12. Visualising action potential propagation along an axon

Visualising action potential propagation along an axon In this simulation, we create a cell with a long axon. We put HH-channels over its surface and give it a short current injection into the soma. We look at the voltage at various points along the axon, and see it propogate.

Code

from morphforge.stdimports import *
from morphforgecontrib.simulation.channels.hh_style.core.mmleak import StdChlLeak
from morphforgecontrib.simulation.channels.hh_style.core.mmalphabeta import StdChlAlphaBeta


# Create the environment:
env = NEURONEnvironment()

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

# Create a cell:
morph = MorphologyBuilder.get_soma_axon_morph(axon_length=3000.0, axon_radius=0.15, soma_radius=9.0, axon_sections=20)
cell = sim.create_cell(name="Cell1", morphology=morph)


lk_chl = env.Channel(
                         StdChlLeak,
                         name="LkChl",
                         conductance=qty("0.3:mS/cm2"),
                         reversalpotential=qty("-54.3:mV"),
                       )

na_state_vars = { "m": {
                      "alpha":[-4.00, -0.10, -1.00, 40.00, -10.00],
                      "beta": [4.00, 0.00, 0.00, 65.00, 18.00]},
                    "h": {
                        "alpha":[0.07, 0.00, 0.00, 65.00, 20.00] ,
                        "beta": [1.00, 0.00, 1.00, 35.00, -10.00]}
                  }

na_chl = env.Channel(
                        StdChlAlphaBeta,
                        name="NaChl", ion="na",
                        equation="m*m*m*h",
                        conductance=qty("120:mS/cm2"),
                        reversalpotential=qty("50:mV"),
                        statevars=na_state_vars,

                       )
k_state_vars = { "n": {
                      "alpha":[-0.55, -0.01, -1.0, 55.0, -10.0],
                      "beta": [0.125, 0, 0, 65, 80]},
                   }

k_chl = env.Channel(
                        StdChlAlphaBeta,
                        name="KChl", ion="k",
                        equation="n*n*n*n",
                        conductance=qty("36:mS/cm2"),
                        reversalpotential=qty("-77:mV"),
                        statevars=k_state_vars,

                       )


# 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'))


# Create the stimulus and record the injected current:
cc = sim.create_currentclamp(name="Stim1", amp=qty("250:pA"), dur=qty("5:ms"), delay=qty("100:ms"), cell_location=cell.soma)
sim.record(cc, what=StandardTags.Current)



# To record along the axon, we create a set of 'CellLocations', at the distances
# specified (start, stop,
for cell_location in CellLocator.get_locations_at_distances_away_from_dummy(cell=cell, distances=range(9, 3000, 100)):

    print " -- ", cell_location.section
    print " -- ", cell_location.sectionpos
    print " -- ", cell_location.get_3d_position()

    # Create a path along the morphology from the centre of the
    # Soma
    path = MorphPath(cell.soma, cell_location)
    print "Distance to Soma Centre:", path.get_length()

    sim.record(cell, what=StandardTags.Voltage, cell_location=cell_location, description="Distance Recording at %0.0f (um)"% path.get_length())


# Define what to record:
sim.record(cell, what=StandardTags.Voltage, name="SomaVoltage", cell_location = cell.soma)

# run the simulation
results = sim.run()

# Display the results:
TagViewer([results], timerange=(97.5, 140)*units.ms)

Figures

../_images/singlecell_simulation060_out1.png

Download Figure

Output

    No handlers could be found for logger "neurounits"
Openning ScriptFlags
/auto/homes/mh735/hw/NeuroUnits/ext_deps
Loading StdLib file: /auto/homes/mh735/hw/NeuroUnits/src/neurounits/../stdlib/stdlib.eqn
 --  <SectionObject: [0.000000, 0.000000, 0.000000, r=9.000000] -> [18.000000, 0.000000, 0.000000, r=9.000000], Length: 18.00, Region:soma, idtag:soma, >
 --  0.5
 --  [ 9.  0.  0.]
Distance to Soma Centre: 0.0
 --  <SectionObject: [18.000000, 0.000000, 0.000000, r=9.000000] -> [168.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_1, >
 --  0.606666666667
 --  [ 109.    0.    0.]
Distance to Soma Centre: 100.0
 --  <SectionObject: [168.000000, 0.000000, 0.000000, r=0.150000] -> [318.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_2, >
 --  0.273333333333
 --  [ 209.    0.    0.]
Distance to Soma Centre: 200.0
 --  <SectionObject: [168.000000, 0.000000, 0.000000, r=0.150000] -> [318.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_2, >
 --  0.94
 --  [ 309.    0.    0.]
Distance to Soma Centre: 300.0
 --  <SectionObject: [318.000000, 0.000000, 0.000000, r=0.150000] -> [468.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_3, >
 --  0.606666666667
 --  [ 409.    0.    0.]
Distance to Soma Centre: 400.0
 --  <SectionObject: [468.000000, 0.000000, 0.000000, r=0.150000] -> [618.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_4, >
 --  0.273333333333
 --  [ 509.    0.    0.]
Distance to Soma Centre: 500.0
 --  <SectionObject: [468.000000, 0.000000, 0.000000, r=0.150000] -> [618.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_4, >
 --  0.94
 --  [ 609.    0.    0.]
Distance to Soma Centre: 600.0
 --  <SectionObject: [618.000000, 0.000000, 0.000000, r=0.150000] -> [768.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_5, >
 --  0.606666666667
 --  [ 709.    0.    0.]
Distance to Soma Centre: 700.0
 --  <SectionObject: [768.000000, 0.000000, 0.000000, r=0.150000] -> [918.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_6, >
 --  0.273333333333
 --  [ 809.    0.    0.]
Distance to Soma Centre: 800.0
 --  <SectionObject: [768.000000, 0.000000, 0.000000, r=0.150000] -> [918.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_6, >
 --  0.94
 --  [ 909.    0.    0.]
Distance to Soma Centre: 900.0
 --  <SectionObject: [918.000000, 0.000000, 0.000000, r=0.150000] -> [1068.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_7, >
 --  0.606666666667
 --  [ 1009.     0.     0.]
Distance to Soma Centre: 1000.0
 --  <SectionObject: [1068.000000, 0.000000, 0.000000, r=0.150000] -> [1218.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_8, >
 --  0.273333333333
 --  [ 1109.     0.     0.]
Distance to Soma Centre: 1100.0
 --  <SectionObject: [1068.000000, 0.000000, 0.000000, r=0.150000] -> [1218.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_8, >
 --  0.94
 --  [ 1209.     0.     0.]
Distance to Soma Centre: 1200.0
 --  <SectionObject: [1218.000000, 0.000000, 0.000000, r=0.150000] -> [1368.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_9, >
 --  0.606666666667
 --  [ 1309.     0.     0.]
Distance to Soma Centre: 1300.0
 --  <SectionObject: [1368.000000, 0.000000, 0.000000, r=0.150000] -> [1518.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_10, >
 --  0.273333333333
 --  [ 1409.     0.     0.]
Distance to Soma Centre: 1400.0
 --  <SectionObject: [1368.000000, 0.000000, 0.000000, r=0.150000] -> [1518.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_10, >
 --  0.94
 --  [ 1509.     0.     0.]
Distance to Soma Centre: 1500.0
 --  <SectionObject: [1518.000000, 0.000000, 0.000000, r=0.150000] -> [1668.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_11, >
 --  0.606666666667
 --  [ 1609.     0.     02013-10-19 15:40:31,010 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:31,010 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-10-19 15:40:32,671 - morphforge.core.logmgr - INFO - Logger Started OK
2013-10-19 15:40:32,671 - 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/ec41fa63d3bbd2677776c59258d6466b.bundle (24k) : 0.795 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_30c2975a245542537b8157858ae7cb90.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_4fe96bbe338ca63bb55bbd7ff98cced3.so
loading membrane mechanisms from /local/scratch/mh735/tmp/morphforge/tmp/modout/mod_13b2f262c38556f5cc10f5fa49fb4fa2.so
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Running Simulation
Time for Extracting Data: (31 records) 0.014641046524
Running simulation : 0.838 seconds
Post-processing : 0.026 seconds
Entire load-run-save time : 1.659 seconds
Suceeded
.]
Distance to Soma Centre: 1600.0
 --  <SectionObject: [1668.000000, 0.000000, 0.000000, r=0.150000] -> [1818.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_12, >
 --  0.273333333333
 --  [ 1709.     0.     0.]
Distance to Soma Centre: 1700.0
 --  <SectionObject: [1668.000000, 0.000000, 0.000000, r=0.150000] -> [1818.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_12, >
 --  0.94
 --  [ 1809.     0.     0.]
Distance to Soma Centre: 1800.0
 --  <SectionObject: [1818.000000, 0.000000, 0.000000, r=0.150000] -> [1968.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_13, >
 --  0.606666666667
 --  [ 1909.     0.     0.]
Distance to Soma Centre: 1900.0
 --  <SectionObject: [1968.000000, 0.000000, 0.000000, r=0.150000] -> [2118.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_14, >
 --  0.273333333333
 --  [ 2009.     0.     0.]
Distance to Soma Centre: 2000.0
 --  <SectionObject: [1968.000000, 0.000000, 0.000000, r=0.150000] -> [2118.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_14, >
 --  0.94
 --  [ 2109.     0.     0.]
Distance to Soma Centre: 2100.0
 --  <SectionObject: [2118.000000, 0.000000, 0.000000, r=0.150000] -> [2268.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_15, >
 --  0.606666666667
 --  [ 2209.     0.     0.]
Distance to Soma Centre: 2200.0
 --  <SectionObject: [2268.000000, 0.000000, 0.000000, r=0.150000] -> [2418.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_16, >
 --  0.273333333333
 --  [ 2309.     0.     0.]
Distance to Soma Centre: 2300.0
 --  <SectionObject: [2268.000000, 0.000000, 0.000000, r=0.150000] -> [2418.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_16, >
 --  0.94
 --  [ 2409.     0.     0.]
Distance to Soma Centre: 2400.0
 --  <SectionObject: [2418.000000, 0.000000, 0.000000, r=0.150000] -> [2568.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_17, >
 --  0.606666666667
 --  [ 2509.     0.     0.]
Distance to Soma Centre: 2500.0
 --  <SectionObject: [2568.000000, 0.000000, 0.000000, r=0.150000] -> [2718.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_18, >
 --  0.273333333333
 --  [ 2609.     0.     0.]
Distance to Soma Centre: 2600.0
 --  <SectionObject: [2568.000000, 0.000000, 0.000000, r=0.150000] -> [2718.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_18, >
 --  0.94
 --  [ 2709.     0.     0.]
Distance to Soma Centre: 2700.0
 --  <SectionObject: [2718.000000, 0.000000, 0.000000, r=0.150000] -> [2868.000000, 0.000000, 0.000000, r=0.150000], Length: 150.00, Region:axon, idtag:axon_19, >
 --  0.606666666667
 --  [ 2809.     0.     0.]
Distance to Soma Centre: 2800.0
PlotMnager:Saving  _output/figures/singlecell_simulation060/{png,svg}/fig000_Autosave_figure_1.{png,svg}