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model of DCN pyramidal neuron
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DCNmodel/examples/test_cells.py

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#!/usr/bin/python
"""
Test the basic membrane physiology of cell types.
Basic Usage: python test_cells.py celltype species [--cc | --vc]
This script generates a cell of the specified type and species, then tests the
cell with a series of current/voltage pulses to produce I/V, F/I, and spike
latency analyses.
"""
import argparse
import os, sys
from neuron import h
import pyqtgraph as pg
import cnmodel
import cnmodel.cells as cells
from cnmodel.protocols import IVCurve, VCCurve
debugFlag = True
ax = None
h.celsius = 22
default_durs = [10.0, 100.0, 20.0]
cclamp = False
cellinfo = {
"types": [
"bushy",
"bushycoop",
"tstellate",
"tstellatenav11",
"dstellate",
"dstellateeager",
"sgc",
"cartwheel",
"pyramidal",
"octopus",
"tuberculoventral",
"mso",
],
"morphology": ["point", "waxon", "stick"],
"nav": ["std", "jsrna", "nav11", "nacncoop"],
"species": ["guineapig", "cat", "rat", "mouse"],
"pulse": ["step", "pulse"],
}
# Format for ivranges is list of tuples. This allows finer increments in selected ranges, such as close to rest
ccivrange = {
"mouse": {
"bushy": {"pulse": [(-1, 1.2, 0.05)]},
"bushycoop": {"pulse": [(-0.5, 0.7, 0.02)]},
"tstellate": {"pulse": [(-1.0, 1.01, 0.05), (-0.015, 0, 0.005)]},
"tstellatenav11": {"pulse": [(-1, 1.0, 0.1)]},
"dstellate": {"pulse": [(-0.3, 0.301, 0.015)]},
"octopus": {"pulse": [(-1.0, 1.0, 0.05)]},
"sgc": {"pulse": [(-0.3, 0.6, 0.02)]},
"cartwheel": {"pulse": [(-0.5, 0.5, 0.05)]},
"pyramidal": {
"pulse": [(-0.3, 0.3, 0.025), (-0.040, 0.025, 0.005)]
}, # , 'prepulse': [(-0.25, -0.25, 0.25)]},
"tuberculoventral": {"pulse": [(-0.35, 1.0, 0.05), (-0.040, 0.01, 0.005)]},
},
"guineapig": {
"bushy": {"pulse": [(-1, 1.2, 0.05)]},
"tstellate": {"pulse": [(-0.15, 0.15, 0.01)]},
"dstellate": {"pulse": [(-0.25, 0.25, 0.025)]},
"dstellateeager": {"pulse": [(-0.6, 1.0, 0.025)]},
"octopus": {"pulse": [(-2.0, 6.0, 0.2)]},
"sgc": {"pulse": [(-0.3, 0.6, 0.02)]},
"mso": {"pulse": [(-1, 1.2, 0.05)]},
},
"rat": {
"pyramidal": {
"pulse": [(-0.3, 0.3, 0.025), (-0.040, 0.025, 0.005)]
} # 'prepulse': [(-0.25, -0.25, 0.25)]},
},
}
# scales holds some default scaling to use in the cciv plots
# argument is {cellname: (xmin, xmax, IVymin, IVymax, FIspikemax,
# offset(for spikes), crossing (for IV) )}
## the "offset" refers to setting the axes back a bit
scale = {
"bushy": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"bushycoop": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"tstellate": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"tstellatenav11": (
-1.0,
-160.0,
1.0,
-40,
0,
40,
"offset",
5,
"crossing",
[0, -60],
),
"tstellatedend": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"dstellate": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"dstellateeager": (
-1.0,
-160.0,
1.0,
-40,
0,
40,
"offset",
5,
"crossing",
[0, -60],
),
"sgc:": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"cartwheel": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"pyramidal": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"tuberculoventral": (
-1.0,
-160.0,
1.0,
-40,
0,
40,
"offset",
5,
"crossing",
[0, -60],
),
"octopus": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
"mso": (-1.0, -160.0, 1.0, -40, 0, 40, "offset", 5, "crossing", [0, -60]),
}
class Tests:
"""
Class to select cells for tests
"""
def __init__(self):
pass
def selectCell(self, args):
"""
Parameters
----------
args : argparse args from command line
Returns
-------
cell
Instantiated cell of the selected celltype
"""
h.celsius = float(args.temp)
#
# Spiral Ganglion cell tests
#
if args.celltype == "sgc": # morphology is always "point" for SGCs
cell = cells.SGC.create(
debug=debugFlag,
species=args.species,
nach=args.nav,
ttx=args.ttx,
modelType=args.type,
)
#
# Bushy tests
#
elif args.celltype == "bushy" and args.morphology == "point":
cell = cells.Bushy.create(
model="RM03",
species=args.species,
modelType=args.type,
ttx=args.ttx,
nach=args.nav,
debug=debugFlag,
)
# cell.soma().klt.gbar = 0.0003
elif args.celltype == "bushy" and args.morphology == "waxon":
cell = cells.Bushy.create(
model="RM03",
species=args.species,
modelType=args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
)
cell.add_axon()
elif args.celltype == "bushy" and args.morphology == "stick":
cell = cells.Bushy.create(
model="RM03",
species=args.species,
modelType=args.type,
morphology="cnmodel/morphology/bushy_stick.hoc",
decorator=True,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
)
h.topology()
elif args.celltype == "bushycoop" and args.morphology == "point":
cell = cells.Bushy.create(
model="RM03",
species=args.species,
modelType=args.type,
ttx=args.ttx,
nach=args.nav,
debug=debugFlag,
)
#
# T-stellate tests
#
elif args.celltype == "tstellate" and args.morphology == "point":
cell = cells.TStellate.create(
model="RM03",
species=args.species,
modelType=args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
)
elif args.celltype == "tstellate" and args.morphology == "stick":
cell = cells.TStellate.create(
model="RM03",
species=args.species,
modelType=args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
morphology="cnmodel/morphology/tstellate_stick.hoc",
decorator=True,
)
elif (
args.celltype == "tstellatenav11" and args.morphology == "point"
): # note this uses a different model...
print("test_cells: Stellate NAV11")
cell = cells.TStellateNav11.create(
model="Nav11",
species=args.species,
modelType=None,
ttx=args.ttx,
debug=debugFlag,
)
elif (
args.celltype == "tstellatenav11" and args.morphology == "stick"
): # note this uses a different model...
cell = cells.TStellateNav11.create(
model="Nav11",
species=args.species,
modelType=None,
morphology="cnmodel/morphology/tstellate_stick.hoc",
decorator=True,
ttx=args.ttx,
debug=debugFlag,
)
h.topology()
#
# Octopus cell tests
#
elif args.celltype == "octopus" and args.morphology == "point":
cell = cells.Octopus.create(
species=args.species,
modelType="RM03", # args.type,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
)
elif (
args.celltype == "octopus" and args.morphology == "stick"
): # Go to spencer et al. model
cell = cells.Octopus.create(
modelType="Spencer",
species=args.species,
morphology="cnmodel/morphology/octopus_spencer_stick.hoc",
decorator=True,
nach=args.nav,
ttx=args.ttx,
debug=debugFlag,
)
h.topology()
#
# D-stellate tests
#
elif args.celltype == "dstellate":
cell = cells.DStellate.create(
debug=debugFlag, species=args.species, ttx=args.ttx, modelType=args.type
)
elif args.celltype == "dstellateeager":
cell = cells.DStellateEager.create(
debug=debugFlag, ttx=args.ttx, modelType=args.type
)
#
# DCN pyramidal cell tests
#
elif args.celltype == "pyramidal":
cell = cells.Pyramidal.create(
modelType=args.type, ttx=args.ttx, debug=debugFlag
)
#
# DCN tuberculoventral cell tests
#
elif args.celltype == "tuberculoventral" and args.morphology == "point":
cell = cells.Tuberculoventral.create(
species="mouse",
modelType="TVmouse",
ttx=args.ttx,
nach=args.nav,
debug=debugFlag,
)
elif args.celltype == "tuberculoventral" and args.morphology == "stick":
cell = cells.Tuberculoventral.create(
species="mouse",
modelType="TVmouse",
morphology="cnmodel/morphology/tv_stick.hoc",
decorator=True,
ttx=args.ttx,
debug=debugFlag,
)
h.topology()
#
# DCN cartwheel cell tests
#
elif args.celltype == "cartwheel":
cell = cells.Cartwheel.create(
modelType=args.type, ttx=args.ttx, debug=debugFlag
)
#
# MSO principal neuron tests
#
elif args.celltype == "mso" and args.morphology == "point":
cell = cells.MSO.create(
model="RM03",
species=args.species,
modelType=args.type,
ttx=args.ttx,
nach=args.nav,
debug=debugFlag,
)
else:
raise ValueError(
"Cell Type %s and configurations nav=%s or config=%s are not available"
% (args.celltype, args.nav, args.morphology)
)
print(cell.__doc__)
self.cell = cell
def run_test(self, sites, ptype, args):
"""
Run either vc or cc test, and plot the result
Parameters
----------
args : argparse args from command line
"""
self.cell.set_temperature(float(args.temp))
print(self.cell.status)
V0 = self.cell.find_i0(showinfo=True)
# self.cell.cell_initialize()
print(
"Currents at nominal Vrest= %.2f I = 0: I = %g "
% (V0, self.cell.i_currents(V=V0))
)
self.cell.print_mechs(self.cell.soma)
instant = self.cell.compute_rmrintau(auto_initialize=False, vrange=None)
print(
" From Inst: Rin = {:7.1f} Tau = {:7.1f} Vm = {:7.1f}".format(
instant["Rin"], instant["tau"], instant["v"]
)
)
if args.cc is True:
# define the current clamp electrode and default settings
self.iv = IVCurve()
self.iv.run(
ccivrange[args.species][args.celltype],
self.cell,
durs=default_durs,
sites=sites,
reppulse=ptype,
temp=float(args.temp),
)
ret = self.iv.input_resistance_tau()
print(
" From IV: Rin = {:7.1f} Tau = {:7.1f} Vm = {:7.1f}".format(
ret["slope"], ret["tau"], ret["intercept"]
)
)
self.iv.show(cell=self.cell)
elif args.rmp is True:
print("temperature: ", self.cell.status["temperature"])
self.iv = IVCurve()
self.iv.run(
{"pulse": (0, 0, 1)},
self.cell,
durs=default_durs,
sites=sites,
reppulse=ptype,
temp=float(args.temp),
)
self.iv.show(cell=self.cell, rmponly=True)
elif args.vc is True:
# define the voltage clamp electrode and default settings
self.vc = VCCurve()
self.vc.run((-120, 40, 5), self.cell)
self.vc.show(cell=self.cell)
else:
raise ValueError("Nothing to run. Specify one of --cc, --vc, --rmp.")
def main():
parser = argparse.ArgumentParser(
description=(
"test_cells.py:",
" Biophysical representations of neurons (mostly auditory), test file",
)
)
parser.add_argument("celltype", action="store")
parser.add_argument("species", action="store", default="guineapig")
parser.add_argument("--type", action="store", default=None)
parser.add_argument(
"--temp", action="store", default=22.0, help=("Temp DegC (22 default)")
)
# species is an optional option....
parser.add_argument(
"-m",
action="store",
dest="morphology",
default="point",
help=("Set morphology: %s " % [morph for morph in cellinfo["morphology"]]),
)
parser.add_argument(
"--nav",
action="store",
dest="nav",
default=None,
help=("Choose sodium channel: %s " % [ch for ch in cellinfo["nav"]]),
)
parser.add_argument(
"--ttx",
action="store_true",
dest="ttx",
default=False,
help=("Use TTX (no sodium current"),
)
parser.add_argument(
"-p",
action="store",
dest="pulsetype",
default="step",
help=("Set CCIV pulse to step or repeated pulse"),
)
clampgroup = parser.add_mutually_exclusive_group()
clampgroup.add_argument(
"--vc", action="store_true", help="Run in voltage clamp mode"
)
clampgroup.add_argument(
"--cc", action="store_true", help="Run in current clamp mode"
)
clampgroup.add_argument(
"--rmp", action="store_true", help="Run to get RMP in current clamp mode"
)
args = parser.parse_args()
if args.celltype not in cellinfo["types"]:
print("cell: %s is not in our list of cell types" % (args.celltype))
print("celltypes: ", cellinfo["types"])
sys.exit(1)
path = os.path.dirname(cnmodel.__file__)
# h.load_file("stdrun.hoc")
# h.load_file(os.path.join(path, "custom_init.hoc")) # replace init with one that gets closer to steady state
# print 'Species: ', args.species
# print 'Morphology configuration: ', args.morphology
sites = None
if args.pulsetype == "step":
ptype = None
else:
ptype = "pulses"
if args.morphology in cellinfo["morphology"]:
print("Morphological configuration %s is ok" % args.morphology)
t = Tests()
t.selectCell(args)
app = pg.mkQApp()
t.run_test(sites, ptype, args)
if sys.flags.interactive == 0:
pg.QtGui.QApplication.exec_()
if __name__ == "__main__":
main()