Cable cells

class arbor.cable_cell

A cable cell is constructed from a morphology and an optional label dictionary.

Note

The regions and locsets defined in the label dictionary are concretised 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('granule.swc')
morph = arbor.morphology(tree, spherical_root=True)

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

# Construct a cable cell.
cell = arbor.cable_cell(morph, labels)
set_properties(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

  • region (str) – name 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].

# Set cell-wide values for properties
cell.set_properties(Vm=-70, cm=0.01, rL=100, tempK=280)
paint(region[, Vm=None, cm=None, rL=None, tempK=None])

Set cable properties on a region.

Parameters

  • region (str) – name 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
cell.paint('"soma"', rL=100)
# Specialize resistivity and capacitance on the axon, where
# axon is defined using a region expression.
cell.paint('(tag 2)', cm=0.05, rL=80)
class arbor.ion

properties of an ionic species.