Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Jul 4, 2025

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Published on: March 8, 2024

Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data.

Ethan Bahl^1,2, Snehajyoti Chatterjee^3,4, Utsav Mukherjee^3,4,5

¹Department of Psychiatry, University of Iowa, Iowa City, IA, USA.

Nature Communications

|January 26, 2024

Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Newly identified invasion drivers define the tumor front in oral squamous cell carcinoma.

Cell death discovery·2026

Same author

Kidney Outcomes After Contrast Exposure in Patients Recovering From Dialysis-Requiring Acute Kidney Injury: A Target Trial Emulation Study.

American journal of kidney diseases : the official journal of the National Kidney Foundation·2026

Same author

Generalisable artificial intelligence ECG trained on public data for outcome prediction after transcatheter aortic valve replacement.

Heart (British Cardiac Society)·2026

Same author

Region- and cell type-specific changes in gene expression in the cerebellum after classical fear conditioning.

Communications biology·2026

Same author

Ancient regulatory evolution shapes individual language abilities in present-day humans.

Science advances·2026

Same author

Repeated sleep deprivation selectively reactivates hippocampal CA1 pyramidal neurons.

Molecular brain·2026

Same journal

Demonstration of a quantum C-NOT gate in a time-multiplexed fully reconfigurable photonic processor.

Nature communications·2026

Same journal

Nonlinear quantum light source with van der Waals ferroelectric NbOX<sub>2</sub> (X = Br, I).

Nature communications·2026

Same journal

Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis.

Nature communications·2026

Same journal

The long tail of nitrate pollution in groundwater challenges governance of global water quality.

Nature communications·2026

Same journal

Select microbial metabolites promote tau aggregation in a murine tauopathy model.

Nature communications·2026

Same journal

Warming climate has lengthened global intense tropical cyclone seasons.

Nature communications·2026

See all related articles

This summary is machine-generated.

We developed NEUROeSTIMator, a deep learning model that uses gene expression to measure neuronal activation. This tool accurately estimates brain activity across species and cell types, aiding neuroscience research.

Area of Science:

Neuroscience
Computational Biology
Genomics

Background:

Neuronal activity-driven gene transcription is crucial for synaptic plasticity, brain development, and memory formation.
Single-cell RNA sequencing (scRNAseq) enables studying gene expression at cellular resolution.
Existing methods lack robustness across diverse biological contexts.

Purpose of the Study:

To introduce NEUROeSTIMator, a deep learning model for estimating neuronal activation from transcriptomic data.
To validate NEUROeSTIMator's accuracy and generalizability across species, cell types, and brain regions.
To apply NEUROeSTIMator to spatial transcriptomics for mapping learning-induced activity patterns.

Main Methods:

Developed a deep learning model (NEUROeSTIMator) integrating transcriptomic signals.

More Related Videos

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Published on: October 26, 2018

Automated Multimodal Stimulation and Simultaneous Neuronal Recording from Multiple Small Organisms

Automated Multimodal Stimulation and Simultaneous Neuronal Recording from Multiple Small Organisms

Published on: March 3, 2023

Related Experiment Videos

Last Updated: Jul 4, 2025

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Published on: March 8, 2024

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Published on: October 26, 2018

Automated Multimodal Stimulation and Simultaneous Neuronal Recording from Multiple Small Organisms

Automated Multimodal Stimulation and Simultaneous Neuronal Recording from Multiple Small Organisms

Published on: March 3, 2023

Validated the model against Patch-seq electrophysiological data.

Applied the model to existing scRNAseq datasets and a spatial transcriptomic study in male mice.

Main Results:

NEUROeSTIMator accurately estimates neuronal activation, correlating with electrophysiological features.
The model demonstrates robustness across different species, cell types, and brain regions.
Identified unique patterns of learning-induced neuronal activity in specific brain regions using spatial transcriptomics.

Conclusions:

NEUROeSTIMator is a powerful and versatile tool for quantifying neuronal activation.
The model enhances the analysis of activity-dependent transcription in neuroscience.
NEUROeSTIMator facilitates the study of brain function and behavior at a molecular level.