Cable cells

class arbor.cable_cell

A cable cell is constructed from a morphology, a label dictionary and a decor.

Note

The regions and locsets defined in the label dictionary are thingified when the cable cell is constructed, and an exception will be thrown if an invalid label expression is found.

There are two reasons an expression might be invalid:

  1. Explicit reference to a location of cable that does not exist in the morphology, for example (branch 12) on a cell with 6 branches.

  2. Reference to an incorrect label: circular reference, or a label that does not exist.

import arbor

# Construct the morphology from an SWC file.
tree = arbor.load_swc_arbor('granule.swc')
morph = arbor.morphology(tree)

# Define regions using standard SWC tags
labels = arbor.label_dict({'soma': '(tag 1)',
                           'axon': '(tag 2)',
                           'dend': '(join (tag 3) (tag 4))'})

# Define decorations
decor = arbor.decor()
decor.paint('"dend"', arbor.density('pas'))
decor.paint('"axon"', arbor.density('hh'))
decor.paint('"soma"', arbor.density('hh'))

# Construct a cable cell.
cell = arbor.cable_cell(morph, decor, labels)
__init__(morphology, decorations, labels)

Constructor.

Parameters:

  • morphology (morphology or segment_tree) – the morphology of the cell

  • labels (label_dict) – dictionary of labeled regions and locsets

  • decorations (decor) – the decorations on the cell

placed_lid_range(index)

Returns the range of local indexes assigned to a placement in the decorations as a tuple of two integers, that define the range of indexes as a half open interval.

Parameters:

index (int) – the unique index of the placement.

Return type:

tuple(int, int)

class arbor.ion

properties of an ionic species.

class arbor.cable_cell_global_properties
property catalogue

All mechanism names refer to mechanism instances in this mechanism catalogue. by default, this is set to point to default_catalogue().

property membrane_voltage_limit

Set a limiter U_max (mV) on the membrane potential; if U > U_max at any point and location the simulation is aborted with an error. Defaults to None, if set to a numeric value the limiter is armed.

property ion_data

Return a read-only view onto concentrations, diffusivity, and reversal potential settings.

property ion_valence

Return a read-only view onto species and charge.

property ion_reversal_potential

Return a read-only view onto reversal potential methods (if set).

property ions

Return a read-only view onto all settings.

set_ion(name, charge, internal_concentration, external_concentration, reversal_potential, reversal_potential_method, diffusivty)

Add a new ion to the global set of known species.

unset_ion(name)

Remove the named ion.

property membrane_potential

Set the default value for the membrane potential. (mV)

property membrane_capacitance

Set the default value for the membrane potential. (F/m²)

property temperature

Set the default value for the temperature (K).

property axial_resistivity

Set the default value for the membrane axial resisitivity. (Ω·cm)

For convenience, neuron_cable_properties is a predefined value that holds values that correspond to NEURON defaults.