Example 16. Compartmentalisation of neuron
Compartmentalisation of neuron
In this set of simulations, we create a cell consisting of a soma and long axon. We use a current-clamp at the soma to start an action potential that propagates along the axon and record the voltages at 10um intervals (~400 recordings) along the axon. In each simulation, we change the number of compartments of the axon.
“CellSegmenter_MaxLengthByID” allows us to specify the maximum length of a compartment based on the Section ID. We see that as the length of the compartments goes up, the number of distinct recordings goes down. When there are very few compartments, the action potential does not propogate.
Custom cell-segmentation algorithms can be written by subclassing from: ‘CellSegmenterStd’ and overridding the method: ‘_get_n_segments(self, section)’, which should query the section and return the number of compartments in the cell.
Code
from morphforge.stdimports import *
from morphforgecontrib.stdimports import *
def run_sim(axon_compartment_length):
env = NEURONEnvironment()
sim = env.Simulation()
# Create a cell, consisting of a soma and long axon:
morphDict1 = {'root': {'length': 20, 'diam': 20, 'id':'soma', 'sections': [ {'length':4000,'diam':0.3, 'id':'axon'} ] } }
m1 = MorphologyTree.fromDictionary(morphDict1)
cell = sim.create_cell(
name="Cell1",
morphology=m1,
segmenter=CellSegmenter_MaxLengthByID(section_id_segment_maxsizes={'soma':20,'axon':axon_compartment_length} )
)
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'))
# 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, user_tags=['AxonCompLength%d'%axon_compartment_length])
# Define a series of points at 50um intervals along the axon to record voltage at:
pts_along_cell = CellLocator.get_locations_at_distances_away_from_dummy(cell=cell, distances= [0] + list(range(20,4000, 10) ) )
x0 = CellLocator.get_location_at_distance_away_from_dummy(cell=cell, distance=20 ).morphlocation
for pt in pts_along_cell:
dist = "Distance%04d"%MorphPath(x0, pt.morphlocation).get_length()
sim.record(cell, what=StandardTags.Voltage, description=dist, user_tags=['AxonCompLength%d'%axon_compartment_length], cell_location = pt)
# run the simulation
results = sim.run()
return results
axon_compartment_lengths = [20,50,100,200,500]
results = [ run_sim(axon_compartment_length=ax_comp_len) for ax_comp_len in axon_compartment_lengths]
TagViewer(results,
timerange=(98, 125)*units.ms,
plots =
[ TagPlot("ALL{Voltage,AxonCompLength%d}"%ax_comp_len, ylabel='Axon comp \n Length:%dum\n (Voltage)'%ax_comp_len, yrange=(-80*units.mV, 50*units.mV), yunit=units.mV, legend_labeller=None, yticklabel_quantisation=Decimal('1')) for ax_comp_len in axon_compartment_lengths] +
[ TagPlot("ALL{Current,AxonCompLength20}", ylabel='Current', yunit=units.picoamp, yticklabel_quantisation=Decimal('1') ) ]
)
Figures
Download Figure
Output
No handlers could be found for logger "neurounits"
2013-12-01 17:12:49,530 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:49,530 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-12-01 17:12:52,033 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:52,034 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/39/399ab3c3877725401738b604d2478a48.bundle (127k) : 0.868 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 /mnt/scratch/tmp/morphforge/tmp/modout/mod_af84455a7bd10be7408061ecd02b589b.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_fb18cab9ab8db5d2c968f5e6fba6a942.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_e1d9b15c15cf730d6ad5de223a1b3007.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_e5e7665427d16493604ff201a9f41d6f.hoc
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Running Simulation
Time for Extracting Data: (400 records) 0.791956186295
Running simulation : 2.628 seconds
Size of results file: 9.4 (MB)
Post-processing : 0.717 seconds
Entire load-run-save time : 4.214 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:12:58,477 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:12:58,478 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/97/97980bb10048c89d42a3eef3291c5e47.bundle (127k) : 0.858 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 /mnt/scratch/tmp/morphforge/tmp/modout/mod_43fa2a5e62c5ab14e6597bea0a23b2cc.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_62a4ddcd4ac772510aa6813825f854fa.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_979e51e8134d9ad14b8ff4498af4abcc.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_f54a863da6f147e2afd48f2738b3031c.hoc
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Running Simulation
Time for Extracting Data: (400 records) 0.763997077942
Running simulation : 1.982 seconds
Size of results file: 7.1 (MB)
Post-processing : 0.570 seconds
Entire load-run-save time : 3.410 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:13:04,178 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:13:04,179 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/4d/4dc66a084e95fa660bbdeeb9d5d0ea02.bundle (128k) : 0.884 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 /mnt/scratch/tmp/morphforge/tmp/modout/mod_1b9db84d43b77ec2fb2e53e206df6e31.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_08fd042f5617092e986b5453289c786a.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_7df4c149812c25e673966e04c457447e.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_2984062baeb71bd0f1f9c5f0f8f6b548.hoc
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Running Simulation
Time for Extracting Data: (400 records) 0.819808006287
Running simulation : 2.087 seconds
Size of results file: 8.0 (MB)
Post-processing : 0.636 seconds
Entire load-run-save time : 3.607 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:13:09,896 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:13:09,896 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/5e/5ea2b0b4473e7d461885ed4b3b57f806.bundle (128k) : 0.864 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 /mnt/scratch/tmp/morphforge/tmp/modout/mod_441d00ac1d6ed2d478a432634287e05e.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_20f6d2c3344f354cb5e5fc2759b4552b.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_493e4afc99901274d3bc57b05062327c.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_5857117db6fa14104cdc3a4d0fb6d936.hoc
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Running Simulation
Time for Extracting Data: (400 records) 0.735677957535
Running simulation : 1.761 seconds
Size of results file: 7.1 (MB)
Post-processing : 0.593 seconds
Entire load-run-save time : 3.218 seconds
Suceeded
No handlers could be found for logger "neurounits"
2013-12-01 17:13:15,352 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:13:15,352 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LD_LIBRARY_PATH', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/a7/a76de9d59e812c6efca64c5346518296.bundle (128k) : 0.860 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 /mnt/scratch/tmp/morphforge/tmp/modout/mod_47e8f16ebc67f13d01a7bd84be614581.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_3bf774ddb40d01137fc04e1ccf2cc5ab.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_5163cbad7d6a5b01abf1db214c811de2.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_ed4e35c9e2aba5162898b1a15d3eeeb7.hoc
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Running Simulation
Time for Extracting Data: (400 records) 0.783655166626
Running simulation : 1.677 seconds
Size of results file: 2.8 (MB)
Post-processing : 0.288 seconds
Entire load-run-save time : 2.826 seconds
Suceeded
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/39//399ab3c3877725401738b604d2478a48.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/97//97980bb10048c89d42a3eef3291c5e47.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/4d//4dc66a084e95fa660bbdeeb9d5d0ea02.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/5e//5ea2b0b4473e7d461885ed4b3b57f806.neuronsim.results.pickle ]
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/a7//a76de9d59e812c6efca64c5346518296.neuronsim.results.pickle ]
PlotManger saving: _output/figures/singlecell_simulation090/{png,svg}/fig000_Autosave_figure_1.{png,svg}