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Stephan Grein edited this page Aug 27, 2020 · 13 revisions

Welcome to the NeuGen wiki

For a detailed description see the README of the devel branch click here.

Build

If you want to build NeuGen from source, you can either make use of the Netbeans Project, i. e. open project in Netbeans, select NeuGen project, then hit clean&build. A NeuGen jar-file in the dist subfolder of the NeuGen base folder is created.

However you can also use Ant (>= 1.8). Then just hit ant in the NeuGen directory where the build.xml is located, you may wish to issue also other ant tasks, e. g. release (creates a fat jar with all dependencies), bundle-NeuGenApp for MacOSX, or others (cf. build.xml).

Please note, that Java Target Level must be Java 1.6 - therefore, if you compile with a later Java version, e. g. 7 or 8, make sure you leave that option untouched, or compile with Java 6.

Run

Note, that currently we provide no installer for Windows or Linux, thus if using Windows or Linux you need to use the Universal release with an installed JRE. For Mac we provided bundled JRE to cope with some Java-specifics on OSX, thus no JRE must be installed but may be installed however.

  • Universal: Unzip neugen2.0.zip, navigate to osx, linux or windows and execute either run.sh or run.bat. Please note however that a working version of JRE >= 6 installation is required for NeuGen 2.0 and the run scripts must be made executable by chmod +x run.sh if the script is not executable already.
  • OSX PKG Installer: Just install by double click the pkg file, then find NeuGen in /Applications and execute it for instance via Finder or commandline. Make sure, that your Gatekeeper settings allow execution of unsigned packages/software to allow the for now unsigned Mac bundle.
  • Windows Installer: TBD
  • Linux Installer: TBD

Releases

2.1

TDB

2.0

The universal build contains Linux, OSX and Windows variants of NeuGen. Each variant can be executed by its corresponding run.sh script respectively run.bat. The only prerequisite is an installed JRE >= 6. In addition we provide installers specificially for your operation system, for now we provide only a installer for OSX as a pkginstaller. Windows and Linux installers may be provided in future (or on demand).

For older releases please see http://atlas.gcsc.uni-frankfurt.de/~neugen/download.html.

Publications

  • NeuGen 2.0

S. Wolf, S. Grein, G. Queisser. NeuGen 2.0 - Employing NeuGen 2.0 to automatically generate realistic morphologies of hippocapal neurons and neural networks in 3D. Neuroinformatics, 2013, 11(2), pp. 137-148, doi: 10.1007/s12021-012-9170-1

  • NeuGen

J. P. Eberhard, A. Wanner, G. Wittum. NeuGen - A tool for the generation of realistic morphology of cortical neurons and neural networks in 3D. Neurocomputing, 70(1-3), pp. 327-343, doi: 10.1016/j.neucom.2006.01.028

NeuGen - A generator for realistic neurons in 3D

NeuGen

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