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.
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.
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 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.
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.
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).
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).
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:
- Add the following line to /etc/apt/sources.list:
deb http://fr.archive.ubuntu.com/ubuntu/ lucid main universe
(you can replace fr.archive.ubuntu.com with the mirror closest to you)
# apt-get update
# apt-get install kdelibs4c2a
Remove the line from /etc/apt/sources.list
# apt-get update
(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
(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
(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
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.
Developer documentation (API) can be found in the source archive in the directory ndmanager-api/html. It is also available online.
August 5 2011 - NDManager Plugins 1.4
- Major overhaul, with numerous new features and bug fixes.
- Single-pass batch processing.
- Revamped Neuralynx conversion code to fix synchronization issues.
- Support for file format version 9, allowing for longer recordings.
- Included spots2pos tracking program (Matlab function, previously part of FMAToolbox).
- New graphical applications (python) to prepare and check files for NDManager.
- New code for PCA.
- Numerous bug fixes.
August 5 2011 - NDManager 1.2.3
- Updated manual to document how to get started with NDManager Plugins. Included template parameter files.
July 5 2011 - NDManager 1.2.2
- Minor fixes (removed obsolete default parameters, corrected description file default name, fixed save bug and restored widow size).
September 17 2007 - NDManager 1.2.1
- Addition of the Data processing action: a terminal screen where processing commands can be entered and at the bottom of the screen, several buttons and popup menus which allow you to quickly open specific session files with the appropriate application.
- Addition of a Units page which lets you list all the units recorded during the session, and provide important information about them: structure, isolation distance, type, quality and notes (thanks to Michaël Zugaro who has done 95% of the work).
This information is diplayed and may be modified in Klusters.
- Addition of the Queries action. Queries are a means to look for specific information in several parameter files at once (this functionnality needs the xpathRead program which can be found on the download page).
A big thanks to Michaël Zugaro who has developped this functionnality.
- The currently opened file can be reloaded
- Bug fixes
- NDManager has been modified to be compatible with the new GCC 3.4 release series (G++ is now much closer to full conformance to the ISO/ANSI C++ standard).
February 7 2005 - NDManager 1.1.1
- This first release allows you to define and set the parameters of your own command-line tools; but does not yet contain the functionality to launch the tools.