Jinghui Geng

HIPPIE: a generative model for electrophysiological analysis across species, technologies, and modalities

Jesus Gonzalez-Ferrer, Julian Lehrer, Bruno Alvarez-Esteban, Avelina Moreno-Ochando et autres

Abstract Neuronal classification from extracellular electrophysiological recordings is challenging due to intrinsic waveform variability, noise, and technical differences across experiments, technologies, and species. We introduce HIPPIE (High-dimensional Interpretation of Physiological Patterns In Intercellular Electrophysiology), a deep learning framework that combines self-supervised pretraining …

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SpikeCanvas: An IoT-based control plane for event-triggered workflow orchestration of high-density neurophysiology data

Jinghui Geng, Kateryna Voitiuk, David F. Parks, Ash Robbins et autres

Microscale maps of bursting dynamics across human hippocampal slices from patients with epilepsy

Matthew A.T. Elliott, John P. Andrews, Tjitse van der Molen, Jinghui Geng et autres

We apply high-density CMOS-based microelectrode arrays to excised patient brain slices, mapping the communication patterns of hundreds of neurons at unprecedented resolution. We developed novel computational techniques to spatially map neuronal dynamics. In patient slices, our findings suggest that recurrent feedback localized …

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Preconfigured neuronal firing sequences in human brain organoids

Tjitse van der Molen, Alex Spaeth, Mattia Chini, Sebastían Hernández et autres

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Incubator-Free Organoid Culture in a Sealed Recirculatory System

Yohei Rosen, Kivilcim E Doganyigit, Santhosh Arul, Eliot Wachtel et autres

Organoids are powerful tools for studying development and disease, offering realistic organ-like human and animal tissues and facilitating experimental observation compared to live animal models. However, traditional organoid culture methods require a humidified incubator. This requirement complicates culture due to evaporative losses …

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Microfluidic Topography Biases Neural Organoid Morphogenesis

John Minnick, Drew Ehrlich, Maryam Moarefian, Jess Sevetson et autres

This study highlights how inherent micro-scale surface topographies can occur in microfluidic chips based on their fabrication modalities and how these surface topographies can bias organoid morphogenesis. Human cortical organoids were cultured and seeded into micro-wells with varying surface topographies for 21 …

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Weighted Graph for Longitudinal Tracking of Neurons in Cortical Organoids on a High-Density Microelectrode Array

Jinghui Geng, Jesus Gonzalez-Ferrer, Kateryna Voitiuk, Spencer T. Seiler et autres

Tracking cortical neurons over several days can provide extensive data for their electrophysiology features, development trajectories, and connectivity with other neurons within neuronal circuits. However, reliably identifying the same neurons over time remains a challenge for high-density microelectrode array (HD-MEA) recordings. In …

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A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring

Kateryna Voitiuk, Spencer T. Seiler, Mirella Pessoa de Melo, Jinghui Geng et autres

The analysis of tissue cultures requires a sophisticated integration and coordination of multiple technologies for monitoring and measuring. We have developed an automated research platform enabling independent devices to achieve collaborative objectives for feedback-driven cell culture studies. Our approach enables continuous, communicative, …

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Self-Organizing Neural Networks in Organoids Reveal Principles of Forebrain Circuit Assembly

Sebastian Hernandez, H. Schweiger, Isabel Cline, Gregory A. Kaurala et autres

SUMMARY The mouse cortex is a canonical model for studying how functional neural networks emerge, yet it remains unclear which topological features arise from intrinsic cellular organization versus external regional cues. Mouse forebrain organoids provide a powerful system to investigate these intrinsic …

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HIPPIE: A Multimodal Deep Learning Model for Electrophysiological Classification of Neurons

Jesus Gonzalez-Ferrer, Julian Lehrer, H. Schweiger, Jinghui Geng et autres

Abstract Extracellular electrophysiological recordings present unique computational challenges for neuronal classification due to noise, technical variability, and batch effects across experimental systems. We introduce HIPPIE (High-dimensional Interpretation of Physiological Patterns In Extracellular recordings), a deep learning framework that combines self-supervised pretraining on …

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Goal-Directed Learning in Cortical Organoids

Ash Robbins, H. Schweiger, Sebastian Hernandez, Alex Spaeth et autres

Abstract Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise as in vitro models of brain development and function. …

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Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices

John P. Andrews, Jinghui Geng, Kateryna Voitiuk, Matthew A.T. Elliott et autres

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