Cell Type FileΒΆ
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 \(cm^2\)). 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 (\(nS / cm^2\)). |
| 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 Channel Type file that contains the parameters of channel. However, any of the fields in the Channel Type file 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 \(10^{-5}\) and standard deviation \(10^{-6}\) (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.