.. _cppcablecell: Cable cells =========== .. toctree:: :maxdepth: 1 morphology probe_sample cable_cell_format .. Warning:: The interface for building and modifying cable cell objects has changed significantly; some of the documentation below is out of date. The C++ cable cell documentation should have the same structure as the Python cable cell documentation. Cable cells, which use the :cpp:enum:`cell_kind` :cpp:expr:`cable`, represent morphologically-detailed neurons as 1-d trees, with electrical and biophysical properties mapped onto those trees. A single cell is represented by an object of type :cpp:type:`cable_cell`. Properties shared by all cable cells, as returned by the recipe :cpp:expr:`get_global_properties` method, are described by an object of type :cpp:type:`cable_cell_global_properties`. The :cpp:type:`cable_cell` object --------------------------------- Cable cells are constructed from a :cpp:type:`morphology`; an optional :cpp:type:`label_dict` that associates names with particular points (:cpp:type:`locset` objects) or subsets (:cpp:type:`region` objects) of the morphology; and an optional :ref:`decor `. Morphologies are constructed from a :cpp:type:`segment_tree`, but can also be generated via the :cpp:type:`stitch_builder`, which offers a slightly higher level interface. Details are described in :ref:`cppcablecell-morphology-construction`. Each cell has particular values for its electrical and ionic properties. These are determined first by the set of global defaults, then the defaults associated with the cell, and finally by any values specified explicitly for a given subsection of the morphology via the ``paint`` interface of the decor (see :ref:`cppcablecell-electrical-properties` and :ref:`cppcablecell-paint-properties`). Ion channels and other distributed dynamical processes are also specified on the cell via the ``paint`` method; while synapses, current clamps, gap junction mechanisms, and the site for testing the threshold potential are specified via the ``place`` method. See :ref:`cppcablecell-dynamics`, below. .. _cppcablecell-dynamics: Cell dynamics ------------- Dynamics are imbued onto the cell by setting a :cpp:type:`decor` object during construction. Each segment in a cell may have attached to it one or more density *mechanisms*, which describe biophysical processes. These are processes that are distributed in space, but whose behaviour is defined purely by the state of the cell and the process at any given point. Cells may also have *point* mechanisms, describing the dynamics at post-synaptic sites. And *junction* mechanisms, describing the dynamics at each site of the two sites of a gap-junction connection. A fourth type of mechanism, which describes ionic reversal potential behaviour, can be specified for cells or the whole model via cell parameter settings, described below. Mechanisms are described by a :cpp:type:`mechanism_desc` object. These specify the name of the mechanism (used to find the mechanism in the mechanism catalogue) and parameter values for the mechanism that apply within a segment. A :cpp:type:`mechanism_desc` is effectively a wrapper around a name and a dictionary of parameter/value settings. Mechanism descriptions can be constructed implicitly from the mechanism name, and mechanism parameter values then set with the :cpp:expr:`set` method. Relevant :cpp:type:`mechanism_desc` methods: .. cpp:function:: mechanism_desc::mechanism_desc(std::string name) Construct a mechanism description for the mechanism named `name`. .. cpp:function:: mechanism_desc& mechanism_desc::set(const std::string& key, double value) Sets the parameter associated with :cpp:expr:`key` in the description. Returns a reference to the mechanism description, so that calls to :cpp:expr:`set` can be chained in a single expression. :cpp:type:`density`, :cpp:type:`synapse` and :cpp:type:`junction` objects are thin wrappers around a :cpp:type:`mechanism_desc`, needed for *painting* and *placing* mechanisms on a :cpp:type:`decor`. Relevant methods: .. cpp:function:: density::density(mechanism_desc mech) Construct a density wrapper from the mechanism `mech`. .. cpp:function:: density::density(mechanism_desc mech, const std::unordered_map& params) For each ``{key, value}`` pair in `params`, set the parameter associated with ``key`` to ``value`` on mechanism ``mech``, then construct a density wrapper from the mechanism `mech`. .. cpp:function:: synapse::synapse(mechanism_desc mech) Construct a synapse wrapper from the mechanism `mech`. .. cpp:function:: synapse::synapse(mechanism_desc mech, const std::unordered_map& params) For each ``{key, value}`` pair in `params`, set the parameter associated with ``key`` to ``value`` on mechanism ``mech``, then construct a synapse wrapper from the mechanism `mech`. .. cpp:function:: junction::junction(mechanism_desc mech) Construct a junction wrapper from the mechanism `mech`. .. cpp:function:: junction::junction(mechanism_desc mech, const std::unordered_map& params) For each ``{key, value}`` pair in `params`, set the parameter associated with ``key`` to ``value`` on mechanism ``mech``, then construct a junction wrapper from the mechanism `mech`. Density mechanisms are associated with a cable cell object with: .. cpp:function:: void decor::paint(const region&, density) Point mechanisms, which are associated with connection end points on a cable cell, are placed on a set of locations given by a locset. The group of generated items are given a label which can be used to create connections in the recipe. Point mechanisms are attached to a cell with: .. cpp:function:: void decor::place(const locset&, synapse, cell_tag_type label) Gap-junction mechanisms, which are associated with gap-junction connection end points on a cable cell, are placed on a single location given by a locset (locsets with multiple locations will raise an exception). The generated item is given a label which can be used to create gap-junction connections in the recipe. Gap-junction mechanisms are attached to a cell with: .. cpp:function:: void decor::place(const locset&, junction, cell_tag_type label) .. todo:: TODO: describe other ``place``-able things: current clamps, threshold potential measurement point. .. _cppcablecell-electrical-properties: Electrical properties and ion values ------------------------------------- On each cell segment, electrical and ion properties can be specified by the :cpp:expr:`parameters` field, of type :cpp:type:`cable_cell_local_parameter_set`. The :cpp:type:`cable_cell_local_parameter_set` has the following members, where an empty optional value or missing map key indicates that the corresponding value should be taken from the cell or global parameter set. .. cpp:class:: cable_cell_local_parameter_set .. cpp:member:: std::unordered_map ion_data The keys of this map are names of ions, whose parameters will be locally overridden. The struct :cpp:type:`cable_cell_ion_data` has three fields: :cpp:type:`init_int_concentration`, :cpp:type:`init_ext_concentration`, and :cpp:type:`init_reversal_potential`. Internal and external concentrations are given in millimolars, i.e. mol/m³. Reversal potential is given in millivolts. .. cpp:member:: util::optional init_membrane_potential Initial membrane potential in millivolts. .. cpp:member:: util::optional temperature Local temperature in Kelvin. .. cpp:member:: util::optional axial_resistivity Local resistivity of the intracellular medium, in ohm-centimetres. .. cpp:member:: util::optional membrane_capacitance Local areal capacitance of the cell membrane, in Farads per square metre. .. cpp:member:: util::optional discretisation Method by which CV boundaries are determined when the cell is discretised. See :ref:`cv-policies`. Default parameters for a cell are given by the :cpp:expr:`default_parameters` field in the :cpp:type:`cable_cell` object. This is a value of type :cpp:type:`cable_cell_parameter_set`, which extends :cpp:type:`cable_cell_local_parameter_set` by adding an additional field describing reversal potential computation: .. cpp:class:: cable_cell_parameter_set: public cable_cell_local_parameter_set .. cpp:member:: std::unordered_map reversal_potential_method Maps the name of an ion to a 'reversal potential' mechanism that describes how it should be computed. When no mechanism is provided for an ionic reversal potential, the reversal potential will be kept at its initial value. Default parameters for all cells are supplied in the :cpp:type:`cable_cell_global_properties` struct. Global properties ----------------- .. cpp:class:: cable_cell_global_properties .. cpp:member:: const mechanism_catalogue* catalogue all mechanism names refer to mechanism instances in this mechanism catalogue. by default, this is set to point to `global_default_catalogue()`, the catalogue that contains all mechanisms bundled with arbor. .. cpp:member:: optional membrane_voltage_limit_mv if set, check to see if the membrane voltage ever exceeds this value in magnitude during the course of a simulation. if so, throw an exception and abort the simulation. .. cpp:member:: bool coalesce_synapses when synapse dynamics are sufficiently simple, the states of synapses within the same discretised element can be combined for better performance. this is true by default. .. cpp:member:: std::unordered_map ion_species every ion species used by cable cells in the simulation must have an entry in this map, which takes an ion name to its charge, expressed as a multiple of the elementary charge. by default, it is set to include sodium "na" with charge 1, calcium "ca" with charge 2, and potassium "k" with charge 1. .. cpp:member:: cable_cell_parameter_set default_parameters the default electrical and physical properties associated with each cable cell, unless overridden locally. in the global properties, *every optional field must be given a value*, and every ion must have its default values set in :cpp:expr:`default_parameters.ion_data`. .. cpp:function:: add_ion(const std::string& ion_name, int charge, double init_iconc, double init_econc, double init_revpot) convenience function for adding a new ion to the global :cpp:expr:`ion_species` table, and setting up its default values in the `ion_data` table. .. cpp:function:: add_ion(const std::string& ion_name, int charge, double init_iconc, double init_econc, mechanism_desc revpot_mechanism) As above, but set the initial reversal potential to zero, and use the given mechanism for reversal potential calculation. For convenience, :cpp:expr:`neuron_parameter_defaults` is a predefined :cpp:type:`cable_cell_local_parameter_set` value that holds values that correspond to NEURON defaults. To use these values, assign them to the :cpp:expr:`default_parameters` field of the global properties object returned in the recipe. .. _cppcablecell-revpot: Reversal potential dynamics --------------------------- If no reversal potential mechanism is specified for an ion species, the initial reversal potential values are maintained for the course of a simulation. Otherwise, a provided mechanism does the work, but it subject to some strict restrictions. A reversal potential mechanism described in NMODL: * May not maintain any STATE variables. * Can only write to the "eX" value associated with an ion. * Can not be given as a POINT mechanism. Essentially, reversal potential mechanisms must be pure functions of cellular and ionic state. If a reversal potential mechanism writes to multiple ions, then if the mechanism is given for one of the ions in the global or per-cell parameters, it must be given for all of them. Arbor's default catalogue includes a "nernst" reversal potential, which is parameterized over a single ion, and so can be assigned to e.g. calcium in the global parameters via .. code:: cable_cell_global_properties gprop; // ... gprop.default_parameters.reversal_potential_method["ca"] = "nernst/ca"; This mechanism has global scalar parameters for the gas constant *R* and Faraday constant *F*, corresponding to the exact values given by the 2019 redefinition of the SI base units. These values can be changed in a derived mechanism in order to use, for example, older values of these physical constants. .. code:: mechanism_catalogue mycat(global_default_catalogue()); mycat.derive("nernst1998", "nernst", {{"R", 8.314472}, {"F", 96485.3415}}); gprop.catalogue = &mycat; gprop.default_parameters.reversal_potential_method["ca"] = "nernst1998/ca"; .. _cppcablecell-paint-properties: Overriding properties locally ----------------------------- .. todo:: TODO: using ``paint`` to specify electrical properties on subsections of the morphology.