Fivox  0.4.0
ITK library to sample events into regular volumes
Fivox Documentation

Introduction

Fivox (Field Voxelization) is a library to generate volumetric images of 3d scalar fields (Local Field Potential, spike densities, voltage sensitive dye), with loaders for the compartment, soma and spike reports generated by the Neuron and NEST simulators used in the Blue Brain Project. Fivox supports time animation.

Fivox can be retrieved by cloning the source code.

The voxelize command line tool can be used to generate volumes for ParaView or other volume rendering applications. When compiled with Livre, launch Livre with one of the URIs used by the voxelize command line tool as the volume parameter. The fivox data source will be loaded automatically and selected through one of the volume URI schemes.

To use the ImageSource programmatically, please refer to the fivox namespace documentation and voxelize command line tool.

3m_spikes_scaled.jpg
Fivox spike densities rendered in Livre
paraview.jpg
Using a Fivox volume in ParaView

Features

Fivox provides the following major features:

  • Converting compartment reports to volumetric LFP-like data
  • Converting spike reports densities to volumetric data
  • Converting compartment and surface area reports to volumetric data
  • Time and animation support

Installation

Build Fivox from source:

1 git clone https://github.com/BlueBrain/Fivox
2 mkdir Fivox/build
3 cd Fivox/build
4 cmake ..
5 make

Usage

The voxelize command line tool supports the following parameters:

About

Fivox uses CMake to create a platform-specific build environment. The following platforms and build environments are tested:

  • Linux: Ubuntu 14.04, RHEL 6.6 (Makefile, x64)
  • Mac OS X 10.9

The API documentation can be found on bluebrain.github.io.