(2.0, self.somaarea) |
|
soma().ihvcn.eh = -43 # Rodrigues and Oertel, 2006 |
|
soma().leak.gbar = nstomho(2.0, self.somaarea) |
|
self.axonsf = 0.5 |
|
elif ( |
|
species == "guineapig" and modelType == "I-II" |
|
): # values from R&M 2003, Type II-I |
|
self.set_soma_size_from_Diam(25.0) |
|
self.adjust_na_chans(soma, gbar=1000.0 * 0.75) |
|
soma().kht.gbar = 0.02 # nstomho(150.0, self.somaarea) |
|
soma().klt.gbar = 0.005 # nstomho(20.0, self.somaarea) |
|
soma().ihvcn.gbar = 0.0002 # nstomho(2.0, self.somaarea) |
|
soma().leak.gbar = 0.0005 # nstomho(2.0, self.somaarea) |
|
self.axonsf = 1.0 |
|
elif ( |
|
species == "cat" and modelType == "I=II" |
|
): # a cat is a big guinea pig Type I |
|
self.set_soma_size_from_Cm(35.0) |
|
self.adjust_na_chans(soma) |
|
soma().kht.gbar = nstomho(150.0, self.somaarea) |
|
soma().klt.gbar = nstomho(20.0, self.somaarea) |
|
soma().ihvcn.gbar = nstomho(2.0, self.somaarea) |
|
soma().leak.gbar = nstomho(2.0, self.somaarea) |
|
self.axonsf = 1.0 |
|
else: |
|
raise ValueError( |
|
"Species %s or species-type %s is not recognized for D-StellateEager cells" |
|
% (species, type) |
|
) |
|
self.status["species"] = species |
|
self.status["type"] = modelType |
|
self.cell_initialize(showinfo=True) |
|
if not silent: |
|
print(" set cell as: ", species) |
|
print(" with Vm rest = %6.3f" % self.vm0) |
|
|
|
def adjust_na_chans(self, soma, gbar=1000.0): |
|
""" |
|
adjust the sodium channel conductance |
|
|
|
Parameters |
|
---------- |
|
soma : soma object (no default) |
|
soma object whose sodium channel complement will have it's |
|
conductances adjusted depending on the channel type |
|
|
|
gbar : float (default: 1000.) |
|
The conductance to be set for the sodium channel |
|
|
|
Returns |
|
------- |
|
Nothing |
|
""" |
|
|
|
if self.status["ttx"]: |
|
gnabar = 0.0 |
|
else: |
|
gnabar = nstomho(gbar, self.somaarea) |
|
nach = self.status["na"] |
|
if nach == "jsrna": |
|
soma().jsrna.gbar = gnabar |
|
soma.ena = self.e_na |
|
if self.debug: |
|
print("using jsrna with gbar: ", soma().jsrna.gbar) |
|
elif nach == "nav11": |
|
soma().nav11.gbar = gnabar * 0.5 |
|
soma.ena = self.e_na |
|
soma().nav11.vsna = 4.3 |
|
if self.debug: |
|
print("using inva11 with gbar:", soma().na.gbar) |
|
print("nav11 gbar: ", soma().nav11.gbar) |
|
elif nach == "na": |
|
soma().na.gbar = gnabar |
|
soma.ena = self.e_na |
|
if self.debug: |
|
print("using na with gbar: ", soma().na.gbar) |
|
elif nach == "nach": |
|
soma().nach.gbar = gnabar |
|
soma.ena = self.e_na |
|
if self.debug: |
|
print(("uwing nacn with gbar: ", soma().nacn.gbar)) |
|
else: |
|
raise ValueError( |
|
"DstellateEager setting Na channels: channel %s not known" % nach |
|
) |
|
# print soma().na.gbar |
|
|
|
def add_axon(self): |
|
""" |
|
Adds an axon to the Eager. et al model |
|
Cell.add_axon(self, nodes=1, c_m=self.c_m, R_a=self.R_a, axonsf=self.axonsf, dia=3.0, len=70, seg=2) |
|
The Eager et al model just uses one cable, 70 microns long and 3 microns in dameter. |
|
|
|
Parameters |
|
---------- |
|
None |
|
|
|
Returns |
|
------- |
|
Nothing |
|
""" |
|
|
|
naxons = 1 |
|
axon = [] |
|
for i in range(naxons): |
|
axon.append(h.Section(cell=self.soma)) |
|
for i in range(naxons): |
|
axon[i].connect(self.soma) |
|
axon[i].L = 70 |
|
axon[i].diam = 3.0 |
|
axon[i].Ra = 500 |
|
axon[i].cm = 0.9 |
|
axon[i].nseg = 2 |
|
axon[i].insert("kht") |
|
axon[i].insert("klt") |
|
axon[i].insert("ihvcn") |
|
axon[i].insert("leak") |
|
axon[i].insert("na") |
|
axon[i].ek = self.e_k |
|
axon[i].ena = self.e_na |
|
axon[i]().leak.erev = self.e_leak |
|
axon[i]().na.gbar = 0.5 |
|
axon[i]().klt.gbar = 0.005 |
|
axon[i]().kht.gbar = 0.02 |
|
axon[i]().ihvcn.gbar = 0.0002 |
|
axon[i]().leak.gbar = 0.0005 |
|
self.status["axon"] = True |
|
self.add_section(axon, "axon") |
|
|
|
def add_dendrites(self): |
|
""" |
|
Adds dendrites to the Eager model. The Eager model uses simple passive dendrites. |
|
|
|
Parameters |
|
---------- |
|
None |
|
|
|
Returns |
|
------- |
|
Nothing |
|
""" |
|
|
|
nDend = range(2) # these will be simple, unbranced, N=4 dendrites |
|
dendrites = [] |
|
for i in nDend: |
|
dendrites.append(h.Section(cell=self.soma)) |
|
for i in nDend: |
|
dendrites[i].connect(self.soma) |
|
dendrites[i].L = 1100 # length of the dendrite (not tapered) |
|
dendrites[i].diam = 3.5 # dendrite diameter |
|
dendrites[i].nseg = 5 # # segments in dendrites |
|
dendrites[i].Ra = 1500 # ohm.cm |
|
dendrites[i].insert("leak") # leak |
|
dendrites[i]().leak.gbar = 0.00025 |
|
dendrites[i]().leak.erev = self.e_leak |
|
self.maindend = dendrites |
|
self.status["dendrites"] = True |
|
self.add_section(self.maindend, "maindend")
|
|
|