[Comp-neuro] SPIKE-distance (incl. new Matlab source codes & movies)

Thomas Kreuz thomaskreuz at yahoo.de
Mon Apr 29 19:39:58 CEST 2013

Dear all, 
may I kindly draw your attention to our paper on the new SPIKE-distance which has just appeared in the Journal of Neurophysiology  (Section 'Innovative methodology'). This improved method opens
up several novel possibilities in spike train analysis. Among others, it allows
to estimate spike train synchrony online and in real-time.
Monitoring spike
train synchrony
Kreuz T, Chicharro D, Houghton C, Andrzejak RG, Mormann F
Abstract: Recently, the SPIKE-distance has been proposed as a parameter-free and
time-scale independent measure of spike train synchrony. This measure is
time-resolved since it relies on instantaneous estimates of spike train
dissimilarity. However, its original definition led to spuriously high
instantaneous values for event-like firing patterns. Here we present a
substantial improvement of this measure which eliminates this shortcoming. The
reliability gained allows us to track changes in instantaneous clustering,
i.e., time-localized patterns of (dis)similarity among multiple spike trains. Additional
new features include selective and triggered temporal averaging as well as the
instantaneous comparison of spike train groups. In a second step, a causal
SPIKE-distance is defined such that the instantaneous values of dissimilarity
rely on past information only so that time-resolved spike train synchrony can
be estimated in real-time. We demonstrate that these methods are capable of
extracting valuable information from field data by monitoring the synchrony
between neuronal spike trains during an epileptic seizure. Finally, the
applicability of both the regular and the real-time SPIKE-distance to
continuous data is illustrated on model electroencephalographic (EEG)
The paper is accessible on the webpage of theJournal of Neurophysiology:
A preprint can also be found on the arXiv (with permission): 

On my webpage you can find improvedMatlab source codes (including documentation):

The updated version uses MEX-  instead of m-files for the most time-consuming calculations. This reduces  the computational cost considerably (on my notebook the code running all the  examples below was faster by a factor of 85). It also uses a new output-structure 'results' which allows easy access not only to the overall  dissimilarity value but also to the measure profiles and the pairwise  distance matrices for all the selected measures. 

The source codes include a file “Distances_Main_Demo” which reproduces the figures 1-9 and the movie
from the paper. To provide a better illustration of what is done the parameter settings for each figure are detailed on the
On the same webpage there are also two movies (in both avi and wmv format) which demonstrate the new
method best. The first one is described in Fig. 9 of the paper, the second one
extends the analysis performed in Fig. 7D-F.

Finally, a short review on the SPIKE-distance can be
found on Scholarpedia:
Kreuz T
Scholarpedia 7(12), 30652 (2012).

Any feedback is very
Best regards,
Thomas Kreuz

Institute for complex systems, CNR
Via Madonna del Piano 10
50119 Sesto Fiorentino (Italy)
Tel: +39-349-0748506
Email: thomas.kreuz at cnr.it
Webpage: http://www.fi.isc.cnr.it/users/thomas.kreuz/
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