14. Visualising the internal states of a neuron

Visualising the internal states of a neuron

We look at the internal states of an HH neuron, and plot the properties on different graphs.

Code

from morphforge.stdimports import *
from morphforgecontrib.stdimports import *



# Create the environment:
env = NEURONEnvironment()

# Create the simulation:
sim = env.Simulation()


# Create a cell:
morphDict1 = {'root': {'length': 20, 'diam': 20, 'id':'soma'} }
m1 = MorphologyTree.fromDictionary(morphDict1)
cell = sim.create_cell(name="Cell1", morphology=m1)


lk_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Lk", env=env)
na_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="Na", env=env)
k_chl = ChannelLibrary.get_channel(modelsrc=StandardModels.HH52, channeltype="K", env=env)


# Apply the channels uniformly over the cell
cell.apply_channel( lk_chl)
cell.apply_channel( na_chl)
cell.apply_channel( k_chl)
cell.set_passive( PassiveProperty.SpecificCapacitance, qty('1.0:uF/cm2'))

# Get a cell_location on the cell:


# Create the stimulus and record the injected current:
cc = sim.create_currentclamp(name="Stim1", amp=qty("250:pA"), dur=qty("100:ms"), delay=qty("100:ms"), cell_location=cell.soma)
sim.record(cc, what=StandardTags.Current)
# Define what to record:
sim.record(cell, what=StandardTags.Voltage, name="SomaVoltage", cell_location = cell.soma)


sim.record(lk_chl, cell_location = cell.soma, what=StandardTags.ConductanceDensity)
sim.record(na_chl, cell_location = cell.soma, what=StandardTags.ConductanceDensity)
sim.record(k_chl,  cell_location = cell.soma, what=StandardTags.ConductanceDensity)

sim.record(lk_chl, cell_location = cell.soma, what=StandardTags.CurrentDensity)
sim.record(na_chl, cell_location = cell.soma, what=StandardTags.CurrentDensity)
sim.record(k_chl,  cell_location = cell.soma, what=StandardTags.CurrentDensity)


sim.record(na_chl, cell_location = cell.soma, what=StandardTags.StateVariable, state="m")
sim.record(na_chl, cell_location = cell.soma, what=StandardTags.StateVariable, state="h")
sim.record(k_chl,  cell_location = cell.soma, what=StandardTags.StateVariable, state="n")


# Also:
#sim.record(na_chl, where = cell.soma, what=StandardTags.StateTimeConstant, state="m")
#sim.record(na_chl, where = cell.soma, what=StandardTags.StateTimeConstant, state="h")
#sim.record(k_chl,  where = cell.soma, what=StandardTags.StateTimeConstant, state="n")

#sim.record(na_chl, where = cell.soma, what=StandardTags.StateSteadyState, state="m")
#sim.record(na_chl, where = cell.soma, what=StandardTags.StateSteadyState, state="h")
#sim.record(k_chl,  where = cell.soma, what=StandardTags.StateSteadyState, state="n")


# run the simulation
results = sim.run()


# Display the results, there is a lot of info for one graph, so lets split it up:
TagViewer([results], timerange=(50, 250)*units.ms, show=False)


TagViewer([results], timerange=(50, 250)*units.ms, show=False,
          plots = [
                       DefaultTagPlots.Voltage,
                       DefaultTagPlots.Current,
                       DefaultTagPlots.CurrentDensity,
                      ])


TagViewer([results], timerange=(100, 120)*units.ms, show=True,
          plots = [
                       DefaultTagPlots.Voltage,
                       DefaultTagPlots.ConductanceDensity,
                       DefaultTagPlots.StateVariable,
                      ])

Figures

../_images/singlecell_simulation070_out2.png

Download Figure

../_images/singlecell_simulation070_out1.png

Download Figure

../_images/singlecell_simulation070_out3.png

Download Figure

Output

    No handlers could be found for logger "neurounits"
2013-10-19 15:40:40,588 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:40,589 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-10-19 15:40:42,181 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:42,181 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
Loading Bundle from: /local/scratch/mh735/tmp/morphforge/tmp/simulationresults/ec/ecf2dde0447333de8ee0864e7877ff6e.bundle (13k) : 0.775 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}

loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_468d766f8a3c48bce3bbb5aa16488aa9.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_10528623af7b919560a2e2606bf0cd9c.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_e53416588be6b02ed52a843da0f43a15.so
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Running Simulation
Time for Extracting Data: (11 records) 0.0158488750458
Running simulation : 0.145 seconds
Post-processing : 0.014 seconds
Entire load-run-save time : 0.934 seconds
Suceeded
Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
PlotMnager:Saving  _output/figures/singlecell_simulation070/{png,svg}/fig000_Autosave_figure_1.{png,svg}
PlotMnager:Saving  _output/figures/singlecell_simulation070/{png,svg}/fig001_Autosave_figure_2.{png,svg}
PlotMnager:Saving  _output/figures/singlecell_simulation070/{png,svg}/fig002_Autosave_figure_3.{png,svg}