How to use the SynapseDistributionGenerator

Introduction

The NeuroBox component SynapseDistributionGenerator is designed to create and manage distributions of synapses on neuron morphologies, which are given as graphs consisting of vertices in a three-dimensional space and edges connecting them.

Supported file format

Neuron morphologies are supported in the ProMesh *.ugx file format (s. http://promesh3d.com/).

Methods

Mandatory

create_synapse_distributor()

This constructor like method initializes a synapse distribution on a user-specified neuron morphology. Already existing synapses in the specified morphology can either be preserved or deleted. The invocation of this method is mandatory for using the following methods.

Optional

place_synapses()

This method enables the user to specify densities in [1/m] by which synapses will be distributed on the subset(s) of choice.

degenerate_synapses()

In this method the user can specify fractions in the range of [0,1] by which synapses will be deleted from the subset(s) of choice. For the new number of synapses fraction concretely means: newNumber = (1-fraction)*oldNumber

print_total_num_synapses()

This method prints the total number of synapses currently contained in the neuron morphology.

print_num_synapses_in_subset()

This method prints the number of synapses currently contained in the specified subset of the neuron morphology.

print_subset_length()

This method prints the the length in [m] of the specified subset the neuron morphology.

export_grid_to_input_grid_path()

This method exports the modified neuron morphology together with the synapse distribution to the path of the input grid file. The filename is user-specified.

export_grid_to()

This method exports the modified neuron morphology together with the synapse distribution to a user-specified file.