FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila
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.
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.Attached Files
Published - journal.pone.0173433.pdf
Submitted - 089714.full.pdf
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Additional details
- PMCID
- PMC5409058
- Eprint ID
- 77910
- Resolver ID
- CaltechAUTHORS:20170602-092136915
- 2008/005
- Swiss SystemsX.ch Initiative
- 200020-121763
- Swiss National Science Foundation (SNSF)
- 200020-144355
- Swiss National Science Foundation (SNSF)
- LT000057/2009
- Human Frontier Science Program
- P300P3_158511
- Swiss National Science Foundation (SNSF)
- 205202
- European Research Council (ERC)
- 615094
- European Research Council (ERC)
- Created
-
2017-06-02Created from EPrint's datestamp field
- Updated
-
2023-06-01Created from EPrint's last_modified field