Cable cell decoration

class arbor.decor

A decor object contains a description of the cell dynamics, to be applied to a morphology when used to instantiate a cable_cell

__init__()

Construct an empty decor description.

Properties for which defaults can be defined over the entire cell, specifically cable properties and ion properties, are set with set_property and set_ion methods.

set_property(Vm=None, cm=None, rL=None, tempK=None)

Set default values of cable properties on the whole cell. Overrides the default global values, and can be overridden by painting the values onto regions.

Parameters

  • Vm (float or None) – Initial membrane voltage [mV].

  • cm (float or None) – Membrane capacitance [F/m²].

  • rL (float or None) – Axial resistivity of cable [Ω·cm].

  • tempK (float or None) – Temperature [Kelvin].

# Set cell-wide values for properties for resistivity and capacitance
decor.set_property(rL=100, cm=0.1)
set_ion(ion, int_con=None, ext_con=None, rev_pot=None, method=None)

Set default value for one or more properties of a specific ion on the whole cell. Set the properties of ion species named ion that will be applied by default everywhere on the cell. Species concentrations and reversal potential can be overridden on specific regions using the paint interface, while the method for calculating reversal potential is global for all CVs in the cell, and can’t be overridden locally.

Parameters

  • ion (str) – description of the ion species.

  • int_con (float or None.) – initial internal concentration [mM].

  • ext_con (float or None.) – initial external concentration [mM].

  • rev_pot (float or None) – reversal potential [mV].

  • method (mechanism or None) – method for calculating reversal potential.

# Set nernst reversal potential method for calcium.
decor.set_ion('ca', method=mech('nernst/x=ca'))

# Set reversal potential and concentration for sodium.
# The reversal potential is fixed, so we set the method to None.
decor.set_ion('na', int_con=5.0, rev_pot=70, method=None)

Various specialisations of the paint method are available for setting properties and mechanisms that are applied to regions.

paint(region, Vm=None, cm=None, rL=None, tempK=None)

Set cable properties on a region.

Parameters

  • region (str) – description of the region.

  • Vm (float or None) – Initial membrane voltage [mV].

  • cm (float or None) – Membrane capacitance [F/m²].

  • rL (float or None) – Axial resistivity of cable [Ω·cm].

  • tempK (float or None) – Temperature [Kelvin].

# Specialize resistivity on soma
decor.paint('"soma"', rL=100)
# Specialize resistivity and capacitance on the axon, where
# axon is defined using a region expression.
decor.paint('(tag 2)', cm=0.05, rL=80)
paint(region, name, int_con=None, ext_con=None, rev_pot=None)

Set ion species properties initial conditions on a region.

Parameters

  • name (str) – name of the ion species.

  • int_con (float or None.) – initial internal concentration [mM].

  • ext_con (float or None.) – initial external concentration [mM].

  • rev_pot (float or None) – reversal potential [mV].

paint(region, mechanism)

Apply a mechanism with a region. Returns a unique identifier that can be used to query the local indexes (see index) assigned to the placed items on the cable cell.

Parameters

  • region (str) – description of the region.

  • mechanism (mechanism) – the mechanism.

paint(region, mech_name)

Apply a mechanism with a region using the name of the mechanism. The mechanism will use the parameter values set in the mechanism catalogue. Returns a unique identifier that can be used to query the local indexes (see index) assigned to the placed items on the cable cell.

Parameters

  • region (str) – description of the region.

  • mechanism (str) – the name of the mechanism.

place(locations, mech_name, label)

Place one instance of the synapse named mech_name to each location in locations and label the group of synapses with label. The label can be used to form connections to one of the synapses in the arbor.recipe by creating a arbor.connection.

Parameters

  • locations (str) – description of the locset.

  • mechanism (str) – the name of the mechanism.

  • label (str) – the label of the group of synapses on the locset.

place(locations, mechanism, label)

Place one instance of the synapse described by mechanism to each location in locations and label the group of synapses with label. The label can be used to form connections to one of the synapses in the arbor.recipe by creating a arbor.connection.

Parameters

  • locations (str) – description of the locset.

  • mechanism (mechanism) – the mechanism.

  • label (str) – the label of the group of synapses on the locset.

place(locations, site, label)

Place one gap junction site at each location in locations and label the group of gap junction sites with label. The label can be used to form connections to/from one of the gap junction sites in the arbor.recipe by creating a arbor.gap_junction_connection.

Parameters

  • locations (str) – description of the locset.

  • site (gap_junction_site) – indicates a gap junction site..

  • label (str) – the label of the group of gap junction sites on the locset.

place(locations, stim, label)

Add a current stimulus at each location in locations and label the group of stimuli with label.

Parameters

  • locations (str) – description of the locset.

  • stim (iclamp) – the current stim.

  • label (str) – the label of the group of stimuli on the locset.

place(locations, d, label)

Add a voltage spike detector at each location in locations and label the group of detectors with label. The label can be used to form connections from one of the detectors in the arbor.recipe by creating a arbor.connection.

Parameters

  • locations (str) – description of the locset.

  • d (threshold_detector) – description of the detector.

  • label (str) – the label of the group of detectors on the locset.

discretization(policy)

Set the cv_policy used to discretise the cell into control volumes for simulation.

Parameters

policy (cv_policy) – The cv_policy.