ArticleCell reports methods2024
MEA-NAP: A flexible network analysis pipeline for neuronal 2D and 3D organoid multielectrode recordings.
Article in Cell reports methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Article
- Redefining ocular safety assessment: retinal organoids as platforms for predicting human ocular toxicology.Genes & genomics · 2026Review
- A human corticospinal organoid-slice connectoid model informs enhancer strategies for post-injury axon regrowth.Cell reports · 2026Article
- Electrophysiological development and functional plasticity in dissociated human cerebral organoids across multiple cell lines.Cell reports methods · 2026Article
- Wnt activation and dual SMAD inhibition for induction and maintenance of hindbrain-like neural stem cell from hiPSCs.Cell reports methods · 2026Article
- Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids.Nature communications · 2026Article
- PTEN variant and genetic backgrounds combine to modify cerebellar neuronal differentiation in autism spectrum disorder.Human molecular genetics · 2026Article
- Context-tuned strategies for marker selection precision in neuronal studies.Frontiers in neuroscience · 2026Review
- Network Analysis Pipeline for Neuronal 2D and 3D Organoid Multielectrode Recordings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Mecp2 deficiency impairs microscale cortical network topology and dynamics in a Rett syndrome mouse model.bioRxiv : the preprint server for biology · 2025Article
- Astrocyte induction of disease-associated microglia is suppressed by acute exposure to fAD neurons in human iPSC triple cultures.Cell reports · 2025Article
- Biomimetic Visual Information Spatiotemporal Encoding Method for In Vitro Biological Neural Networks.Biomimetics (Basel, Switzerland) · 2025Article
- Bioengineering innovations for neural organoids with enhanced fidelity and function.Cell stem cell · 2025Review
- MEA-Based Graph Deviation Network for Early Autism Syndrome Signatures in Human Forebrain Organoids.Cyborg and bionic systems (Washington, D.C.) · 2025Article
- Established and emerging new approach methodologies in neuroscience.Frontiers in neuroscience · 2025Review
- Multiscale Cloud-Based Pipeline for Neuronal Electrophysiology Analysis and Visualization.bioRxiv : the preprint server for biology · 2024Article
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Abstract
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.
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