Cable cell probing and sampling#

Cable cell probes#

Various properties of a cable cell can be sampled. They fall into two classes: scalar probes are associated with a single real value, such as a membrane voltage or mechanism state value at a particular location; vector probes return multiple values corresponding to a quantity sampled at a set of points on the cell.

The sample data associated with a cable cell probe will either be a double for scalar probes, or a cable_sample_range describing a half-open range of double values:

using cable_sample_range = std::pair<const double*, const double*>

The probe metadata passed to the sampler will be a const pointer to:

mlocation for most scalar probes;
cable_probe_point_info for point mechanism state queries;
mcable_list for most vector queries;
std::vector<cable_probe_point_info> for cell-wide point mechanism state queries.

The type cable_probe_point_info holds metadata for a single target on a cell:

struct cable_probe_point_info {
    // Target number of point process instance on cell.
    cell_lid_type target;

    // Number of combined instances at this site.
    unsigned multiplicity;

    // Point on cell morphology where instance is placed.
    mlocation loc;
};

Note that the multiplicity will always be 1 if synapse coalescing is disabled.

Cable cell probes that contingently do not correspond to a valid measurable quantity are ignored: samplers attached to them will receive no values. Mechanism state queries however will throw a cable_cell_error exception at simulation initialization if the requested state variable does not exist on the mechanism.

Cable cell probeset addresses that are described by a locset may generate more than one concrete probe: there will be one per location in the locset that is satisfiable. Sampler callback functions can distinguish between different probes with the same address and id by examining their index and/or probe-specific metadata found in the probe_metadata parameter.

Membrane voltage#

struct cable_probe_membrane_voltage {
    locset locations;
};

Queries cell membrane potential at each site in locations.

Sample value: double. Membrane potential in millivolts.
Metadata: mlocation. Location of probe.

struct cable_probe_membrane_voltage_cell {};

Queries cell membrane potential across whole cell.

Sample value: cable_sample_range. Each value is the average membrane potential in millivolts across an unbranched component of the cell, as determined by the discretisation.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

Axial current#

struct cable_probe_axial_current {
    locset locations;
};

Estimate intracellular current at each site in locations, in the distal direction.

Sample value: double. Current in nanoamperes.
Metadata: mlocation. Location as of probe.

Transmembrane current#

struct cable_probe_ion_current_density {
    locset locations;
    std::string ion;
};

Membrane current density attributed to a particular ion at each site in locations.

Sample value: double. Current density in amperes per square metre.
Metadata: mlocation. Location of probe.

struct cable_probe_ion_current_cell {
    std::string ion;
};

Membrane current attributed to a particular ion across components of the cell.

Sample value: cable_sample_range. Each value is the current in nanoamperes across an unbranched component of the cell, as determined by the discretisation.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

struct cable_probe_total_ion_current_density {
    locset locations;
};

Membrane current density at given locations _excluding_ capacitive currents.

Sample value: double. Current density in amperes per square metre.
Metadata: mlocation. Location of probe.

struct cable_probe_total_ion_current_cell {};

Membrane current _excluding_ capacitive currents and stimuli across components of the cell.

Sample value: cable_sample_range. Each value is the current in nanoamperes across an unbranched component of the cell, as determined by the discretisation.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

struct cable_probe_total_current_cell {};

Total membrance current excluding current stimuli across components of the cell.

Sample value: cable_sample_range. Each value is the current in nanoamperes across an unbranched component of the cell, as determined by the discretisation.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

struct cable_probe_stimulus_current_cell {};

Total stimulus currents applied across components of the cell.

Sample value: cable_sample_range. Each value is the current in nanoamperes across an unbranched component of the cell, as determined by the discretisation. Components of CVs where no stimulus is present will report a corresponding stimulus value of zero.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

Ion concentration#

struct cable_probe_ion_int_concentration {
    locset locations;
    std::string ion;
};

Ionic internal concentration of ion at each site in locations.

Sample value: double. Ion concentration in millimoles per litre.
Metadata: mlocation. Location of probe.

struct cable_probe_ion_int_concentration_cell {
    std::string ion;
};

Ionic external concentration of ion across components of the cell.

Sample value: cable_sample_range. Each value is the concentration in millimoles per lire across an unbranched component of the cell, as determined by the discretisation.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

struct cable_probe_ion_ext_concentration {
    mlocation location;
    std::string ion;
};

Ionic external concentration of ion at each site in locations.

Sample value: double. Ion concentration in millimoles per litre.
Metadata: mlocation. Location of probe.

struct cable_probe_ion_ext_concentration_cell {
    std::string ion;
};

Ionic external concentration of ion across components of the cell.

Sample value: cable_sample_range. Each value is the concentration in millimoles per lire across an unbranched component of the cell, as determined by the discretisation.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

Ionic diffusion concrentration.

struct cable_probe_ion_diff_concentration {
    locset locations;
    std::string ion;
};

Diffusive ionic concentration of the given ion at the sites specified by locations.

struct cable_probe_ion_diff_concentration_cell {
    std::string ion;
};

Ionic diffusion concrentration attributed to a particular ion across CVs of the cell.

Mechanism state#

struct cable_probe_density_state {
    locset locations;
    std::string mechanism;
    std::string state;
};

Value of state variable in a density mechanism in each site in locations. If the mechanism is not defined at a particular site, that site is ignored.

Sample value: double. State variable value.
Metadata: mlocation. Location as given in the probeset address.

struct cable_probe_density_state_cell {
    std::string mechanism;
    std::string state;
};

Value of state variable in a density mechanism across components of the cell.

Sample value: cable_sample_range. State variable values from the mechanism across unbranched components of the cell, as determined by the discretisation and mechanism extent.
Metadata: mcable_list. Each cable in the cable list describes the unbranched component for the corresponding sample value.

struct cable_probe_point_state {
    cell_lid_type target;
    std::string mechanism;
    std::string state;
};

Value of state variable in a point mechanism associated with the given target. If the mechanism is not associated with this target, the probe is ignored.

Sample value: double. State variable value.
Metadata: cable_probe_point_info. Target number, multiplicity and location.

struct cable_probe_point_state_cell {
    std::string mechanism;
    std::string state;
};

Value of state variable in a point mechanism for each of the targets in the cell with which it is associated.

Sample value: cable_sample_range. State variable values at each associated target.
Metadata: std::vector<cable_probe_point_info>. Target metadata for each associated target.

Sampling API#

The new API replaces the flexible but irreducibly inefficient scheme where the next sample time for a sampling was determined by the return value of the sampler callback.

Definitions#

probe: A location or component of a cell that is available for monitoring.
sample: A record of data corresponding to the value at a specific probe at a specific time.
sampler: A function or function object that receives a sequence of sample records.
schedule: A function or function object that, given a time interval, returns a list of sample times within that interval.

Probes#

Probes are specified in the recipe objects that are used to initialize a simulation; the specification of the item or value that is subjected to a probe will be specific to a particular cell type.

 struct probe_info {
    cell_tag_type tag;     // opaque key, returned in sample record
    any address;           // cell-type specific location info

    template <typename X>
    probe_info(X&& x, nullptr_t) = delete;

    template <typename X>
    probe_info(X&& x, const cell_tag_type& tag):
        tag(tag), address(std::forward<X>(x)) {}
};

std::vector<probe_info> recipe::get_probes(cell_gid_type gid);

The tag field identifies the probe locally on this global id gid, e.g. it is used in conjunction to attach samplers, as cell_address_type{gid, tag}.

Probeset addresses are decoupled from the cell descriptions themselves — this allows a recipe implementation to construct probes independently of the cells themselves. It is the responsibility of a cell group implementation to parse the probeset address objects wrapped in the any address field, thus the order of probes returned is important.

One probeset address may describe more than one concrete probe, depending upon the interpretation of the probeset address by the cell group. In this instance, each of the concrete probes will be associated with the same probe-id. Samplers can distinguish between different probes with the same id by their probe index (see below).

Samplers and sample records#

Data collected from probes (according to a schedule described below) will be passed to a sampler function or function object:

struct probe_metadata {
    cell_address_type id; // probeset id
    unsigned index;       // index of probe source within those supplied by probeset id
    util::any_ptr meta;   // probe-specific metadata
};

using sampler_function =
    std::function<void (probe_metadata, size_t, const sample_record*)>;

where the parameters are respectively the probe metadata, the number of samples, and finally a pointer to the sequence of sample records.

The probeset_id, identifies the probe by its probe-id (see above).

The index identifies which of the possibly multiple probes associated with the probe-id is the source of the samples.

The any_ptr value in the metadata points to const probe-specific metadata; the type of the metadata will depend upon the probeset address specified in the probe_info provided by the recipe.

One sample_record struct contains one sample of the probe data at a given simulation time point:

struct sample_record {
    time_type time;    // simulation time of sample
    any_ptr data;      // sample data
};

The data field points to the sample data, wrapped in any_ptr for type-checked access. The exact representation will depend on the nature of the object that is being probed, but it should depend only on the cell type and probeset address.

The data pointed to by data, and the sample records themselves, are only guaranteed to be valid for the duration of the call to the sampler function. A simple sampler implementation for double data, assuming one probe per probeset id, might be as follows:

using sample_data = std::map<cell_address_type, std::vector<std::pair<double, double>>>;

struct scalar_sampler {
    sample_data& samples;

    explicit scalar_sample(sample_data& samples): samples(samples) {}

    void operator()(probe_metadata pm, size_t n, const sample_record* records) {
        for (size_t i=0; i<n; ++i) {
            const auto& rec = records[i];

            const double* data = any_cast<const double*>(rec.data);
            assert(data);
            samples[pm.id].emplace_back(rec.time, *data);
        }
    }
};

The use of any_ptr allows type-checked access to the sample data, which may differ in type from probe to probe.

Model and cell group interface#

Polling rates and sampler functions are set through the simulation interface, after construction from a recipe.

using sampler_association_handle = std::size_t;
using cell_member_predicate = std::function<bool (cell_member_type)>;

sampler_association_handle simulation::add_sampler(
    cell_member_predicate probeset_ids,
    schedule sched,
    sampler_function fn)

void simulation::remove_sampler(sampler_association_handle);

void simulation::remove_all_samplers();

Multiple samplers can then be associated with the same probe locations. The handle returned is only used for managing the lifetime of the association. The cell_member_predicate parameter defines the set of probeset ids in terms of a membership test.

We provide a few helper functions are provided for making cell_member_predicate objects:

// Match all probeset ids.
cell_member_predicate
all_probes = [](const cell_address_type& pid) { return true; };

// Match just one probeset id.
cell_member_predicate
one_probe(const cell_address_type& pid) { return [pid](const auto& x) { return pid==x; }; }

// Match all probes on a given ``gid``.
cell_member_predicate
one_gid(const cell_gid_type& gid) { return [gid](const auto& x) { return gid==x.gid; }; }

// Match all probes with a given ``tag``.
cell_member_predicate
one_tag(const cell_tag_type& tag) { return [tag](const auto& x) { return tag==x.tag; }; }

The simulation object will pass on the sampler setting request to the cell group that owns the given probeset id. The cell_group interface will be correspondingly extended:

void cell_group::add_sampler(sampler_association_handle h,
                            cell_member_predicate probeset_ids,
                            sample_schedule sched,
                            sampler_function fn);

void cell_group::remove_sampler(sampler_association_handle);

void cell_group::remove_all_samplers();

Cell groups will invoke the corresponding sampler function directly, and may aggregate multiple samples with the same probeset id in one call to the sampler. Calls to the sampler are synchronous, in the sense that processing of the cell group state does not proceed while the sampler function is being executed, but the times of the samples given to the sampler will typically precede the time corresponding to the current state of the cell group. It should be expected that this difference in time should be no greater the the duration of the integration period (i.e. mindelay/2).

Schedules#

Schedules represent a non-negative, monotonically increasing sequence of time points, and are used to specify the sampling schedule in any given association of a sampler function to a set of probes.

A schedule object has two methods:

void schedule::reset();

time_event_span events(time_type t0, time_type t1)

A time_event_span is a std::pair of pointers const time_type*, representing a view into an internally maintained collection of generated time values.

The events(t0, t1) method returns a view of monotonically increasing time values in the half-open interval [t0, t1). Successive calls to events — without an intervening call to reset() — must request strictly subsequent intervals.

The data represented by the returned time_event_span view is valid for the lifetime of the schedule object, and is invalidated by any subsequent call to reset() or events().

The reset() method resets the state such that events can be retrieved from again from time zero. A schedule that is reset must then produce the same sequence of time points, that is, it must exhibit repeatable and deterministic behaviour.

The schedule object itself uses type-erasure to wrap any schedule implementation class, which can be any copy–constructable class that provides the methods reset() and events(t0, t1) above. Three schedule implementations are provided by the engine:

// Schedule at integer multiples of dt:
schedule regular_schedule(time_type dt);

// Schedule at a predetermined (sorted) sequence of times:
template <typename Seq>
schedule explicit_schedule(const Seq& seq);

// Schedule according to Poisson process with lambda = 1/mean_dt
template <typename RandomNumberEngine>
schedule poisson_schedule(time_type mean_dt, const RandomNumberEngine& rng);

The schedule class and its implementations are found in schedule.hpp.

Helper classes for probe/sampler management#

The simulation and cable_cell_group classes use classes defined in scheduler_map.hpp to simplify the management of sampler–probe associations and probe metadata.

sampler_association_map wraps an unordered_map between sampler association handles and tuples (schedule, sampler, probe set), with thread-safe accessors.

Batched sampling in `cable_cell_group`#

The fvm_multicell implementations for CPU and GPU simulation of multi-compartment cable neurons perform sampling in a batched manner: when their integration is initialized, they take a sequence of sample_event objects which are used to populate an implementation-specific event_stream that describes for each cell the sample times and what to sample over the integration interval.

When an integration step for a cell covers a sample event on that cell, the sample is satisfied with the value from the cell state at the beginning of the time step, after any postsynaptic spike events have been delivered.

It is the responsibility of the cable_cell_group::advance() method to create the sample events from the entries of its sampler_association_map, and to dispatch the sampled values to the sampler callbacks after the integration is complete. Given an association tuple (schedule, sampler, probe set) where the schedule has (non-zero) n sample times in the current integration interval, the cable_cell_group will call the sampler callback once for probe in probe set, with n sample values.

Note

When the time values returned by a call to a schedule’s events(t0, t1) method do not perfectly coincide with the boundaries of the numerical time step grid, \([t_0, t_0 + dt, t_0 + 2\, dt, \, \cdots \, , t_1)\), the samples will be taken at the closest possible point in time. In particular, any sample times \(t_s \in \left( t_i - dt/2,~ t_i + dt/2\right]\) are attributed to simulation time step \(t_i = t_0 + i\,dt\).

LIF cell probing and sampling#

Membrane voltage#

struct lif_probe_voltage {};

Queries cell membrane potential.

Sample value: double. Membrane potential (mV).
Metadata: none

Cable cell probing and sampling#

Cable cell probes#

Membrane voltage#

Axial current#

Transmembrane current#

Ion concentration#

Mechanism state#

Sampling API#

Definitions#

Probes#

Samplers and sample records#

Model and cell group interface#

Schedules#

Helper classes for probe/sampler management#

Batched sampling in cable_cell_group#

LIF cell probing and sampling#

Membrane voltage#

Batched sampling in `cable_cell_group`#