Automated annotation of birdsong with a neural network that segments spectrograms

  1. Yarden Cohen  Is a corresponding author
  2. David Aaron Nicholson
  3. Alexa Sanchioni
  4. Emily K Mallaber
  5. Viktoriya Skidanova
  6. Timothy J Gardner  Is a corresponding author
  1. Weizmann Institute of Science, Israel
  2. Emory University, United States
  3. Boston University, United States
  4. University of Oregon, United States

Abstract

Songbirds provide a powerful model system for studying sensory-motor learning. However, many analyses of birdsong require time-consuming, manual annotation of its elements, called syllables. Automated methods for annotation have been proposed, but these methods assume that audio can be cleanly segmented into syllables, or they require carefully tuning multiple statistical models. Here we present TweetyNet: a single neural network model that learns how to segment spectrograms of birdsong into annotated syllables. We show that TweetyNet mitigates limitations of methods that rely on segmented audio. We also show that TweetyNet performs well across multiple individuals from two species of songbirds, Bengalese finches and canaries. Lastly, we demonstrate that using TweetyNet we can accurately annotate very large datasets containing multiple days of song, and that these predicted annotations replicate key findings from behavioral studies. In addition, we provide open-source software to assist other researchers, and a large dataset of annotated canary song that can serve as a benchmark. We conclude that TweetyNet makes it possible to address a wide range of new questions about birdsong.

Data availability

Datasets of annotated Bengalese finch song are available at:https://figshare.com/articles/Bengalese_Finch_song_repository/4805749https://figshare.com/articles/BirdsongRecognition/3470165Datasets of annotated canary song are available at:https://doi.org/10.5061/dryad.xgxd254f4Model checkpoints, logs, and source data files are available at:http://dx.doi.org/10.5061/dryad.gtht76hk4Source data files for figure are in the repository associated with the paper:https://github.com/yardencsGitHub/tweetynet(version 0.4.3, 10.5281/zenodo.3978389).

The following data sets were generated
The following previously published data sets were used
    1. Koumura
    2. Takuya
    (2016) BirdsongRecognition.
    Figshare, https://doi.org/10.6084/m9.figshare.3470165.v1.

Article and author information

Author details

  1. Yarden Cohen

    Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
    For correspondence
    yarden.j.cohen@weizmann.ac.il
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8149-6954
  2. David Aaron Nicholson

    Department of Biology, Emory University, Atlanta, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Alexa Sanchioni

    Department of Biology, Boston University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Emily K Mallaber

    Department of Biology, Boston University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Viktoriya Skidanova

    Department of Biology, Boston University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Timothy J Gardner

    Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, United States
    For correspondence
    timg@uoregon.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1744-3970

Funding

National Institute of Neurological Disorders and Stroke (R01NS104925)

  • Alexa Sanchioni
  • Emily K Mallaber
  • Viktoriya Skidanova
  • Timothy J Gardner

National Institute of Neurological Disorders and Stroke (R24NS098536)

  • Alexa Sanchioni
  • Emily K Mallaber
  • Viktoriya Skidanova
  • Timothy J Gardner

National Institute of Neurological Disorders and Stroke (R01NS118424)

  • Timothy J Gardner

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All procedures were approved by the Institutional Animal Care and Use Committees of Boston University (protocol numbers 14-028 and 14-029). Song data were collected from adult male canaries (n = 5). Canaries were individually housed for the entire duration of the experiment and kept on a light-dark cycle matching the daylight cycle in Boston (42.3601 N). The birds were not used in any other experiments.

Copyright

© 2022, Cohen 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.

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  1. Yarden Cohen
  2. David Aaron Nicholson
  3. Alexa Sanchioni
  4. Emily K Mallaber
  5. Viktoriya Skidanova
  6. Timothy J Gardner
(2022)
Automated annotation of birdsong with a neural network that segments spectrograms
eLife 11:e63853.
https://doi.org/10.7554/eLife.63853

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https://doi.org/10.7554/eLife.63853