NeuroScience Objects Library
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README.md

README.md

build status coverage report

NSOL - Neuroscience Objects Library

(c) 2015. GMRV / URJC

www.gmrv.es gmrv@gmrv.es

Introduction

nsol is a library that provides data structures to handle basic neuroscientific data, mainly cortex morphologies and structures as Spine, Soma, Neuron, Column, etc... It also provides some readers and writers to load and store dataset in swc (as used by NeuroMorpho) and XML file formats.
It also reads circuits and morphologies using Brion, which is an optional dependency.
It is used in projects as NeuroScheme, ViSimpl and NeuroLOTs

Dependencies

  • Required dependencies:
    • Eigen3 (*1)
  • Optional dependencies:
    • FiReS (*2)
    • Brion (*2)
    • Boost's Unit Test Framework
    • Qt5Core

(*1) Install linux package libeigen3-dev or download sources from http://eigen.tuxfamily.org/
(*2) This dependencies can be built uncommenting theirs corresponding line in the file .gitsubprojects

Building

nsol has been successfully built and used on Ubuntu 17.04/16.04, Mac OSX Yosemite/Capitan/Sierra and Windows 7/8/10 (Visual Studio 2015 Win64). The following steps should be enough to build it under linux/Mac OSX:

git clone --recursive https://github.com/gmrvvis/nsol
mkdir nsol/build && cd nsol/build
cmake .. -DCMAKE_BUILD_TYPE=Release -DCLONE_SUBPROJECTS=ON
make

Testing

After building NSOL, you can run some examples in bin directory. For example, to manually run a simple test that parses an input .swc file and dumps some statistics about it, use the command:

./bin/nsolScene testData/scene.xml

Documentation

You can access the online API documentation generated from the source (using Doxygen ) in https://gmrvvis.github.io/doc/nsol/