title: ToolConnect: A Functional Connectivity Toolbox for In vitro Networks.
abstract: Nowadays, the use of in vitro reduced models of neuronal networks to investigate the interplay between structural-functional connectivity and the emerging collective dynamics is a widely accepted approach. In this respect, a relevant advance for this kind of studies has been given by the recent introduction of high-density large-scale Micro-Electrode Arrays (MEAs) which have favored the mapping of functional connections and the recordings of the neuronal electrical activity. Although, several toolboxes have been implemented to characterize network dynamics and derive functional links, no specifically dedicated software for the management of huge amount of data and direct estimation of functional connectivity maps has been developed. toolconnect offers the implementation of up to date algorithms and a user-friendly Graphical User Interface (GUI) to analyze recorded data from large scale networks. It has been specifically conceived as a computationally efficient open-source software tailored to infer functional connectivity by analyzing the spike trains acquired from in vitro networks coupled to MEAs. In the current version, toolconnect implements correlation- (cross-correlation, partial-correlation) and information theory (joint entropy, transfer entropy) based core algorithms, as well as useful and practical add-ons to visualize functional connectivity graphs and extract some topological features. In this work, we present the software, its main features and capabilities together with some demonstrative applications on hippocampal recordings.
authors.affiliation: Neuroengineering and Bio-Nano Technology Lab, Department of Informatics, Bioengineering, Robotics, System Engineering, University of Genoa Genoa, Italy.
authors.forename: Vito Paolo
authors.initials: VP
authors.lastname: Pastore
authors.affiliation: Neuroengineering and Bio-Nano Technology Lab, Department of Informatics, Bioengineering, Robotics, System Engineering, University of Genoa Genoa, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Poli
authors.affiliation: Neuroengineering and Bio-Nano Technology Lab, Department of Informatics, Bioengineering, Robotics, System Engineering, University of Genoa Genoa, Italy.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Godjoski
authors.affiliation: Neuroengineering and Bio-Nano Technology Lab, Department of Informatics, Bioengineering, Robotics, System Engineering, University of GenoaGenoa, Italy; Institute of Biophysics, National Research CouncilGenova, Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Martinoia
authors.affiliation: Neuroengineering and Bio-Nano Technology Lab, Department of Informatics, Bioengineering, Robotics, System Engineering, University of Genoa Genoa, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Massobrio
keywords: correlation algorithms; functional connectivity; in vitro; information theory algorithms; micro-electrode arrays; multi-threading; neural networks; windows form application