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 a 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.