What is Klusters?
Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists
sort action potentials recorded from multiple neurons on groups of electrodes (e.g.,
tetrodes or multisite silicon probes).
Klusters is part of a larger data analysis framework, including
NeuroScope (advanced viewer for electrophysiological and behavioral data) and other utilities which are currently under development.
Klusters was developed by Lynn Hazan in
G. Buzsáki's lab (CMBN, Rutgers Newark, USA).
What is cluster cutting?
Neurophysiological experiments investigating the functional properties of neuronal networks
involve recording brain signals with large numbers of electrodes.
Because each of the electrodes used in these experiments generally records from
multiple neurons, the first step before analyzing the data is to sort out the action
potentials emitted by each individual neuron.
Hence, each putative action potential or "spike" must be grouped together with other spikes
that are thought to belong to the same neuron. Such a group of spikes is referred to as
a "cluster", and the whole process of sorting out the action potentials is thus known as
"spike sorting" or "cluster cutting".
How is Klusters distributed?
Klusters is a free software distributed under the
General Public License (GPL).
Who uses Klusters?
Klusters is actively used to analyze neuronal recordings from hippocampus and cortex in
G. Buzsáki's lab
(CMBN, Rutgers Newark, USA).
September 17 2007: Klusters 1.6.2 released
- Addition of the capability to add information (structure, isolation distance, type, quality and notes) to cluster in the Cluster Palette.
This information is saved in the parameter file. Note that Klusters is no more backward compatible and the information is only saved in the xml version of the parameter file.
January 28 2004: Klusters 1.6released
- Addition of the capability to browse spikes in the Trace View.
- Klusters 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).
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 28 2004: Klusters 1.6 released
- Ability to open several Correlation Views in a single display. This allows you to examine spike train properties at different time scales.
- Cross-correlograms are displayed in gray when the background is white or very light (including while printing with the "Use white background" option on).
- Bug fixes.
October 26 2004: Klusters at the Society for Neuroscience 34th Annual Meeting in San Diego
- The abstract reference is: L.Hazan et al, Soc.Neurosci Abstr 34,768.3, 2004
October 11 2004: Klusters 1.5.2 released
- Labels displayed next to the traces in the Trace View.
- Bug fixes.
September 20 2004: Klusters 1.5.1 released
- Ability to open data files recorded with a 14 bits recording system.
- Bug fixes.
September 13 2004:Klusters 1.5 released
- The parameter file format was changed. However, Klusters is backward compatible and can still read the old parameter files. see user manual for detail.
- Addition of a new type of view, the Trace View. The Trace View displays spikes on the wide-band signals.
This view is available only if the wide-band data file is present in the same directory as the other files and the new parameter file format is used.
- When moving the mouse over the Correlation View, the clusters corresponding to the underlying correlogram are shown in the status bar.
- Bug fixes.
July 27 2004: Klusters 1.4.2 released
Bug fixes.
July 22 2004: Klusters 1.4.1 released
- Klusters runs on Slackware 10.
- rpms for Mandrake 9.1
- Bug fixes.
July 16 2004: new release of Klusters 1.4
The source archive klusters-1.4.tar.gz released on July 08 did not compiled on certain distributions, this is now corrected.
If you have encounter this problem, please download a copy of the corrected archive and try again. [This does not affect the debian package].
In addition a layout bug was corrected in the documentation. [This affects both the source archive and the debian package].
New Feature:
July 08 2004: Klusters 1.4 released
New Feature:
- Printing, and exporting to a PostScript file (.ps) or Portable Document File (.pdf), see user manual for detail.
Bug fixes.
April 19 2004: Klusters 1.3.3 released
Bug fixes.
April 09 2004: Klusters 1.3.2 released !
New Features:
- When moving the mouse over the Correlation View, the time corresponding to the underlying correlogram is shown in the status bar.
- In the Error Matrix View, clicking twice with the CTRL key on a cell of the Error Matrix will unselect the corresponding pair of clusters (which were selected by the first click).
Bug fixes.
March 08 2004: Klusters 1.3.1 released !
Minor release which fixes bugs and adds the ability to open another session file without closing the current one (this will actually start another instance of Klusters).
February 23 2004: Klusters 1.3 released !
New Features:
- The user interface is now more flexible, allowing you to dynamically compose custom combinations of views, and lay them out as you like.
These combinations are referred to as displays, and the term views is now more restrictively used to designate
a specific type of data representation (i.e., the 'building blocks': Clusters View, Waveform View, Correlation View and Error Matrix View).
- Views can be added and removed from a display.
- Views can be moved around in a display.
- A display can contain several Cluster Views, each presenting a different two-dimensional projection of the feature space.
- Display titles (tab labels) can be edited.
- These changes are now reflected in the application menus and User Manual.
- Thread interruptions are now much faster, resulting in a more responsive interface (this reduces the delays
when closing a display, the data files or the application).
Bug fixes.
February 11 2004: Klusters on sourceForge !
February 06 2004: Klusters 1.2 released !
New Features:
- Firing rates displayed in the Correlation View.
- Automatic Reclustering: besides the ability to manually reshape existing clusters,
Klusters now provides a mechanism to invoke an external automatic cluster cutting program such as Kenneth D. Harris' KlustaKwik
to selectively recluster currently selected clusters.
- User Manual written by Micha� B. Zugaro.
- An icon for Klusters.
Bug fixes.
January 21 2004: Klusters 1.1 released !
This release corrects some bugs and adds the Grouping Assistant feature. This feature helps you to find similar clusters by displaying
an Error Matrix. Each element in the Matrix indicates how likely it is that the two clusters corresponding to the row and column of the element contain spikes from the same neuron.
The user manual can be acessed in Klusters from the Help menu. It is also available online.
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Developers' documentation
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The developers' documentation (API) can be found in the source archive in the directory klusters-api/html.
It is also available online.
Klusters is known to compile and work on several GNU/Linux distributions: Mandrake 9.1, RedHat 9, RedHat Fedora, SuSE 9.1, Slackware 10 and Debian testing/unstable (KNOPPIX).
Klusters requires KDE >= 3.1, QT >= 3.1 and libxml2 >= 2.5.4
To build Klusters from source, you will also need the corresponding devel packages and an ANSI C++ Standard compliant compiler (gcc version 3.2.2 is known to work).
If you are upgrading Klusters uninstall the previous version first by doing the following:
# cd klusters-1.6.1
# su
(type root password)
# make uninstall
Download the archive, extract the source files, build and install the application by doing the following:
On Ubuntu
# tar xvzf klusters-1.6.2.tar.gz
# cd klusters-1.6.2
# kde_htmldir=/usr/share/doc/kde/HTML ./configure --prefix=$(kde-config --prefix)
# make
# sudo make install
On other distributions
# tar xvzf klusters-1.6.2.tar.gz
# cd klusters-1.6.2
# ./configure --prefix=$(kde-config --prefix)
# make
# su
(type root password)
# make install
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Installing the debian binary package
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Download the binary package (.deb) and install the application by doing the following:
# su
(type root password)
# dpkg -i klusters_1.6.1-1_i386.deb
You are done :0)
To make sure Klusters compiled properly, try it on these
example files (courtesy of Derek Buhl).
Simply extract the files and in Klusters, select File->Open and choose any of the files ending with the extension ".2"
To try out the new feature (
Trace View), use these
example files (16.7MB, courtesy of David Robbe).
