PySpike - A Python library for analyzing spike train synchrony

Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is introduced, a Python package for spike train analysis providing parameter-free and time-scale independent measures of spike train synchrony. It allows to compute similarity and dissimilarity profiles, averaged values and distance matrices. Although mainly focusing on neuroscience, PySpike can also be applied in other contexts like climate research or social sciences. The package is available as Open Source on Github and PyPI.Comment: 7 pages, 6 figure

A guide to time-resolved and parameter-free measures of spike train synchrony

Measures of spike train synchrony have proven a valuable tool in both experimental and computational neuroscience. Particularly useful are time-resolved methods such as the ISI- and the SPIKE-distance, which have already been applied in various bivariate and multivariate contexts. Recently, SPIKE-Synchronization was proposed as another time-resolved synchronization measure. It is based on Event-Synchronization and has a very intuitive interpretation. Here, we present a detailed analysis of the mathematical properties of these three synchronization measures. For example, we were able to obtain analytic expressions for the expectation values of the ISI-distance and SPIKE-Synchronization for Poisson spike trains. For the SPIKE-distance we present an empirical formula deduced from numerical evaluations. These expectation values are crucial for interpreting the synchronization of spike trains measured in experiments or numerical simulations, as they represent the point of reference for fully randomized spike trains.Comment: 8 pages, 4 figure

Measuring spike train synchrony

Estimating the degree of synchrony or reliability between two or more spike trains is a frequent task in both experimental and computational neuroscience. In recent years, many different methods have been proposed that typically compare the timing of spikes on a certain time scale to be fixed beforehand. Here, we propose the ISI-distance, a simple complementary approach that extracts information from the interspike intervals by evaluating the ratio of the instantaneous frequencies. The method is parameter free, time scale independent and easy to visualize as illustrated by an application to real neuronal spike trains obtained in vitro from rat slices. In a comparison with existing approaches on spike trains extracted from a simulated Hindemarsh-Rose network, the ISI-distance performs as well as the best time-scale-optimized measure based on spike timing.Comment: 11 pages, 13 figures; v2: minor modifications; v3: minor modifications, added link to webpage that includes the Matlab Source Code for the method (http://inls.ucsd.edu/~kreuz/Source-Code/Spike-Sync.html

Which spike train distance is most suitable for distinguishing rate and temporal coding?

Background: It is commonly assumed in neuronal coding that repeated presentations of a stimulus to a coding neuron elicit similar responses. One common way to assess similarity are spike train distances. These can be divided into spike-resolved, such as the Victor-Purpura and the van Rossum distance, and time-resolved, e.g. the ISI-, the SPIKE- and the RI-SPIKE-distance. New Method: We use independent steady-rate Poisson processes as surrogates for spike trains with fixed rate and no timing information to address two basic questions: How does the sensitivity of the different spike train distances to temporal coding depend on the rates of the two processes and how do the distances deal with very low rates? Results: Spike-resolved distances always contain rate information even for parameters indicating time coding. This is an issue for reasonably high rates but beneficial for very low rates. In contrast, the operational range for detecting time coding of time-resolved distances is superior at normal rates, but these measures produce artefacts at very low rates. The RI-SPIKE-distance is the only measure that is sensitive to timing information only. Comparison with Existing Methods: While our results on rate-dependent expectation values for the spike-resolved distances agree with \citet{Chicharro11}, we here go one step further and specifically investigate applicability for very low rates. Conclusions: The most appropriate measure depends on the rates of the data being analysed. Accordingly, we summarize our results in one table that allows an easy selection of the preferred measure for any kind of data.Comment: 14 pages, 6 Figures, 1 Tabl

Bootstrap testing for cross-correlation under low firing activity

A new cross-correlation synchrony index for neural activity is proposed. The index is based on the integration of the kernel estimation of the cross-correlation function. It is used to test for the dynamic synchronization levels of spontaneous neural activity under two induced brain states: sleep-like and awake-like. Two bootstrap resampling plans are proposed to approximate the distribution of the test statistics. The results of the first bootstrap method indicate that it is useful to discern significant differences in the synchronization dynamics of brain states characterized by a neural activity with low firing rate. The second bootstrap method is useful to unveil subtle differences in the synchronization levels of the awake-like state, depending on the activation pathway.Comment: 22 pages, 7 figure