Analysis of ultrasonic vocalizations from mice using computer vision and machine learning
Abstract
Mice emit ultrasonic vocalizations (USV) that communicate socially-relevant information. To detect and classify these USVs, here we describe VocalMat. VocalMat is a software that uses image-processing and differential geometry approaches to detect USVs in audio files, eliminating the need for user-defined parameters. VocalMat also uses computational vision and machine learning methods to classify USVs into distinct categories. In a dataset of >4,000 USVs emitted by mice, VocalMat detected over 98% of manually labeled USVs and accurately classified ~86% of the USVs out of eleven USV categories. We then used dimensionality reduction tools to analyze the probability distribution of USV classification among different experimental groups, providing a robust method to quantify and qualify the vocal repertoire of mice. Thus, VocalMat makes it possible to perform automated, accurate, and quantitative analysis of USVs without the need for user inputs, opening the opportunity for detailed and high-throughput analysis of this behavior.
Data availability
All the data and code used in this work is publicly available and can be found in the links below: https://osf.io/bk2uj/https://www.dietrich-lab.org/vocalmatThis information is also present in the manuscript at section 4.12 (Code and data availability).
Article and author information
Author details
Funding
National Institute of Diabetes and Digestive and Kidney Diseases
- Marcelo O Dietrich
Howard Hughes Medical Institute (Gilliam Fellowship)
- Gabriela M Bosque Ortiz
- Marcelo O Dietrich
Brain and Behavior Research Foundation
- Marcelo O Dietrich
Whitehall Foundation
- Marcelo O Dietrich
Charles H. Hood Foundation
- Marcelo O Dietrich
Foundation for Prader-Willi Research
- Marcelo O Dietrich
Reginald and Michiko Spector Award in Neuroscience
- Marcelo O Dietrich
Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Sérgio Bampi
- Marcelo O Dietrich
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Antonio H O Fonseca
- Gustavo M Santana
- Sérgio Bampi
- Marcelo O Dietrich
Yale Center for Clinical Investigation Scholar Award
- Marcelo O Dietrich
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocol was reviewed and approved by the Yale University Institutional Animal Care and Use Committee (IACUC). All of the animals were handled according to the approved IACUC protocol (#2018-20042) of the Yale University School of Medicine.
Copyright
© 2021, Fonseca et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 7,449
- views
-
- 658
- downloads
-
- 72
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Neuroscience
Dendrites are crucial for receiving information into neurons. Sensory experience affects the structure of these tree-like neurites, which, it is assumed, modifies neuronal function, yet the evidence is scarce, and the mechanisms are unknown. To study whether sensory experience affects dendritic morphology, we use the Caenorhabditis elegans' arborized nociceptor PVD neurons, under natural mechanical stimulation induced by physical contacts between individuals. We found that mechanosensory signals induced by conspecifics and by glass beads affect the dendritic structure of the PVD. Moreover, developmentally isolated animals show a decrease in their ability to respond to harsh touch. The structural and behavioral plasticity following sensory deprivation are functionally independent of each other and are mediated by an array of evolutionarily conserved mechanosensory amiloride-sensitive epithelial sodium channels (degenerins). Calcium imaging of the PVD neurons in a micromechanical device revealed that controlled mechanical stimulation of the body wall produces similar calcium dynamics in both isolated and crowded animals. Our genetic results, supported by optogenetic, behavioral, and pharmacological evidence, suggest an activity-dependent homeostatic mechanism for dendritic structural plasticity, that in parallel controls escape response to noxious mechanosensory stimuli.
-
- Neuroscience
Data-driven models of neurons and circuits are important for understanding how the properties of membrane conductances, synapses, dendrites, and the anatomical connectivity between neurons generate the complex dynamical behaviors of brain circuits in health and disease. However, the inherent complexity of these biological processes makes the construction and reuse of biologically detailed models challenging. A wide range of tools have been developed to aid their construction and simulation, but differences in design and internal representation act as technical barriers to those who wish to use data-driven models in their research workflows. NeuroML, a model description language for computational neuroscience, was developed to address this fragmentation in modeling tools. Since its inception, NeuroML has evolved into a mature community standard that encompasses a wide range of model types and approaches in computational neuroscience. It has enabled the development of a large ecosystem of interoperable open-source software tools for the creation, visualization, validation, and simulation of data-driven models. Here, we describe how the NeuroML ecosystem can be incorporated into research workflows to simplify the construction, testing, and analysis of standardized models of neural systems, and supports the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles, thus promoting open, transparent and reproducible science.