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 string where.

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 mechanism mechanism at the sites specified by the location expression where.

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 mechanism mechanism 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 process mechanism associated with the target index target 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 process mechanism 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 string where.

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 string where.

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.