Thursday, April 3, 2014

[Comp-neuro] Article on data sharing/analysis of multielectrode array

I'd like to highlight the following article from our group that I hope
will be of use to the community. Code and data are available via the
project site:

Best wishes, Stephen

Eglen SJ, Weeks M, Jessop M, Simonotto J, Jackson T, Sernagor E (2014)

A data repository and analysis framework for spontaneous neural activity
recordings in developing retina. Gigascience 3:3.



During early development, neural circuits fire spontaneously, generating
activity episodes with complex spatiotemporal patterns. Recordings of
spontaneous activity have been made in many parts of the nervous system
over the last 25 years, reporting developmental changes in activity
patterns and the effects of various genetic perturbations.


We present a curated repository of multielectrode array recordings of
spontaneous activity in developing mouse and ferret retina. The data
have been annotated with minimal metadata and converted into HDF5. This
paper describes the structure of the data, along with examples of
reproducible research using these data files. We also demonstrate how
these data can be analysed in the CARMEN workflow system. This article
is written as a literate programming document; all programs and data
described here are freely available.


1. We hope this repository will lead to novel analysis of spontaneous
activity recorded in different laboratories. 2. We encourage published
data to be added to the repository. 3. This repository serves as an
example of how multielectrode array recordings can be stored for
long-term reuse.


Retinal waves; Spontaneous activity; Electrophysiology; HDF5;
Multielectrode arrays
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