Measuring Electrophysiological Activity in Acute Brain Slices, Spheroids, and Organoids Using 3D High-Density Multielectrode Arrays.
Paper
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The authors' code
Python · 1,693 lines · 58 KB · no license
HD-MEA NEUROPulse.py, no license · at the source
Overview
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Brain Organoid Hub, Atlanta, GA, USA
- Brain AG, Pfäffikon, Switzerland
- Department of Pharmacology (DIFAR), University of Genoa, Genoa, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), Italy
- Digital Neuroscience Center, IRCCS Mondino Foundation, Pavia, Italy
Abstract
Animal and human stem cell–derived three-dimensional models to study physio-pathological brain functioning are becoming a gold standard for in vitro electrophysiology, as they enable the recapitulation of complex network properties by accounting for spatial architectural features that better reflect in vivo conditions than simpler 2D models. Standard planar multielectrode arrays (MEAs), typically providing tens of recording electrodes, are commonly used to record activity from 2D neuronal cultures. However, when adapted for use with 3D models, planar 2D MEAs showed limited effectiveness. The main issues are limited specimen adhesion to the chip, a low number of sensing elements, inability to retrieve signals from within the tissue, and reduced perfusion and vitality of the tissue in contact with sensors. To overcome these limitations, a new generation of microchip-based 3D high-density MEAs (3D HD-MEA) has been developed and validated in recent years. This technological advancement has improved the sensing capabilities and the vitality of 3D models, providing a tool tailored to maximize their potential. Here, we present an optimized protocol for neural network activity recordings in 3D models (including acute slices, brain spheroids, and organoids) from various brain regions using 3D HD-MEAs. First, we summarize the critical steps for 1) obtaining viable acute slices from the mouse cerebellum, cortico-hippocampal circuit, and prefrontal cortex, 2) establishing efficient coupling of the slices with the chip, and 3) performing recordings and analyses. We then describe the main procedures required to obtain human and animal brain spheroids and neural organoids, as well as standardized routines to perform effective recordings and analyses. For each section, we highlight the crucial steps, identify tips for specific applications, and propose troubleshooting procedures. For example, the same type of preparation (e.g., acute slices) requires different adjustments when working with different brain areas. The specific information provided here is intended to assist researchers in their daily efforts to obtain efficient and reproducible functional recordings from 3D models by using the cutting-edge technique of 3D HD-MEA.
Key features
• Comprehensive all-in-one guide covering the complete workflow for acquiring electrophysiological data from brain slices, neural region-specific organoids, and brain spheroids.
• Intuitive, step-by-step protocol for brain slice preparation, enriched with practical tips and expert recommendations to ensure high-quality tissue viability.
• Detailed instructions for optimal use of 3D HD-MEA technology, including proper handling of the sample holder for recordings from brain slices, neural organoids, and spheroids.
• In-depth guidance on BrainWave6 software, providing clear procedures for data acquisition, signal detection, and advanced electrophysiological analysis across all sample types.
Reproduced under the paper's license (CC BY-NC), from the paper cited above.
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Zenodo 13908319
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Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 17 authors, 7 keywords, 38 references.
Cite
This paper
Pali, E., Pellavio, G., Conforti, M., Sarkissian, A. A., Aliya, B., Sciacca, G., Wariyar, S. S., Mainardi, F., Tedesco, M., Verduci, I., Cadiao, G., Cervetto, C., Andersen, J., Birey, F., Maccione, A., D’Angelo, E., & Mapelli, L. (2026). Measuring Electrophysiological Activity in Acute Brain Slices, Spheroids, and Organoids Using 3D High-Density Multielectrode Arrays. Bio-protocol, 16(11), e5708. https://
BibTeX
@article{pali2026measuri
author = {Pali, Eleonora and Pellavio, Giorgia and Conforti, Maria and Sarkissian, Arvin A. and Aliya, Berna and Sciacca, Giacomo and Wariyar, Supriya S. and Mainardi, Francesco and Tedesco, Mariateresa and Verduci, Ivan and Cadiao, Gendenver and Cervetto, Chiara and Andersen, Jimena and Birey, Fikri and Maccione, Alessandro and D’Angelo, Egidio and Mapelli, Lisa},
title = {{Measuring Electrophysiological Activity in Acute Brain Slices, Spheroids, and Organoids Using 3D High-Density Multielectrode Arrays}},
journal = {Bio-protocol},
year = {2026},
month = jun,
volume = {16},
number = {11},
pages = {e5708},
publisher = {Bio-protocol, LLC},
issn = {2331-8325},
doi = {10.21769/
url = {https://
pmid = {42305135},
pmcid = {PMC13266469}
}
RIS
TY - JOUR
AU - Pali, Eleonora
AU - Pellavio, Giorgia
AU - Conforti, Maria
AU - Sarkissian, Arvin A.
AU - Aliya, Berna
AU - Sciacca, Giacomo
AU - Wariyar, Supriya S.
AU - Mainardi, Francesco
AU - Tedesco, Mariateresa
AU - Verduci, Ivan
AU - Cadiao, Gendenver
AU - Cervetto, Chiara
AU - Andersen, Jimena
AU - Birey, Fikri
AU - Maccione, Alessandro
AU - D’Angelo, Egidio
AU - Mapelli, Lisa
TI - Measuring Electrophysiological Activity in Acute Brain Slices, Spheroids, and Organoids Using 3D High-Density Multielectrode Arrays
T2 - Bio-protocol
J2 - Bio Protoc
PY - 2026
DA - 2026/
VL - 16
IS - 11
SP - e5708
SN - 2331-8325
PB - Bio-protocol, LLC
DO - 10.21769/
UR - https://
LA - en
ER -
CSL-JSON
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