Project Summary

on Tuesday, 28 February 2012. Posted in Project

Project context and objectives. Work performed and main results reached. The expected final results and their potential impact and use.

Project context and objectives

Enhancing recovery of cognitive and motor functions after localized brain injuries which disrupt connections between brain and body is widely recognized as a priority in healthcare. Nowadays, neurological diseases implying severe motor impairment are among the most common causes of adult-onset disability. Millions of people worldwide are affected by paralysis, and this number is likely to increase in coming years, because of the rapidly ageing population. Current assistive technology is still limited since only a minority of survivors with hemiparesis is able to achieve independence in simple activities of daily living. The frequent lack of complete recovery makes a desirable goal the development of novel neurobiological or neurotechnological strategies for brain repair.

Over the last decade Brain-Machine Interfaces (BMIs) and generally neuro-prostheses (Nicolelis, 2003; Hochberg et al., 2006; Nicolelis & Lebedev, 2009; Hochberg et al., 2012) have been object of extensive research and may represent a valid treatment for such disabilities. The development of these devices has and will hopefully have a profound social impact on the quality of life. Nevertheless, modern neural interfaces are mainly devoted to restore lost motor functions, because of injuries at the level of the spinal cord (Collinger et al., 2012; van den Brand et al., 2012), or recover sensorial capabilities, e.g. through artificial retinal or cochlear implants (Chader et al., 2009). However, the majority of motor disabilities are caused by brain diseases, such as stroke and traumatic brain injury - TBI - (33%) and not by spinal cord injury (23%).

Only very recently scientific interest has been devoted to in vivo cognitive neural prostheses. The first ever hippocampal prosthesis improving memory function in behaving rats has been presented in recent papers (Berger et al., 2011; Berger et al., 2012). Lately the same group tested a similar device in primate prefrontal cortex aimed at restoring impaired cognitive functions (Hampson et al., 2012; Opris et al., 2012).

The realization of such prostheses implies that we know how to interact with neuronal cell assemblies, taking into account the intrinsic spontaneous activation of neuronal networks and understanding how to drive them into a desired state in order to produce a specific behaviour. The long-term goal of replacing damaged brain areas with artificial devices requires the development of neural network models to be fed with the recorded electrophysiological patterns to yield the correct brain stimulation aimed at recovering the desired functions. All these issues are extremely difficult to investigate in vivo, due to the inherent complexity and low controllability of the system. On the other hand, we believe that important insights (e.g. structure-dynamics relationship, neural coding) might be gained by using in vitro systems of increasing architectural complexity, which can be easily and wholly accessed, monitored, manipulated, and thus modelled.


The final goal of the European project BRAIN BOW is to build a test-bed for the development and the study of a new generation of neuro-prostheses capable to restore the communication between neuronal circuitries lost because of a traumatic brain injury.

This topic is extremely up-to-date and represents one of the most important challenges over the next years in terms of clinical impacts and translational medicine. This is demonstrated, not only by the literature over the past years, but also by new US funding programmes in this specific direction (see e.g. DARPA website:, programmes REPAIR and REMIND). In particular, the group of T. Berger (University of California at Irvine, CA, USA) published several papers in 2013 regarding the development of hippocampal prosthesis (both on in vitro and in vivo experimental models) for memory enhancement (Deadwyler et al., 2013; Hampson et al., 2013; Hsiao et al., 2013). On December 2013, another very interesting paper came out from the group led by R. Nudo, very active in clinical studies related to stroke and TBI (Guggenmos et al., 2013). In this paper the very first example of a unidirectional ‘neural bridge’ aimed at promoting functional connection between two motor areas (i.e. the premotor cortex and the sensory cortex) in a rat model of TBI was demonstrated. Our project BRAIN BOW is exactly along the same line, but with the goal to make even a step forward with respect to these studies: design a chip for network replacement able to operate in a closed-loop fashion. The preliminary results demonstrating that a biological network and an artificial one are able to communicate and influence, in a bi-directional way, their intrinsic dynamics, constitute one of the most promising results of the second year and represent the basis for the activities of the third and final year.

Work performed and main results in the second year

Studies of healthy and lesioned in vitro neuronal circuits are presented (cf. Section 3.2) in parallel to the development of in silico neuronal networks, which will be exploited to establish a bi-directional communication with the injured neuronal network. In an attempt to develop an experimental and computational platform for the prototyping of neuro-prostheses, we have been following a bottom-up approach, where in vitro biological neuronal systems with increasing structural complexity are used. Our approach takes advantage of the unique features of in vitro neuronal cultures, which represent a powerful experimental model to investigate the inherent properties of neuronal cell assemblies as a complement to artificial computational models. We are using engineered networks of increasing structural complexity, from isolated finite-size networks up to interacting assemblies, as a model of intercommunicating neuronal circuitries. Moreover, we are scaling our studies up to the isolated whole brain (IWB) of guinea pig as a model of intact neuronal system preserving its native cytoarchitecture and circuit organization.


A Traumatic Brain Injury (TBI) was modelled as a ‘lesion’ in our experimental preparations. In particular, we used a laser dissector to cut connections in the in vitro cultures, while we cut the connections through a very fine surgical blade in case of IWB.

In the second year of the project, all the experiments related to the characterization of the spontaneous and evoked activity of the different experimental models have been performed both in healthy and injured neuronal systems. 2D patterned cultures have been realized for coverslips and Micro Electrode Arrays (MEAs) in order to characterize them from both the electrophysiological and the optical point of view. Regarding stimulation tests, 3D cultures have been tested for electrical stimulation for the first time and the first optical stimulation has been performed on 2D networks.

Data analysis, performed on a large experiment dataset, aimed at identifying peculiar patterns recorded during spontaneous activity and changes showed before and after the lesion, also provided the basis for the parameter tuning for the computational models. Large-scale computational models of both uniform and modular cultures have been implemented in the NEST environment, through the implementation of the architecture for modeling interconnected 2D networks, the realization of simulations, the development of ad hoc routines to make the output simulations compatible with the data analysis sw developed during the second year.

The same network model has been configured into the FPGA board, which represents the core of the neuromorphic device and contains the artificial neural network, the spike detection module and one block for external communication.

Colsed loop

The preliminary results demonstrating that a biological network and an artificial one are able to communicate constitute one of the most important results of the second year and constitute the promising basis for third and final year of the project.

The expected final results and their potential impact and use

In the last decades, great efforts have been made to develop neuro-prostheses to restore lost sensory or motor functions (Taylor et al., 2002; Chader et al., 2009; Collinger et al., 2012), but very few groups focused on studying neuro-prostheses targeting lesions at the level of the CNS and aimed at recovering lost cognitive capabilities (Berger et al., 2011; Prueckl et al., 2011; Bamford et al., 2012; Hampson et al., 2012; Opris et al., 2012). Although in this project our efforts are limited to simplified in vitro models of cell assemblies, their final aim is to provide useful insights for the design of future cognitive brain prostheses. In fact, we believe that the adopted approach would help us understand how we can influence/drive the dynamics of a neuronal assembly by interfacing it to an artificial one, either implemented in software or hardware. This is not the first ever attempt to realize an in vitro closed-loop system (DeMarse et al., 2001; Martinoia et al., 2004; Wagenaar et al., 2005; Wallach et al., 2011), either involving a robotic actuator or a control algorithm aimed at clamping the network activity to a desired level. In this project, however, we seek to extend these approaches by investigating the possibility of replacing a real biological network with a simulated one and hence by studying the bi-directional communication between biological and simulated networks and its effects on the resultant output dynamics.

This research project will build on previously published results in the field of in vitro closed-loop electrophysiology (Arsiero et al., 2007) and generalize previous findings to a more structured experimental model like the in vitro whole brain of a guinea pig, which lies between in vivo (as it retains the original 3D architecture) and in vitro (as it is disconnected from any sensory input/motor output). We will exploit the unique advantages of in vitro electrophysiology, namely accessibility, visibility and control of physical and chemical conditions, to study neural information processing in neuronal assemblies and understand which parameters are relevant for effectively interfacing biological and artificial networks. Moreover, in vitro system allows to standardize the type of injury down to single connection level, and thus to characterize the consequent electrophysiological changes respect to the increased number of severed connections. Therefore, a quantitative analysis of the network dynamics of the involved neuronal assembly could provide the basic procedure to restore the electrophysiological features in the specific cases of increased/decreased activity of neuronal assembly or their reciprocal activity desynchronization. For the above reasons, we are convinced that our approach will produce a number of subsidiary findings, mainly related to how the network structure constrains/drives the network dynamics which can be eventually exploited also in vivo studies. All this can open the venue for a continuation of the project exactly along this line.

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The BrainBow project acknowledges the financial support of the Future and Emerging Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, under FET-Open grant number: FP7-284772.