SpiCoDyn: A Toolbox for the Analysis of Neuronal Network Dynamics and Connectivity from Multi-Site Spike Signal Recordings

Abstract

We implemented an automated and efficient open-source software for the analysis of multi-site neuronal spike signals. The software package, named SPICODYN, has been developed as a standalone windows GUI application, using C# programming language with Microsoft Visual Studio based on .NET framework 4.5 development environment. Accepted input data formats are HDF5, level 5 MAT and text files, containing recorded or generated time series spike signals data. SPICODYN processes such electrophysiological signals focusing on: spiking and bursting dynamics and functional-effective connectivity analysis. In particular, for inferring network connectivity, a new implementation of the transfer entropy method is presented dealing with multiple time delays (temporal extension) and with multiple binary patterns (high order extension). SPICODYN is specifically tailored to process data coming from different Multi-Electrode Arrays setups, guarantying, in those specific cases, automated processing. The optimized implementation of the Delayed Transfer Entropy and the High-Order Transfer Entropy algorithms, allows performing accurate and rapid analysis on multiple spike trains from thousands of electrodes.

Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings

“…Functional connectivity and topological analysis . The FNCCH used to infer functional connectivity, as well as the metrics used to characterize the topological features of the cortical networks (Small-World Index, Clustering Coefficient, average shortest Path Length) were collected in an update version of the SpiCoDyn software [ 71 ].…”

Simulation of Large Scale Neural Networks for Evaluation Applications

“…However, the complexity and topology of commonly used in silico neural networks and thus the evaluation results can vary. For example, the accuracy of Transfer Entropy, a widely used algorithm for connectivity estimation, varies greatly depending on the model used for the evaluation [15,16].…”

“…Whereas SII topologies are used in many evaluations, e.g. without delay times [15], with delay times, and with different use of STDP [16,17], more realistic scale-free topologies are rarely used for evaluations [3]. One can concluded that searching for the best algorithms can be confusing, since apparently better results are not synonymous with physiologic relevance for real biological neural networks.…”

Human neuronal networks on micro-electrode arrays are a highly robust tool to study disease-specific genotype-phenotype correlationsin vitro

“…We obtained connectivity matrix for each culture by applying the Filtered Cross-Correlation algorithm (Gorkin et al 2014, Pastore et al 2018) available in the free software SPICODYN (Pastore et al 2018, Bastle et al 2019). Cross correlograms were obtained using a bin size of 0.1 ms and a correlation window of 150 ms. Matrices were then analyzed using custom script in MATLAB.…”