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FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila

Uhlmann, Virginie and Ramdya, Pavan and Delgado-Gonzalo, Ricard and Benton, Richard and Unser, Michael (2017) FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila. PLOS ONE, 12 (4). Art. No. e0173433. ISSN 1932-6203. PMCID PMC5409058. https://resolver.caltech.edu/CaltechAUTHORS:20170602-092136915

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[img] Video (QuickTime) (S3 Video. A fly grooming its forelegs) - Supplemental Material
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[img] Video (QuickTime) (S5 Video. A fly grooming its abdomen) - Supplemental Material
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Abstract

Understanding the biological underpinnings of movement and action requires the development of tools for quantitative measurements of animal behavior. Drosophila melanogaster provides an ideal model for developing such tools: the fly has unparalleled genetic accessibility and depends on a relatively compact nervous system to generate sophisticated limbed behaviors including walking, reaching, grooming, courtship, and boxing. Here we describe a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving D. melanogaster. We show that this approach yields a more than 6-fold reduction in user intervention when compared with fully manual annotation and can be used to annotate videos with low spatial or temporal resolution for a variety of locomotor and grooming behaviors. FlyLimbTracker, the software implementation of this method, is open-source and our approach is generalizable. This opens up the possibility of tracking leg movements in other species by modifications of underlying active contour models.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1371/journal.pone.0173433DOIArticle
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173433PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5409058/PubMed CentralArticle
https://doi.org/10.1371/journal.pone.0173433.s001DOIS1 Video. A fly walking straight
https://doi.org/10.1371/journal.pone.0173433.s002DOIS2 Video. A fly turning
https://doi.org/10.1371/journal.pone.0173433.s003DOIS3 Video. A fly grooming its forelegs
https://doi.org/10.1371/journal.pone.0173433.s004DOIS4 Video. A fly grooming its head
https://doi.org/10.1371/journal.pone.0173433.s005DOIS5 Video. A fly grooming its abdomen
https://doi.org/10.1371/journal.pone.0173433.s006DOIS6 Video. A fly walking straight (video 1), annotated using FlyLimbTracker
https://doi.org/10.1371/journal.pone.0173433.s007DOIS7 Video. A fly turning (video 2), annotated using FlyLimbTracker
https://doi.org/10.1371/journal.pone.0173433.s008DOIS8 Video. A fly grooming its forelegs (video 3), annotated using FlyLimbTracker
https://doi.org/10.1371/journal.pone.0173433.s009DOIS9 Video. A fly grooming its head (video 4), annotated using FlyLimbTracker
https://doi.org/10.1371/journal.pone.0173433.s010DOIS10 Video. A fly grooming its abdomen (video 5), annotated using FlyLimbTracker
https://doi.org/10.1101/089714DOIDiscussion Paper
Additional Information:© 2017 Uhlmann et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: January 1, 2017; Accepted: February 11, 2017; Published: April 28, 2017. We thank Cédric Vonesch, Michael Rusterholz, and Loic Perruchoud for early contributions to the body tracking algorithm. Data Availability Statement: User instructions, FlyLimbTracker software, sample data, and a video demonstration of a complete data analysis pipeline can be found at: http://bigwww.epfl.ch/algorithms/FlyLimbTracker/ and at https://doi.org/10.6084/m9.figshare.4688962.v1. This work was supported by Swiss SystemsX.ch Initiative, Grant#: 2008/005, http://www.systemsx.ch/, VU, RDG, MU; Swiss National Science Foundation, Grant#: 200020-121763 and 200020-144355, http://www.snf.ch/en/Pages/default.aspx, VU, RDG, MU; Human Frontier Science Program, Grant#: LT000057/2009, http://www.hfsp.org/, PR; Swiss National Science Foundation, Grant#: P300P3_158511, http://www.snf.ch/en/Pages/default.aspx, PR; European Research Council, Grant#: 205202 and 615094, https://erc.europa.eu/, RB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Contributions: Conceptualization: PR VU MU. Data curation: PR VU. Formal analysis: VU RDG PR. Funding acquisition: PR RB MU. Investigation: PR VU. Methodology: VU RDG MU. Project administration: PR MU. Resources: RB MU. Software: VU RDG PR. Supervision: PR RB MU. Validation: VU RDG PR. Visualization: PR VU. Writing – original draft: PR VU. Writing – review & editing: PR VU RDG RB MU. The authors have declared that no competing interests exist.
Funders:
Funding AgencyGrant Number
Swiss SystemsX.ch Initiative2008/005
Swiss National Science Foundation (SNSF)200020-121763
Swiss National Science Foundation (SNSF)200020-144355
Human Frontier Science ProgramLT000057/2009
Swiss National Science Foundation (SNSF)P300P3_158511
European Research Council (ERC)205202
European Research Council (ERC)615094
Issue or Number:4
PubMed Central ID:PMC5409058
Record Number:CaltechAUTHORS:20170602-092136915
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170602-092136915
Official Citation:Uhlmann V, Ramdya P, Delgado-Gonzalo R, Benton R, Unser M (2017) FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila. PLoS ONE 12(4): e0173433. https://doi.org/10.1371/journal.pone.0173433
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:77910
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:02 Jun 2017 18:19
Last Modified:03 Oct 2019 18:03

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