Search research articles

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

A hierarchical cascade of sleep rhythms supports motor memory and is hijacked by epileptic spikes in human epilepsy.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Distinct cell-type contributions and network topography of theta-nested gamma oscillations in the medial entorhinal cortex.

bioRxiv : the preprint server for biology·2026

Same author

Correction: Nonnegative matrix factorization for analyzing state dependent neuronal network dynamics in calcium recordings.

Scientific reports·2025

Same author

CaNetiCs - An Open-Source Toolbox for Standardized Dimensionality Reduction of Neuronal Calcium Activity.

bioRxiv : the preprint server for biology·2025

Same author

Reactivation of memory-associated neurons induces downstream suppression of competing neuronal populations.

Proceedings of the National Academy of Sciences of the United States of America·2025

Same author

Publisher Correction: An implantable piezoelectric ultrasound stimulator (ImPULS) for deep brain activation.

Nature communications·2024

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: Jun 7, 2025

Functional Calcium Imaging in Developing Cortical Networks

Functional Calcium Imaging in Developing Cortical Networks

Published on: October 22, 2011

Nonnegative matrix factorization for analyzing state dependent neuronal network dynamics in calcium recordings.

Daniel Carbonero^1,2,3, Jad Noueihed^1,2,3, Mark A Kramer^4,2

¹Department of Biomedical Engineering, Boston University, Boston, MA, USA.

Scientific Reports

|November 13, 2024

Summary

Nonnegative Matrix Factorization (NMF) effectively analyzes complex calcium imaging data by preserving neuronal activity dynamics. This method outperforms traditional approaches, offering a more accurate understanding of neural responses in vivo.

Keywords:

Calcium imaging Dimensionality reduction Neuronal network analysis Neuronal network dynamics Nonnegative matrix factorization

More Related Videos

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

Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis

Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis

Published on: February 18, 2020

Related Experiment Videos

Last Updated: Jun 7, 2025

Functional Calcium Imaging in Developing Cortical Networks

Functional Calcium Imaging in Developing Cortical Networks

Published on: October 22, 2011

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

Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis

Fluorescent Calcium Imaging and Subsequent In Situ Hybridization for Neuronal Precursor Characterization in Xenopus laevis

Published on: February 18, 2020

Area of Science:

Neuroscience
Computational Biology
Data Science

Background:

Calcium imaging enables high-throughput recording of neuronal activity in vivo, capturing single-cell resolution.
Analyzing the multidimensional nature of calcium imaging data presents significant challenges.
Traditional statistical methods often average neuronal responses, losing critical temporal dynamics and relative activity patterns.

Purpose of the Study:

To adapt and evaluate Nonnegative Matrix Factorization (NMF) as a dimensionality reduction (DR) technique for calcium imaging data analysis.
To compare the performance of NMF against alternative DR methods using both simulated and in vivo neural recordings.

Main Methods:

Dimensionality Reduction (DR) techniques were applied to calcium imaging datasets.
Nonnegative Matrix Factorization (NMF), a DR method with positivity and linearity constraints, was specifically adapted.
NMF performance was benchmarked against other DR methods using artificial and in vivo neuronal activity data.

Main Results:

NMF accurately captures the underlying dynamics present in calcium imaging recordings.
The adapted NMF method demonstrated superior performance compared to commonly used alternative DR techniques.
NMF effectively reduces data dimensions while preserving essential variance and temporal information.

Conclusions:

Nonnegative Matrix Factorization is a well-suited and powerful tool for analyzing complex calcium imaging data.
NMF offers a more comprehensive analysis of neuronal activity, preserving temporal dynamics lost in traditional methods.
This study highlights NMF's potential to advance the interpretation of in vivo neural recordings.