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
andset_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 inlocations
and label the group of synapses withlabel
. The label can be used to form connections to one of the synapses in thearbor.recipe
by creating aarbor.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 inlocations
and label the group of synapses withlabel
. The label can be used to form connections to one of the synapses in thearbor.recipe
by creating aarbor.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 withlabel
. The label can be used to form connections to/from one of the gap junction sites in thearbor.recipe
by creating aarbor.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 withlabel
.- 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 withlabel
. The label can be used to form connections from one of the detectors in thearbor.recipe
by creating aarbor.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.