Cell Type File
==============

Each *Cell Type* file is a JSON file that describes the membrane properties of a particular class of neuron in the simulation. Note that many of these properties are specified as densities (e.g. nanosiemens per square centimetre) that are scaled by the surface area (``sa``) parameter to give the actual value that is used in the simulation.

A *Cell Type* file should contain a single JSON object with the following fields. Each field is required unless otherwise specified.

==================== ======= ===========
Field                Type    Description
==================== ======= ===========
``cell_type``        string  A name for the neuron type. There should not be more than one neuron type with the same name in a simulation.
``sa``               decimal The surface area of the neuron (in :math:`cm^2`). This is used to calculate "final" values for capacitance, conductances and permeabilities, which are specified as densities in this file.
``sa_stdev``         decimal *Optional.* If this is specified, the actual surface area of each neuron is drawn from a Gaussian (normal) distribution, with mean ``sa`` and standard deviation ``sa_stdev``.
``gmax_lk``          decimal The maximum conductance density of passive leak channels (:math:`nS / cm^2`).
``erev_lk``          decimal The reversal potential of passive leak channels (mV).
``channels``         array   A list of active (gated) channels in the membrane. See below for details.
==================== ======= ===========

The ``channels`` array specifies the ionic channels that are present in the membrane. It takes the form of a list of objects, each of which contains only one mandatory field called ``file``, which is a string giving the path of the :doc:`Channel Type file <file_channel_type>` that contains the parameters of channel. However, any of the fields in the :doc:`Channel Type file <file_channel_type>` can also be specified here, in which case the value from the file will be overriden.

The following example shows an entire example *Cell Type* file. Each neuron of this type will have a surface area that is drawn from a Gaussian distribution with mean :math:`10^{-5}` and standard deviation :math:`10^{-6}` (line 3). The neuron type contains two ionic channels: sodium (``na``) and potassium (``k``). The conductance of the sodium channel is not specified here, so the value from its *Channel Type* file will be used; however, a new value is specified for the potassium channel conductance and so this value will override the one from the *Channel Type* file.::

   {
      "cell_type": "SimpleNeuron",
      "sa": 1e-5, "sa_stdev": 2e-7,
      "cap": 10e5,
      "gmax_lk": 1.405e5, "erev_lk": -52.0,
      "channels": [
         { "file": "Channels/na.json" },
         { "file": "Channels/k.json", "gmax": 12.0e" }
      ]
   }

.. hint:: If you wish to specify whole-cell values (rather than densities) for the capacitance and channel conductances/permeabilities, set the surface area (``sa`` field) equal to 1.0.