A new version of NDManager will soon be available
NDManager will soon become a pure Qt4 application. This means that you will again be able to easily install it on any recent GNU/Linux distribution, as well as on MacOS and Windows (although the Plugins will only work on GNU/Linux). Because this transition represents an enormous effort involving numerous people, it is difficult for us to estimate when new version will actually be available — hopefully within a few weeks.

Current pre-release snapshot packages for Kubuntu 12.04: shared libraries, application and mimetypes [last update 23/08/2013]

In the meantime...
Until the new version becomes available though, an interim solution for (K)Ubuntu was provided by our users (it is described below).


Developed by Lynn Hazan in G. Buzsáki's lab (CMBN, Rutgers Newark, USA).
Distributed under the General Public License (GPL).



If you use NDManager for your analyses, please be kind enough to cite the following article in your publications:

L. Hazan, M. Zugaro, G. Buzsáki (2006). Klusters, NeuroScope, NDManager: a Free Software Suite
for Neurophysiological Data Processing and Visualization
, J. Neurosci. Methods 155:207-216.




General

What is NDManager?
NDManager (Neurophysiological Data Manager) is a simple graphical application designed to help neurophysiologists manage their experimental recording parameters (e.g., number of channels and sampling rate of the acquisition system) and process their data (data filtering, spike extraction, PCA, etc.) NDManager is part of a larger data analysis framework, including Klusters (a powerful and easy-to-use cluster cutting application), NeuroScope (an advanced viewer for electrophysiological and behavioral data), and FMAToolbox (a Matlab toolbox for data analyses). NDManager was developed by Lynn Hazan in G. Buzsáki's lab (CMBN, Rutgers Newark, USA).

How is NDManager distributed?
NDManager is a free software distributed under the General Public License (GPL).

Who uses NDManager?
NeuroScope is used to process neuronal recordings from the hippocampus and cortex by dozens of teams around the world, including those of G. Buzsáki (Univ. Rutgers, USA), M. Zugaro and S. Wiener (CNRS-Collège de France, France), A. Sirota (Univ. Tübingen, Germany), K. Benchenane (CNRS, France), K. Diba (Univ. Wisconsin, USA), D. Robbe (IDIBAPS, Spain), H. Hirase (RIKEN, Japan), D. Isbrandt (Univ. Hamburg, Germany), V. Crunelli (Univ. Cardiff, UK), G. Laurent (Caltech, USA), E. Kandel (Univ. Columbia, USA), J. Knierim (Univ. Johns Hopkins, USA) and many more...

NDManager Plugins

Standard Plugins
NDManager Plugins include a number of scripts and programs to automatically pre-process files recorded with data acquisition systems: file conversion (from vendor-specific, proprietary formats to open formats used by e.g. Klusters and NeuroScope), channel resampling and reordering, high-pass filtering and spike detection, waveform feature extraction (PCA) for subsequent spike sorting, video transcoding and LED tracking, etc.

Make sure you download, build and install both NDManager and the Plugins.

Custom Plugins
You can easily integrate your own processing tools within our framework without code modification. Only a simple 'front-end' shell script is required to read and check the parameters from the XML parameter file (rather than from the command-line or legacy configuration files), and pass them along to the processing tools. This intermediate shell script is usually very simple because we also provide a program (xpathReader) and convenience functions (ndm_functions) to easily parse the XML file. Reading our code should help you get started: look at ndm_start, and e.g. ndm_extractchannels.

Installation

Warning: NDManager requires Qt3 and kdelibs from KDE3, and can no longer run on recent GNU/Linux distributions that have dropped support for these libraries (including e.g. Kubuntu >=11.10). To solve this issue, the code will soon be ported to Qt4. In the meantime, please use (older) distributions that support Qt3 and kdelibs from KDE3.

Good news: Thanks to user feedback, a very simple solution is now available for more recent versions of (K)Ubuntu (>=11.10 Oneiric).

Supported Systems
NDManager was developed for GNU/Linux, but can also run on MacOS, and even on Windows, using a virtual machine such as VirtualBox (see instructions contributed by Lucile Belliveau).

Packages
Readily-installable packages are provided for (K)Ubuntu. For other platforms, you will need to compile the sources.

If you use a recent version of (K)Ubuntu (>=11.10 Oneiric), you can get kdelibs4c2a and its dependencies from the repositories for Lucid. This can be done either graphically using your favorite package manager, or at the command-line like this: (Thanks to C. Rodgers and C. Schmidt-Hieber).

Building from Source
Before you start, make sure you have a working building environment (GCC C++ compiler and GNU make). All distributions provide packages ready for installation. Use your favorite package manager to install them, either graphically (Synaptic, KPackageKit, YaST, etc.) or from the command-line (apt-get on Debian/Ubuntu, yum on Fedora/Redhat, etc.) Next, install the libraries and headers for kdelibs (KDE3), qt3 and libxml2. Again, use the packages provided by your distribution. Usually, packages for headers have the same name as those for libraries, followed by a suffix such as '-dev' or '-devel'.

The general procedure consists in extracting the archive, configuring the build process, building the sources, and installing:
   # tar xvzf ndmanager-1.2.2.tar.gz
   # cd ndmanager
   # ./configure --prefix=$(kde-config --prefix) --without-arts
   # make
   # su
     (type root password)
   # make install
Compiling NDManager requires KDE3 and libxml2 development libraries.

For NDManager Plugins:
   # tar xvzf ndmanager-plugins_1.4.tar.gz
   # cd ndmanager-plugins
   # make
   # su
     (type root password)
   # make install
Compiling NDManager Plugins requires libsamplerate and libgsl development libraries. Some plugins also require mplayer (mencoder) and python-qt4 to run.

If you need help, contact Michaël Zugaro at michael.zugaro at college-de-france.fr

Getting Started

The user manual can be acessed in NDManager from the Help menu. It is also available online. Make sure you read it, it contains quite a lot of detailed information to get you started.

Contributing

Developer documentation (API) can be found in the source archive in the directory ndmanager-api/html. It is also available online.





History

August 5 2011 - NDManager Plugins 1.4

August 5 2011 - NDManager 1.2.3

July 5 2011 - NDManager 1.2.2

September 17 2007 - NDManager 1.2.1
February 7 2005 - NDManager 1.1.1

SourceForge.net Logo