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898 lines
33 KiB
898 lines
33 KiB
2 years ago
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from __future__ import print_function
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from neuron import h
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from ..util import nstomho
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from .cell import Cell
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from ..util import Params
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from .. import synapses
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from .. import data
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__all__ = ["DStellate", "DStellateRothman", "DStellateEager"]
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class DStellate(Cell):
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type = "dstellate"
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@classmethod
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def create(cls, model="RM03", **kwds):
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if model == "RM03":
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return DStellateRothman(**kwds)
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elif model == "Eager":
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return DStellateEager(**kwds)
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elif model == "dummy":
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return DummyDStellate(**kwds)
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else:
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raise ValueError("DStellate type %s is unknown", type)
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def __init__(self):
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Cell.__init__(self)
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self.spike_source = (
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None
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) # used by DummyDStellate to connect VecStim to terminal
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def make_psd(self, terminal, psd_type, **kwds):
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"""
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Connect a presynaptic terminal to one post section at the specified location, with the fraction
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of the "standard" conductance determined by gbar.
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The default condition is designed to pass the unit test (loc=0.5)
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Parameters
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----------
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terminal : Presynaptic terminal (NEURON object)
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psd_type : either simple or multisite PSD for bushy cell
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kwds: dictionary of options.
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Two are currently handled:
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postsize : expect a list consisting of [sectionno, location (float)]
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AMPAScale : float to scale the ampa currents
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"""
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if (
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"postsite" in kwds
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): # use a defined location instead of the default (soma(0.5)
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postsite = kwds["postsite"]
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loc = postsite[1] # where on the section?
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uname = (
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"sections[%d]" % postsite[0]
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) # make a name to look up the neuron section object
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post_sec = self.hr.get_section(uname) # Tell us where to put the synapse.
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else:
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loc = 0.5
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post_sec = self.soma
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if psd_type == "simple":
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if terminal.cell.type in ["sgc", "dstellate", "tuberculoventral"]:
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weight = data.get(
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"%s_synapse" % terminal.cell.type,
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species=self.species,
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post_type=self.type,
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field="weight",
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)
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tau1 = data.get(
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"%s_synapse" % terminal.cell.type,
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species=self.species,
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post_type=self.type,
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field="tau1",
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)
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tau2 = data.get(
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"%s_synapse" % terminal.cell.type,
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species=self.species,
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post_type=self.type,
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field="tau2",
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)
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erev = data.get(
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"%s_synapse" % terminal.cell.type,
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species=self.species,
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post_type=self.type,
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field="erev",
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)
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return self.make_exp2_psd(
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post_sec,
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terminal,
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weight=weight,
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loc=loc,
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tau1=tau1,
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tau2=tau2,
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erev=erev,
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)
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else:
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raise TypeError(
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"Cannot make simple PSD for %s => %s"
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% (terminal.cell.type, self.type)
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)
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elif psd_type == "multisite":
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if terminal.cell.type == "sgc":
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# Max conductances for the glu mechanisms are calibrated by
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# running `synapses/tests/test_psd.py`. The test should fail
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# if these values are incorrect
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self.AMPAR_gmax = (
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data.get(
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"sgc_synapse",
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species=self.species,
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post_type=self.type,
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field="AMPAR_gmax",
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)
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* 1e3
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)
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self.NMDAR_gmax = (
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data.get(
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"sgc_synapse",
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species=self.species,
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post_type=self.type,
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field="NMDAR_gmax",
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)
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* 1e3
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)
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self.Pr = data.get(
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"sgc_synapse", species=self.species, post_type=self.type, field="Pr"
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)
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# adjust gmax to correct for initial Pr
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self.AMPAR_gmax = self.AMPAR_gmax / self.Pr
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self.NMDAR_gmax = self.NMDAR_gmax / self.Pr
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# old values:
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# AMPA_gmax = 0.22479596944138733*1e3 # factor of 1e3 scales to pS (.mod mechanisms) from nS.
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# NMDA_gmax = 0.12281291946623739*1e3
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if "AMPAScale" in kwds:
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self.AMPAR_gmax = (
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self.AMPAR_gmax * kwds["AMPAScale"]
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) # allow scaling of AMPA conductances
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if "NMDAScale" in kwds:
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self.NMDAR_gmax = self.NMDAR_gmax * kwds["NMDAScale"]
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return self.make_glu_psd(
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post_sec, terminal, self.AMPAR_gmax, self.NMDAR_gmax, loc=loc
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)
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elif terminal.cell.type == "dstellate":
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# Get GLY kinetic constants from database
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return self.make_gly_psd(post_sec, terminal, psdtype="glyfast", loc=loc)
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elif terminal.cell.type == "tuberculoventral":
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# Get GLY kinetic constants from database
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return self.make_gly_psd(post_sec, terminal, psdtype="glyfast", loc=loc)
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else:
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raise TypeError(
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"Cannot make PSD for %s => %s" % (terminal.cell.type, self.type)
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)
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else:
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raise ValueError("Unsupported psd type %s" % psd_type)
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def make_terminal(self, post_cell, term_type, **kwds):
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if term_type == "simple":
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return synapses.SimpleTerminal(
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self.soma, post_cell, spike_source=self.spike_source, **kwds
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)
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elif term_type == "multisite":
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if post_cell.type in [
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"dstellate",
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"tuberculoventral",
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"pyramidal",
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"bushy",
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"tstellate",
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]:
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nzones = data.get(
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"dstellate_synapse",
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species=self.species,
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post_type=post_cell.type,
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field="n_rsites",
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)
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delay = data.get(
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"dstellate_synapse",
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species=self.species,
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post_type=post_cell.type,
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field="delay",
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)
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else:
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raise NotImplementedError(
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"No knowledge as to how to connect D stellate cell to cell type %s"
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% type(post_cell)
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)
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pre_sec = self.soma
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return synapses.StochasticTerminal(
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pre_sec,
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post_cell,
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nzones=nzones,
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spike_source=self.spike_source,
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delay=delay,
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**kwds
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)
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else:
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raise ValueError("Unsupported terminal type %s" % term_type)
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class DStellateRothman(DStellate):
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"""
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VCN D-stellate model:
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as a type I-II from Rothman and Manis, 2003
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"""
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def __init__(
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self,
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morphology=None,
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decorator=None,
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nach=None,
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ttx=False,
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species="guineapig",
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modelType=None,
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modelName=None,
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debug=False,
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):
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"""
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initialize a radial stellate (D-stellate) cell, using the default parameters for guinea pig from
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R&M2003, as a type I-II cell.
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Modifications to the cell can be made by calling methods below. These include:
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* changing the sodium channel
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* Changing "species" to mouse or cat (scales conductances)
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* Shifting model type
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Parameters
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----------
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morphology : string (default: None)
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Name of a .hoc file representing the morphology. This file is used to constructe
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an electrotonic (cable) model.
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If None (default), then a "point" (really, single cylinder) model is made, exactly according to RM03.
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decorator : Python function (default: None)
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decorator is a function that "decorates" the morphology with ion channels according
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to a set of rules.
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If None, a default set of channels is inserted into the first soma section, and the
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rest of the structure is "bare".
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nach : string (default: None)
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nach selects the type of sodium channel that will be used in the model. A channel mechanism
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by that name must exist. A value of None will set the channel to a default for the model (nacn).
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ttx : Boolean (default: False)
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If ttx is True, then the sodium channel conductance is set to 0 everywhere in the cell.
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This flag duplicates the effects of tetrodotoxin in the model. Currently, the flag is not implemented.
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species: string (default 'guineapig')
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species defines the pattern of ion channel densities that will be inserted, according to
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prior measurements in various species. Note that
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if a decorator function is specified, this argument is ignored as the decorator will
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specify the channel density.
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modelType: string (default: None)
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modelType specifies the subtype of the cell model that will be used (e.g., "II", "II-I", etc).
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modelType is passed to the decorator, or to species_scaling to adjust point (single cylinder) models.
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debug: boolean (default: False)
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When True, there will be multiple printouts of progress and parameters.
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Returns
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-------
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Nothing
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"""
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super(DStellateRothman, self).__init__()
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if modelType == None:
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modelType = "I-II"
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if species == "guineapig":
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modelName = "RM03"
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temp = 22.0
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if nach == None:
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nach = "nacn"
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if species == "mouse":
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temp = 34.0
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if modelName is None:
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modelName = "XM13"
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if nach is None:
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nach = "na"
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self.debug = debug
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# if modelType == None: # allow us to pass None to get the default
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# modelType = 'I-II'
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# if nach == None:
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# nach = 'na'
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self.status = {
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"soma": True,
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"axon": False,
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"dendrites": False,
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"pumps": False,
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"na": nach,
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"species": species,
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"modelType": modelType,
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"modelName": modelName,
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"ttx": ttx,
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"name": "DStellate",
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"morphology": morphology,
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"decorator": decorator,
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"temperature": None,
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}
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self.i_test_range = {
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"pulse": [(-0.3, 0.3, 0.03), (-0.05, 0.0, 0.005)]
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} # set range for ic command test
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self.vrange = [-75.0, -55.0]
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self.spike_threshold = (
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-40.0
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) # matches threshold in released CNModel (set in base cell class)
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if morphology is None:
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"""
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instantiate a basic soma-only ("point") model
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"""
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soma = h.Section(
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name="DStellate_Soma_%x" % id(self)
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) # one compartment of about 29000 um2
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soma.nseg = 1
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self.add_section(soma, "soma")
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else:
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"""
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instantiate a structured model with the morphology as specified by
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the morphology file
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"""
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self.set_morphology(morphology_file=morphology)
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# decorate the morphology with ion channels
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if decorator is None: # basic model, only on the soma
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self.mechanisms = ["klt", "kht", "ihvcn", "leak", nach]
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for mech in self.mechanisms:
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self.soma.insert(mech)
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self.soma.ena = self.e_na
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self.soma.ek = self.e_k
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self.soma().leak.erev = self.e_leak
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self.c_m = 0.9
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self.set_soma_size_from_Cm(12.0)
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self.species_scaling(
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silent=True, species=species, modelType=modelType
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) # set the default type II cell parameters
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else: # decorate according to a defined set of rules on all cell compartments
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self.decorate()
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self.save_all_mechs() # save all mechanisms inserted, location and gbar values...
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self.get_mechs(self.soma)
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if self.debug:
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print("<< D-stellate: JSR Stellate Type I-II cell model created >>")
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def get_cellpars(self, dataset, species="guineapig", modelType="I-II"):
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cellcap = data.get(
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dataset, species=species, model_type=modelType, field="soma_Cap"
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)
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chtype = data.get(
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dataset, species=species, model_type=modelType, field="na_type"
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)
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pars = Params(cap=cellcap, natype=chtype)
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# pars.show()
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if self.status["modelName"] == "RM03":
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for g in [
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"%s_gbar" % pars.natype,
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"kht_gbar",
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"klt_gbar",
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"ka_gbar",
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"ih_gbar",
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"leak_gbar",
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"leak_erev",
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"ih_eh",
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"e_k",
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"e_na",
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]:
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pars.additem(
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g, data.get(dataset, species=species, model_type=modelType, field=g)
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)
|
||
|
|
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")
|