[Comp-neuro] SPIKY and PySpike – Two free software packages for monitoring spike train synchrony

Thomas Kreuz thomaskreuz at gmail.com
Mon Jun 22 01:07:08 CEST 2015


Dear all,

we would like to draw your attention to our two most recent papers and to
two new software packages.

*1. Two new papers:*

This paper provides a detailed description of *SPIKY* (see 2.) and
introduces our new measure *SPIKE-synchronization*:

•    Kreuz T, Mulansky M, Bozanic N:
     SPIKY: A graphical user interface for monitoring spike train synchrony.
     JNeurophysiol <http://jn.physiology.org/content/113/9/3432> 113, 3432
(2015) [PDF]
<http://www.fi.isc.cnr.it/users/thomas.kreuz/images/Kreuz_JNeurophysiol_2015_SPIKY.pdf>.



An overview of all three of our measures (*ISI-distance, SPIKE-distance and
SPIKE-synchronization*) and their mathematical properties can be found in

•    Mulansky M, Bozanic N, Sburlea A, Kreuz T:
     A guide to time-resolved and parameter-free measures of spike train
synchrony.
     IEEE Proceedings (in press) and arXiv [PDF]
<http://arxiv.org/pdf/1502.02027v2.pdf> (2015).


*2. SPIKY, graphical user interface (Matlab) for monitoring spike train
synchrony*

Implementations of ISI-distance, SPIKE-distance, and SPIKE-Synchronization
Distances, time profiles, distance matrices, selective averaging, triggered
averages, dendrograms, etc.
Plotting, movie generation
Spike train generator, event detector (for continuous data such as EEG)
Matlab with C backend (MEX)
Matlab fallback if no MEX-compiler is not available
Extensive documentation includes many illustrative movies

Matlab source codes and all relevant papers are available on our

*SPIKY download page*
http://www.fi.isc.cnr.it/users/thomas.kreuz/Source-Code/SPIKY.html

For further information about new features and updates please check the

*SPIKY Facebook page*           https://www.facebook.com/SPIKYgui

Here you'll also find a lot of documentation including many images and
movies that illustrate how to use SPIKY. All of these movies can also be
found on the

*SPIKY Youtube channel*         https://www.youtube.com/user/SPIKYgui1


*3. PySpike, open source Python library hosted on github*

Implementations of ISI-distance, SPIKE-distance, and SPIKE-Synchronization
Library of functions to compute distances and profiles (bivariate and
multivariate),
distance matrices, selective averages, etc.
Helper functions for plotting, spike train generation
Cython backend for optimal performance (factor 100-200 over plain Python)
Python fallback if Cython is not available
Extensive unit-tests that cover the API as well as the numerics
Automatic build and test runs
Documentation

The github issues system can be used to file bug reports or request new
functionality and features.

*PySpike webpage*         http://www.pyspike.de
*PySpike github page*    https://github.com/mariomulansky/PySpike

Any feedback on both the papers and the software packages is very welcome.

Best wishes,
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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