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Open Access Highly Accessed Research

A data repository and analysis framework for spontaneous neural activity recordings in developing retina

Stephen John Eglen1*, Michael Weeks2, Mark Jessop2, Jennifer Simonotto34, Tom Jackson2 and Evelyne Sernagor5

Author Affiliations

1 Cambridge Computational Biology Institute, University of Cambridge, Wilberforce Road, CB3 0WA Cambridge, UK

2 Advanced Computer Architecture Group, Computer Science Department, University of York, YO10 5GH York, UK

3 School of Computing Science, Newcastle University, NE1 7RU, Newcastle, UK

4 National Heart and Lung Institute, Imperial College London, Hammersmith Campus, W12 0NN, London, UK

5 Institute of Neuroscience, Faculty of Medical Sciences, Framlington PlaceNE2 4HH, Newcastle, UK

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GigaScience 2014, 3:3  doi:10.1186/2047-217X-3-3

Published: 26 March 2014

Abstract

Background

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.

Results

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.

Conclusions

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.

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