Mauro Gandolfo

A novel algorithm for precise identification of spikes in extracellularly recorded neuronal signals.

The spike represents the fundamental bit of information transmitted by the neurons within a network in order to communicate. Then, given the importance of the spike rate as well as the spike time for coding the activity generated at the level of a cell assembly, a relevant issue in extracellular electrophysiology is the correct identification of the spike in multisite recordings from brain areas or neuronal networks. In this paper, we present a novel spike detection algorithm, named Precise Timing Spike Detection (PTSD), aimed at (i) reducing the number of false positives and false negatives, in order to optimize the rate code, and (ii) improving the time precision of the identified spike, in order to optimize the spike timing. The PTSD algorithm considers consecutive portions of the signal and looks for the Relative Maximum/Minimum whose peak-to-peak amplitude is above a defined differential threshold and responds to specific requirements. To validate the algorithm, the presented spike detection has been compared with other methods either commercially available or proposed in the literature by using two benchmarking procedures: (i) visual inspection by a group of experts of a portion of signal recorded from a rat cortical culture and (ii) detection of the spikes generated by a realistic neuronal network model. In both cases our algorithm produced the best performances in terms of efficiency and precision. The ROC curve analysis further proved that the best results are reached by the application of the PTSD.

Following the ontogeny of retinal waves: pan‐retinal recordings of population dynamics in the neonatal mouse

Novel pan‐retinal recordings of mouse retinal waves were obtained at near cellular resolution using a large‐scale, high‐density array of 4096 electrodes to investigate changes in wave spatiotemporal properties from postnatal day 2 to eye opening. Early cholinergic waves are large, slow and random, with low cellular recruitment. A developmental shift in GABAA signalling from depolarizing to hyperpolarizing influences the dynamics of cholinergic waves. Glutamatergic waves that occur just before eye opening are focused, faster, denser, non‐random and repetitive. These results provide a new, deeper understanding of developmental changes in retinal spontaneous activity patterns, which will help researchers in the investigation of the role of early retinal activity during wiring of the visual system.

Extracellular recordings from locally dense microelectrode arrays coupled to dissociated cortical cultures.

High-density microelectrode arrays (MEAs) enabled by recent developments of microelectronic circuits (CMOS-MEA) and providing spatial resolutions down to the cellular level open the perspective to access simultaneously local and overall neuronal network activities expressed by in vitro preparations. The short inter-electrode separation results in a gain of information on the micro-circuit neuronal dynamics and signal propagation, but requires the careful evaluation of the time resolution as well as the assessment of possible cross-talk artifacts. In this respect, we have realized and tested Pt high-density (HD)-MEAs featuring four local areas with 10microm inter-electrode spacing and providing a suitable noise level for the assessment of the high-density approach. First, simulated results show how possible artifacts (duplicated spikes) can be theoretically observed on nearby microelectrodes only for very high-shunt resistance values (e.g. R(sh)=50 kOmega generates up to 60% of false positives). This limiting condition is not compatible with typical experimental conditions (i.e. dense but not confluent cultures). Experiments performed on spontaneously active cortical neuronal networks show that spike synchronicity decreases by increasing the time resolution and analysis results show that the detected synchronous spikes on nearby electrodes are likely to be unresolved (in time) fast local propagations. Finally, functional connectivity analysis results show stronger local connections than long connections spread homogeneously over the whole network demonstrating the expected gain in detail provided by the spatial resolution.

Experimental investigation on spontaneously active hippocampal cultures recorded by means of high-density MEAs: analysis of the spatial resolution effects

Based on experiments performed with high-resolution Active Pixel Sensor microelectrode arrays (APS-MEAs) coupled with spontaneously active hippocampal cultures, this work investigates the spatial resolution effects of the neuroelectronic interface on the analysis of the recorded electrophysiological signals. The adopted methodology consists, first, in recording the spontaneous activity at the highest spatial resolution (interelectrode separation of 21 μm) from the whole array of 4096 microelectrodes. Then, the full resolution dataset is spatially downsampled in order to evaluate the effects on raster plot representation, array-wide spike rate (AWSR), mean firing rate (MFR) and mean bursting rate (MBR). Furthermore, the effects of the array-to-network relative position are evaluated by shifting a subset of equally spaced electrodes on the entire recorded area. Results highlight that MFR and MBR are particularly influenced by the spatial resolution provided by the neuroelectronic interface. On high-resolution large MEAs, such analysis better represent the time-based parameterization of the network dynamics. Finally, this work suggest interesting capabilities of high-resolution MEAs for spatial-based analysis in dense and low-dense neuronal preparation for investigating signaling at both local and global neuronal circuitries.

Microelectronics, bioinformatics and neurocomputation for massive neuronal recordings in brain circuits with large scale multielectrode array probes.

Deciphering neural network function in health and disease requires recording from many active neurons simultaneously. Developing approaches to increase their numbers is a major neurotechnological challenge. Parallel to recent advances in optical Ca(2+) imaging, an emerging approach consists in adopting complementary-metal-oxide-semiconductor (CMOS) technology to realize MultiElectrode Array (MEA) devices. By implementing signal conditioning and multiplexing circuits, these devices allow nowadays to record from several thousands of single neurons at sub-millisecond temporal resolution. At the same time, these recordings generate very large data streams which become challenging to analyze. Here, at first we shortly review the major approaches developed for data management and analysis for conventional, low-resolution MEAs. We highlight how conventional computational tools cannot be easily up-scaled to very large electrode array recordings, and custom bioinformatics tools are an emerging need in this field. We then introduce a novel approach adapted for the acquisition, compression and analysis of extracellular signals acquired simultaneously from 4096 electrodes with CMOS MEAs. Finally, as a case study, we describe how this novel large scale recording platform was used to record and analyze extracellular spikes from the ganglion cell layer in the wholemount retina at pan-retinal scale following patterned light stimulation.

Analysis of simultaneous multielectrode recordings with 4,096 channels: changing dynamics of spontaneous activity in the developing retina

provide a complete characterisation of the dynamics of retinal waves during the first two postnatal weeks, and present several methods for the analysis of such activity patterns. In the mammalian retina, the earliest waves propagate through gap junctions (Stage I, prenatal in mouse), followed by lateral propagation between cholinergic starburst amacrine cells (Stage II) and finally by activity that depends on glutamatergic synaptic transmission (Stage III). Consistent with an earlier analysis of 60 channel MEA recordings [6], we found that Stage II waves exhibit a high degree of randomness with respect to initiation points, trajectories , sizes and durations. Stage III waves, on the other hand, were significantly faster and they were more restricted spatially, following several clear repetitive, non-random propagation patterns that appear to tile the retina, mostly starting from the periphery and propagating towards the centre. This latter effect can not be identified in recordings with conventional 60 channel MEAs, underscoring the importance of probing and analysing neural circuits at a near-cellular resolution.