TOOLCONNECT: A powerful toolbox for functional connectivity analysis of in vitro neural networks

Abstract

Event Abstract Back to Event TOOLCONNECT: A powerful toolbox for functional connectivity analysis of in vitro neural networks Vito P. Pastore1*, Aleksandar Godjoski1, Sergio Martinoia1 and Paolo Massobrio1 1 University of Genova, Department of Informatics, Bioengineering, Robotics, System Engineering , Italy Motivation One of the goal of contemporary neuroscience is to study the interplay between topology, structure, functional-effective connectivity and neuronal dynamics at different level of complexity and on different experimental models (from simple in-vitro networks to whole brain areas). Functional connectivity is defined as the strength of the influence one network member has on another during ongoing behavior [1]. The analysis of multiple neural spike train data recorded from experimental models has gained tremendous relevance recently with the widespread application of Micro-Electrode Arrays (MEAs) [2]. At present, to the best of our knowledge, there is no available dedicated software that puts together a set of different functional connectivity analysis methods. Thus, we developed a user-friendly toolbox [3] in order to provide the researchers community a powerful tool to perform functional connectivity analysis on in-vitro neuronal networks coupled to standard and high-density MEAs, while guaranteeing computational efficiency and high accuracy. Material and Methods We implemented 'ToolConnect' toolbox as a standalone windows Graphical User Interface (GUI) application, using C# and Microsoft Visual Studio with .NET framework 4.5 development environment. The software is designed to be intuitive and straightforward to use. It is based on several windows forms and a friendly and modular GUI through which provides the user with powerful tools to manipulate and analyze data. ToolConnect offers functional connectivity analysis based on two correlation (cross-correlation and partial correlation) and two information theory based methods (transfer entropy and joint entropy). Cross correlation measures the frequency at which one cell fires as a function of time relative to the firing of a spike in another cell [4]. Partial correlation allows to distinguish between direct and indirect connections by removing the portion of the relationship between two spike trains that can be attributed to linear relationships with recorded spike trains from other neurons [5, 6]. Transfer Entropy is an information theoretic measure able to estimate causal relationships between time series taking into account their past activity [7]. Joint Entropy analyzes the cross Inter-Spike-Intervals (cISI): if two neurons are strongly connected the cISI histogram will show a peak and Joint Entropy will be close to zero, otherwise the cISI histogram will be almost flat, and the Joint Entropy will be high. The graphical section offers dedicated interfaces and allows the user to: i) plot the correlograms between each couple of the set of analyzed electrodes (for cross- and partial correlation); ii) manage, thresh and plot the Connectivity Matrix (CM) and the connectivity graph; iii) compute some powerful metrics that allow to extract the main topological features (degree, cluster coefficient, path length). One of the major features of the toolbox is its independence from the acquisition system (e.g. Multi Channel Systems, Qwane Biosciences, 3Brain) and from the MEA layout (number of microelectrodes and spatial organization). Results We designed and developed ToolConnect taking care to satisfy the user-friendliness requirement. According to this, our software has a GUI, which permits also to inexperienced users to perform functional connectivity analysis, to graphically represent the results, hiding the algorithms implementation specifics and software’s code design. Figure 1 shows a screenshot of ToolConnect’s GUI. Figure 2 shows the connectivity graphs obtained from the analysis of cortical networks coupled to the MEA60 and the MEA2100 acquisition systems of Multi Channel Systems (www.multichannelsystems.com; MCS, Reutlingen, Germany) and the BioCam acquisition system of 3Brain Systems. To assess the performances of tool connect we performed functional-connectivity analysis based on the cross-correlation method on hippocampal neuronal networks coupled to the MEA 60 from Multi-Channel Systems (MCS), during spontaneous and stimulus-evoked activity[3]. Discussion To the best of our knowledge, ToolConnect is the first functional connectivity toolbox dedicated to the analysis of multiple spike trains recorded from in-vitro neural networks coupled to MEAs. It provides the user with a complete set of computational and graphical tools of intuitive and straightforward usage through a dedicated and modular GUI. ToolConnect is implemented taking care of the optimization of the resources usage (requested RAM) and the reduction of the computational time. We were able to obtain acceptable performances with computational time lower than 2 minutes (for 10 minutes of recording sampled at 10 kHz). These performances make ToolConnect compatible with high-density recording systems (e.g., the 4096 electrodes of the 3brain system). In this way, it will be possible to perform functional connectivity analysis on neural networks with dimensions of thousands of neurons preserving an acceptable spatial and temporal resolution, hence allowing to obtain realistic and complete information on the dynamics and the topology of such systems.