What is NeuroScope?
NeuroScope is an advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. NeuroScope is part of a larger data analysis framework, including Klusters
(powerful and easy-to-use cluster cutting application) and NDManager
. NeuroScope was developed by Lynn Hazan in G. Buzsáki's lab
(CMBN, Rutgers Newark, USA).
How is NeuroScope distributed?
NeuroScope is a free software distributed under the General Public License (GPL)
Who uses NeuroScope?
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...
Warning: NeuroScope 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).
NeuroScope was developed for GNU/Linux, but can also run on MacOS, and even on Windows, using a virtual machine such as VirtualBox
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 Natty
. 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/ natty 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 neuroscope-1.3.5.tar.gz
# cd neuroscope
# ./configure --prefix=$(kde-config --prefix) --without-arts
(type root password)
# make install
Compiling NeuroScope requires KDE3 and libxml2 development libraries.
If you need help, contact Michaël Zugaro at michael.zugaro at college-de-france.fr
The user manual can be acessed in NeuroScope from the Help menu. It is also available online
NeuroScope can be tested using these example files
(16.7MB, courtesy of David Robbe).
Developer documentation (API) can be found in the source archive in the directory neuroscope-api/html. It is also available online
June 29 2011 - NeuroScope 1.3.5
- Minor corrections to have NeuroScope compile with the new versions of gcc.
September 17 2007 - NeuroScope 1.3.3
- Display the traces on a picture.
- Use of floating number for a certain number of parameters.
- Bug fixes.
February 28 2005 - NeuroScope 1.3.2
- Ability to modify the space ratio for spike rasters versus traces.
- Display the events on the spatial map.
- Bug fixes.
January 26 2005 - NeuroScope 1.3.1
- Modifications to make the application compatible with the new GCC 3.4 release series (G++ is now much closer to full conformance to the ISO/ANSI C++ standard). This version has been tested on Fedora Core3 linux with the gcc 3.4.2 and on KNOPPIX 3.7 with the gcc 3.4.4 20041218 (prerelease)(Debian 3.4.3-6).
December 30 2004 - NeuroScope 1.3
- Addition of a temporary movable time line to quickly assess the temporal relationships between physiological events occurring on different channels.
- Ability to redefine the default offsets.
- Modification of some of the icons.
- Bug fixes.
October 26 2004 - NeuroScope at SfN
- Klusters was presented at the Society for Neuroscience 34th Annual Meeting in San Diego
- The abstract reference is: L.Hazan et al, Soc Neurosci Abstr 34, 768.2, 2004
October 11 2004 - NeuroScope 1.2.5
September 29 2004 - NeuroScope 1.2.4
September 13 2004 - NeuroScope 1.2.3