Intra-burst firing characteristics as network state parameters

Introduction \ud In our group we are aiming to demonstrate learning and memory capabilities of cultured networks of cortical neurons. A first step is to identify parameters that accurately describe changes in the network due to learning. Usually, such parameters are calculated from the responses to test-stimuli before and after a learning experiment. We propose that parameters should be calculated from the spontaneous activity before and after a learning experiment, as the applying of test-stimuli itself may alter the network. Since bursting is dominant in our cultures, we have investigated its spatio-temporal structure. \ud \ud Methods \ud Networks of cortical neurons were cultured on a MEA. Over a period from 9 to 35 DIV, the spontaneous activity has been measured on a regular basis. Measurements on a single day are always continuous; otherwise cultures are kept in a stove under controlled conditions (37 ˚C, 5% CO2, 100% humidity). Network bursts were detected by analysing the Array-Wide Spiking Rate (AWSR, the sum of activity over all electrodes). Next, we estimated the instantaneous AWSR during a burst by convolving spike-occurrences with a Gaussian function. We investigated the changes in burst profiles over time by aligning them to their peak AWSR. In 4 hour recording sessions, we grouped the burst profiles over 1 hour, resulting in 4 average burst profiles per day. In addition, a sufficient amount of aligned bursts yielded enough data to calculate the contribution of each recording site. \ud \ud Results \ud The burst profiles, calculated over a period of 1 hour, generally show little variation (figure 1). In subsequent hours, the profiles gradually change shape. Over a period of days however, the shape can change dramatically (figure 2). The relatively slow changes over the period of hours indicate an underlying probabilistic structure in the AWSR during bursts. The apparent structure in the burst profiles result from the relationships between individual recording sites, and thus also on the connectivity in the neural network. This is revealed in more detail by showing the contributions of individual sites (figure 3). The spike envelopes have a shape that is too detailed to be described accurately by a small set of parameters. \ud \ud Discussion \ud The burst profiles prove to be stable over a period of one hour, and gradually change their shape over several hours, as has also been suggested in [1]. The day-to-day changes in burst profiles may be the result of these gradual changes, thereby suggesting an intrinsically changing network. However, they can also be the result of putting the cultures back in the stove. The spike envelopes per recording site offer more detailed descriptions of the network state than the burst profiles. This may however be the amount of detail required to reveal the changes made during learning experiments. A subsequent refinement can be made by identifying distinct subgroups of bursts, as has been suggested in [2]

A new approach to the spatio-temporal pattern identification in neuronal multi-electrode registrations

A lot of methods were created in last decade for the spatio-temporal analysis of multi-electrode array (MEA) neuronal data sets. All these methods were implemented starting from a channel to channel analysis, with a great computational effort and onerous spatial pattern recognition task. 
Our idea is to approach the MEA data collection from a different point of view, i.e. considering all channels simultaneously. We transform the 2D plus time MEA signal in a mono-dimensional plus time signal and elaborate it as a normal 1D signal, using the Space-Amplitude Transform method. 
This geometrical transformation is completely invertible and allows to employ very fast processing algorithms. 
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Spiking Signatures of Spontaneous Activity Bursts in Hippocampal Cultures

Dense dissociated hippocampal cultures are known to generate spontaneous bursting electrical activity which can be recorded by multielectrode arrays. We have analyzed spatio-temporal profiles of the distribution of spikes in the bursts recorded after 2 weeks in vitro. We have found a statistically significant similarity between the spiking patterns in sequential bursting events, we refer to these spiking patterns as spiking signatures. Such spiking signatures may appear in different parts of the bursts, including the activation patterns – the first spike times in the bursts, and deactivation patterns – the last spike times in the bursts. Moreover, these patterns may display apparent time scaling, e.g., they may be replayed in the subsequent bursts at different speeds, while preserving the spiking order. We discuss how such properties of the bursts may be associated with the formation of repeatable signaling pathways in cultured networks in vitro

Development of statistical and computational methods to estimate functional connectivity and topology in large-scale neuronal assemblies

One of the most fundamental features of a neural circuit is its connectivity since the single neuron activity is not due only to its intrinsic properties but especially to the direct or indirect influence of other neurons1. It is fundamental to elaborate research strategies aimed at a comprehensive structural description of neuronal interconnections as well as the networks\u2019 elements forming the human connectome. The connectome will significantly increase our understanding of how functional brain states emerge from their underlying structural substrate, and will provide new mechanistic insights into how brain function is affected if this structural substrate is disrupted. The connectome is characterized by three different types of connectivity: structural, functional and effective connectivity. It is evident that the final goal of a connectivity analysis is the reconstruction of the human connectome, thus, the application of statistical measures to the in vivo model in both physiological and pathological states. Since the system under study (i.e. brain areas, cell assemblies) is highly complex, to achieve the purpose described above, it is useful to adopt a reductionist approach. During my PhD work, I focused on a reduced and simplified model, represented by neural networks chronically coupled to Micro Electrodes Arrays (MEAs). Large networks of cortical neurons developing in vitro and chronically coupled to MEAs2 represent a well-established experimental model for studying the neuronal dynamics at the network level3, and for understanding the basic principles of information coding4 learning and memory5. Thus, during my PhD work, I developed and optimized statistical methods to infer functional connectivity from spike train data. In particular, I worked on correlation-based methods: cross-correlation and partial correlation, and information-theory based methods: Transfer Entropy (TE) and Joint Entropy (JE). More in detail, my PhD\u2019s aim has been applying functional connectivity methods to neural networks coupled to high density resolution system, like the 3Brain active pixel sensor array with 4096 electrodes6. To fulfill such an aim, I re-adapted the computational logic operations of the aforementioned connectivity methods. Moreover, I worked on a new method based on the cross-correlogram, able to detect both inhibitory and excitatory links. I called such an algorithm Filtered Normalized Cross-Correlation Histogram (FNCCH). The FNCCH shows a very high precision in detecting both inhibitory and excitatory functional links when applied to our developed in silico model. I worked also on a temporal and pattern extension of the TE algorithm. In this way, I developed a Delayed TE (DTE) and a Delayed High Order TE (DHOTE) version of the TE algorithm. These two extension of the TE algorithm are able to consider different temporal bins at different temporal delays for the pattern recognition with respect to the basic TE. I worked also on algorithm for the JE computation. Starting from the mathematical definition in7, I developed a customized version of JE capable to detect the delay associated to a functional link, together with a dedicated shuffling based thresholding approach. Finally, I embedded all of these connectivity methods into a user-friendly open source software named SPICODYN8. SPICODYN allows the user to perform a complete analysis on data acquired from any acquisition system. I used a standard format for the input data, providing the user with the possibility to perform a complete set of operations on the input data, including: raw data viewing, spike and burst detection and analysis, functional connectivity analysis, graph theory and topological analysis. SPICODYN inherits the backbone structure from TOOLCONNECT, a previously published software that allowed to perform a functional connectivity analysis on spike trains dat

Synthesis of neural networks for spatio-temporal spike pattern recognition and processing

The advent of large scale neural computational platforms has highlighted the lack of algorithms for synthesis of neural structures to perform predefined cognitive tasks. The Neural Engineering Framework offers one such synthesis, but it is most effective for a spike rate representation of neural information, and it requires a large number of neurons to implement simple functions. We describe a neural network synthesis method that generates synaptic connectivity for neurons which process time-encoded neural signals, and which makes very sparse use of neurons. The method allows the user to specify, arbitrarily, neuronal characteristics such as axonal and dendritic delays, and synaptic transfer functions, and then solves for the optimal input-output relationship using computed dendritic weights. The method may be used for batch or online learning and has an extremely fast optimization process. We demonstrate its use in generating a network to recognize speech which is sparsely encoded as spike times.Comment: In submission to Frontiers in Neuromorphic Engineerin

A NEW APPROACH TO THE SPATIO-TEMPORAL PATTERN IDENTIFICATION IN NEURONAL MULTI-ELECTRODE REGISTRATIONS

A lot of methods were created in last decade for the spatio-temporal analysis of multi-electrode array (MEA) neuronal data sets. All these methods were implemented starting from a channel to channel analysis, with a great computational effort and onerous spatial pattern recognition task. Our idea is to approach the MEA data collection from a different point of view, i.e. considering all channels simultaneously. We transform the 2D plus time MEA signal in a mono-dimensional plus time signal and elaborate it as a normal 1D signal, using the Space-Amplitude Transform method. This geometrical transformation is completely invertible and allows to employ very fast processing algorithms

Model-free reconstruction of neuronal network connectivity from calcium imaging signals

A systematic assessment of global neural network connectivity through direct electrophysiological assays has remained technically unfeasible even in dissociated neuronal cultures. We introduce an improved algorithmic approach based on Transfer Entropy to reconstruct approximations to network structural connectivities from network activity monitored through calcium fluorescence imaging. Based on information theory, our method requires no prior assumptions on the statistics of neuronal firing and neuronal connections. The performance of our algorithm is benchmarked on surrogate time-series of calcium fluorescence generated by the simulated dynamics of a network with known ground-truth topology. We find that the effective network topology revealed by Transfer Entropy depends qualitatively on the time-dependent dynamic state of the network (e.g., bursting or non-bursting). We thus demonstrate how conditioning with respect to the global mean activity improves the performance of our method. [...] Compared to other reconstruction strategies such as cross-correlation or Granger Causality methods, our method based on improved Transfer Entropy is remarkably more accurate. In particular, it provides a good reconstruction of the network clustering coefficient, allowing to discriminate between weakly or strongly clustered topologies, whereas on the other hand an approach based on cross-correlations would invariantly detect artificially high levels of clustering. Finally, we present the applicability of our method to real recordings of in vitro cortical cultures. We demonstrate that these networks are characterized by an elevated level of clustering compared to a random graph (although not extreme) and by a markedly non-local connectivity.Comment: 54 pages, 8 figures (+9 supplementary figures), 1 table; submitted for publicatio

Spatio-temporal dependencies in functional connectivity in rodent cortical cultures

Models of functional connectivity in cortical cultures on multi-electrodes arrays may aid in understanding how cognitive pathways form and improve techniques that aim to interface with neuronal systems. To enable research on such models, this study uses both data- and model-driven approaches to determine what dependencies are present in and between functional connectivity networks derived from bursts of extracellularly recorded activity. Properties of excitation in bursts were analysed using correlative techniques to assess the degree of linear dependence and then two parallel techniques were used to assess functional connectivity. Three models presenting increasing levels of spatio-temporal dependency were used to capture the dynamics of individual functional connections and their consistencies were verified using surrogate data. By comparing network-wide properties between model generated networks and functional networks from data, complex interdependencies were revealed. This indicates the persistent co-activation of neuronal pathways in spontaneous bursts, as can be found in whole brain structures

A combined experimental and computational approach to investigate emergent network dynamics based on large-scale neuronal recordings

Sviluppo di un approccio integrato computazionale-sperimentale per lo studio di reti neuronali mediante registrazioni elettrofisiologich