Two new papers: analysis of large scale microelectrode array recordings

We just published two new papers on the analysis of recordings with a high-density 4,096 channel microelectode array.

The first one deals with the perhaps biggest problems that comes with recording with so many channels at near-cellular resolution - how to assign the detected spikes to the originating neurons? This is a complex task as we are usually dealing with many millions of events from a single preparation (the longest recording from the same preparation I have seen has about 90 million events). These come from potentially thousands of neurons, so the combinatorics clearly work against us. We have developed a method that solves this task efficiently and reliably, essentially exploiting the fact that dense arrays provide pretty good positional information about the events.

All software we have developed in this project is available at this website.

G. Hilgen, M. Sorbaro, S. Pirmoradian, J.-O. Muthmann, I. Kepiro, S. Ullo, C. Juarez Ramirez, A. Puente Encinas, A. Maccione, L. Berdondini, V. Murino, D. Sona, F. Cella Zanacchi, E. Sernagor, M.H. Hennig (2016). Unsupervised spike sorting for large scale, high density multielectrode arrays. Cell Reports 18, 2521–2532. bioRxiv doi:

The second paper is simply a comprehensive characterisations of the light responses of mouse retinal neurons over the course of its development (starting at around eye opening, when light responses can be first seen). Unlike previous work, we could rely on very large cell samples from single preparations, which reveals properties that are easily missed when pooling multiple retinas - it turns out differences between individual retinas can be substantial, and we are quite certain this is not due to experimental factors. We hope this is a useful resource for everyone working using the mouse visual system as a model for neural development. In fact, a surprising and still unexplained finding in this project was that the development proceeds differently for different cell types, and also depends on retinal location.

G. Hilgen, S. Pirmoradian, D. Pamplona, P. Kornprobst, B. Cessac, M.H. Hennig, E. Sernagor (2016). Pan-retinal characterisation of Light Responses from Ganglion Cells in the Developing Mouse Retina. Scientific Reports 7, Article number: 42330. bioRxiv doi:

In the light of current events it is worth noting that this work was funded by the EU, and would almost certainly never have happened had it not been for this international collaboration.