Cable cell probing and sampling¶
Cable cell probe addresses are defined analogously to their counterparts in the C++ API (see 5. Probes for details). Sample data recorded by the Arbor simulation object is returned in the form of a NumPy array, with the first column holding sample times, and subsequent columns holding the corresponding scalar- or vector-valued sample.
Location expressions will be realised as zero or more specific sites on a cell; probe addresses defined over location expressions will describe zero, one, or more probes, one per site. They are evaluated in the context of the cell on which the probe is attached.
Each of the functions described below generates an opaque probe
object for use in the recipe get_probes()
method.
More information on probes, probe metadata, and sampling can be found
in the documentation for the class simulation
.
- Membrane voltage
- cable_probe_membrane_voltage(where)¶
Cell membrane potential (mV) at the sites specified by the location expression string
where
. This value is spatially interpolated.Metadata: the explicit
location
of the sample site.- cable_probe_membrane_voltage_cell()¶
Cell membrane potential (mV) associated with each cable in each CV of the cell discretization.
Metadata: the list of corresponding
cable
objects.- Axial current
- cable_probe_axial_current(where)¶
Estimation of intracellular current (nA) in the distal direction at the sites specified by the location expression string
where
.Metadata: the explicit
location
of the sample site.- Ionic current
- cable_probe_ion_current_density(where, ion)¶
Transmembrane current density (A/m²) associated with the given
ion
at sites specified by the location expression stringwhere
.Metadata: the explicit
location
of the sample site.- cable_probe_ion_current_cell(ion)¶
Transmembrane current (nA) associated with the given
ion
across each cable in each CV of the cell discretization.Metadata: the list of corresponding
cable
objects.- Total ionic current
- cable_probe_total_ion_current_density(where)¶
Transmembrane current density (A/m²) _excluding_ capacitive currents at the sites specified by the location expression string
where
.Metadata: the explicit
location
of the sample site.- cable_probe_total_ion_current_cell()¶
Transmembrane current (nA) _excluding_ capacitive currents across each cable in each CV of the cell discretization. Stimulus currents are not included.
Metadata: the list of corresponding
cable
objects.- Total transmembrane current
- cable_probe_total_current_cell()¶
Transmembrane current (nA) _including_ capacitive currents across each cable in each CV of the cell discretization. Stimulus currents are not included.
Metadata: the list of corresponding
cable
objects.- Total stimulus current
- cable_probe_stimulus_current_cell()¶
Total stimulus current (nA) across each cable in each CV of the cell discretization.
Metadata: the list of corresponding
cable
objects.- Density mechanism state variable
- cable_probe_density_state(where, mechanism, state)¶
The value of the state variable
state
in the density mechanismmechanism
at the sites specified by the location expressionwhere
.Metadata: the explicit
location
of the sample site.- cable_probe_density_state_cell(mechanism, state)¶
The value of the state variable
state
in the density mechanismmechanism
on each cable in each CV of the cell discretixation.Metadata: the list of corresponding
cable
objects.- Point process state variable
- cable_probe_point_state(target, mechanism, state)¶
The value of the state variable
state
in the point processmechanism
associated with the target indextarget
on the cell. If the given mechanism is not associated with the target index, no probe will be generated.Metadata: an object of type
cable_point_probe_info
, comprising three fields:target
: target index on the cell;multiplicity
: number of targets sharing the same state in the discretization;location
:location
object corresponding to the target site.
- cable_probe_point_state_cell(mechanism, state)¶
The value of the state variable
state
in the point processmechanism
at each of the targets where that mechanism is defined.Metadata: a list of
cable_point_probe_info
values, one for each matching target.- Ionic internal concentration
- cable_probe_ion_int_concentration(where, ion)¶
Ionic internal concentration (mmol/L) of the given
ion
at the sites specified by the location expression stringwhere
.Metadata: the explicit
location
of the sample site.- cable_probe_ion_int_concentration_cell(ion)¶
Ionic internal concentration (mmol/L) of the given
ion
in each able in each CV of the cell discretization.Metadata: the list of corresponding
cable
objects.- Ionic external concentration
- cable_probe_ion_ext_concentration(where, ion)¶
Ionic external concentration (mmol/L) of the given
ion
at the sites specified by the location expression stringwhere
.Metadata: the explicit
location
of the sample site.- cable_probe_ion_ext_concentration_cell(ion)¶
Ionic external concentration (mmol/L) of the given
ion
in each able in each CV of the cell discretization.Metadata: the list of corresponding
cable
objects.