MEA-NAP: A flexible network analysis pipeline for neuronal 2D and 3D organoid multielectrode recordings
Microelectrode array (MEA) recordings are commonly used to compare firing and burst rates in neuronal cultures. MEA recordings can also reveal microscale functional connectivity, topology, and network dynamics-patterns seen in brain networks across spatial scales. Network topology is frequently characterized in neuroimaging with graph theoretical metrics. However, few computational tools exist for analyzing microscale functional brain networks from MEA recordings. Here, we present a MATLAB MEA network analysis pipeline (MEA-NAP) for raw voltage time series acquired from single- or multi-well MEAs. Applications to 3D human cerebral organoids or 2D human-derived or murine cultures reveal differences in network development, including topology, node cartography, and dimensionality. MEA-NAP incorporates multi-unit template-based spike detection, probabilistic thresholding for determining significant functional connections, and normalization techniques for comparing networks. MEA-NAP can identify network-level effects of pharmacologic perturbation and/or disease-causing mutations and thus can provide a translational platform for revealing mechanistic insights and screening new therapeutic approaches. VIDEO ABSTRACT.
Authors
- Stephen J. Eglen (ORCID: https://orcid.org/0000-0001-8607-8025)
- George M. Gibbons
- David Oluigbo
- András Lakatos (ORCID: https://orcid.org/0000-0002-1301-2292)
- Mahsa Khayat-Khoei (ORCID: https://orcid.org/0000-0002-3003-002X)
- Martin Hemberg (ORCID: https://orcid.org/0000-0001-8895-5239)
- Ole Paulsen (ORCID: https://orcid.org/0000-0002-2258-5455)
- Francesco De Angelis (ORCID: https://orcid.org/0000-0002-8354-6820)
- Erik Hemberg (ORCID: https://orcid.org/0000-0002-2153-3506)
- Hugo Smith (ORCID: https://orcid.org/0009-0006-5331-7740)
- Alexander WE Dunn (ORCID: https://orcid.org/0000-0003-1504-499X)
- Alessio Boschi (ORCID: https://orcid.org/0009-0002-0593-0090)
- Timothy P.H. Sit (ORCID: https://orcid.org/0000-0003-1149-0466)
- Susanna B. Mierau (ORCID: https://orcid.org/0000-0002-1220-6423)
- Rachael C. Feord (ORCID: https://orcid.org/0000-0001-7801-8137)
- Madeline A. Lancaster (ORCID: https://orcid.org/0000-0003-2324-8853)
- Jeremi Chabros (ORCID: https://orcid.org/0000-0001-7114-1108)
- Yuan Yin (ORCID: https://orcid.org/0009-0005-8405-3381)
- Elise Chang
- Lance Burn (ORCID: https://orcid.org/0009-0006-0449-5786)
Institutions
- Brigham and Women's Hospital (US)
- Harvard University (US)
- MRC Laboratory of Molecular Biology (GB)
- University of Cambridge (GB)
- Cambridge University Hospitals NHS Foundation Trust (GB)
- Italian Institute of Technology (IT)
- Bridge University (SS)
- National Hospital for Neurology and Neurosurgery (GB)
- University College London (GB)
- Massachusetts Institute of Technology (US)
Publication Details
- Journal
- Cell Reports Methods
- Published
- 2024-11-01
- DOI
- https://doi.org/10.1016/j.crmeth.2024.100901
- Citations
- 14
- Primary Topic
- Neural dynamics and brain function
- Type
- article
- Field-Weighted Citation Impact
- 4.80
Funders
- UK Research and Innovation
- European Commission
- National Institutes of Health
- Medical Research Council
- National Institute of Neurological Disorders and Stroke