Lpar is the parameter structure that defines the cell populations from which axonal and dendritic densities are generated. The figure below shows the structure of lpar. Any field with a lighter color is itself a struct.
The fields of lpar are:
| nDim: | The number of dimensions |
|---|---|
| nSigRange: | cut-off range for gaussians (number of standard deviations from the centre) |
| vox.voxPerDim: | The number of voxels in each dimension. If a scalar is given, all dimensions have that many voxels |
| vox.voxelSize: | A scalar giving the size of a voxel. |
| neurPop: | A cell array of structs defining all populations in the current model |
| neurPop.seed: | A random seed for this populations |
| neurpop.Nn: | The number of neurons in this populations |
| neurpop.isPre: | Whether or not this is a presynaptic population |
| neurpop.name: | The name of this population, as in identifier* |
| neurpop.number: | The number of this population, as an identifier* |
| neurpop.typeSpec: | |
| a struct specifying the density of the neurons | |
| typeSpec.generator: | |
| function handle specifying the generator to use | |
| typeSpec.parameters: | |
| Different parameters are required depending on the generator | |
| typeSpec.Distributions: | |
| Can be used to define distributions over parameters ,* | |
| typeSpec.wVec: | Defines the relative weight of the different Gaussians. Does not have to be normalized* |
| neurPop.soma: | struct containing the specification of the soma distribution |
| soma.area: | Defines in coordinates normalized to [0,1] the range in the tissue at hand where the soma are to be generated, alternatively a scalar soma.edge can be given which gives the amount of somaless area from the edge in normalized coordinates (so it should be from [0,0.5) ) |
| soma.distribution: | |
| Defines the distribution of the soma | |
| soma.seed: | A new seed to generate soma locations from. If none is given, the population seed, the generator, the rotation and the number of neurons determine the soma distribution* |
| neurPop.rot: | struct defining the rotation of the target densities. Rotations are processed first around X, then Y, then Z.* |
| rot.X: | Rotation around the X axis* |
| rot.XDistr: | Distribution of rotation around the X axis*,** |
| rot.Y: | Rotation around the Y axis* |
| rot.YDistr: | Distribution of rotation around the Y axis*,** |
| rot.Z: | Rotation around the Z axis* |
| rot.ZDistr: | Distribution of rotation around the Z axis*,** |
| neurPop.mst: | Struct defining the parameters for the weighted minimum spanning tree algorithm used to grow the trees |
| mst.bf: | Balancing factor, setting this to 0 creates a minimum spanning tree. |
| mst.thr: | Threshold, giving the maximum branch length. A branch spans from one point to another. |
*Optional
**Distributions are defined by appending Distr to the parameter name. (See ExampleScript 1 for instance) For options, see help randSample