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J Neurosci Methods. 2012 Jun 15;207(2):161-71. doi: 10.1016/j.jneumeth.2012.04.002. Epub 2012 Apr 9.

Multiscale functional connectivity estimation on low-density neuronal cultures recorded by high-density CMOS Micro Electrode Arrays.

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Department of Neuroscience and Brain Technologies - Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy.


We used electrophysiological signals recorded by CMOS Micro Electrode Arrays (MEAs) at high spatial resolution to estimate the functional-effective connectivity of sparse hippocampal neuronal networks in vitro by applying a cross-correlation (CC) based method and ad hoc developed spatio-temporal filtering. Low-density cultures were recorded by a recently introduced CMOS-MEA device providing simultaneous multi-site acquisition at high-spatial (21 μm inter-electrode separation) as well as high-temporal resolution (8 kHz per channel). The method is applied to estimate functional connections in different cultures and it is refined by applying spatio-temporal filters that allow pruning of those functional connections not compatible with signal propagation. This approach permits to discriminate between possible causal influence and spurious co-activation, and to obtain detailed maps down to cellular resolution. Further, a thorough analysis of the links strength and time delays (i.e., amplitude and peak position of the CC function) allows characterizing the inferred interconnected networks and supports a possible discrimination of fast mono-synaptic propagations, and slow poly-synaptic pathways. By focusing on specific regions of interest we could observe and analyze microcircuits involving connections among a few cells. Finally, the use of the high-density MEA with low density cultures analyzed with the proposed approach enables to compare the inferred effective links with the network structure obtained by staining procedures.

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