ABSTRACT
Negative geotaxis (climbing) performance is a useful metric for quantifying Drosophila health. Manual methods to quantify climbing performance are tedious and often biased, while many available computational methods have challenging hardware or software requirements. We present an alternative: FreeClimber. This open source, Python-based platform subtracts a video's static background to improve detection for flies moving across heterogeneous backgrounds. FreeClimber calculates a cohort's velocity as the slope of the most linear portion of a mean vertical position versus time curve. It can run from a graphical user interface for optimization or a command line interface for high-throughput and automated batch processing, improving accessibility for users with different expertise. FreeClimber outputs calculated slopes, spot locations for follow-up analyses (e.g. tracking), and several visualizations and plots. We demonstrate FreeClimber's utility in a longitudinal study for endurance exercise performance in Drosophila mitonuclear genotypes using six distinct mitochondrial haplotypes paired with a common D. melanogaster nuclear background.
Footnotes
Competing interests
The authors declare no competing or financial interests.
Author contributions
Conceptualization: A.N.S., D.M.R.; Methodology: A.N.S., C.-T.Z.; Software: A.N.S., C.-T.Z.; Validation: A.N.S.; Formal analysis: A.N.S., D.Y.; Investigation: A.N.S., D.Y.; Resources: D.M.R.; Writing - original draft: A.N.S., D.M.R.; Writing - review & editing: A.N.S., D.Y., D.M.R.; Visualization: A.N.S.; Supervision: D.M.R.; Funding acquisition: D.M.R.
Funding
A.N.S., C.T.Z. and this work were supported by the National Institutes of Health [R01 GM067862 and 1R01AG027849 to D.M.R.]. D.Y. was supported by a Brown University Undergraduate Research and Teaching Award (UTRA). The Power Tower was supported by a Sigma Xi Grants-in-Aid of Research (to A.N.S.). This research was partially supported by Institutional Development Award Number P20GM109035 from the National Institute of General Medical Sciences of the National Institutes of Health, which funds COBRE Center for Computational Biology of Human Disease. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Deposited in PMC for release after 12 months.
Data availability
FreeClimber source code, tutorial, examples and result files used for statistical analysis are available online from the GitHub repository (https://github.com/adamspierer/FreeClimber/tree/JEB_release). The most updated version of FreeClimber can be found at: https://github.com/adamspierer/FreeClimber/
Supplementary information
Supplementary information available online at https://jeb.biologists.org/lookup/doi/10.1242/jeb.229377.supplemental
- Received July 27, 2020.
- Accepted November 5, 2020.
- © 2021. Published by The Company of Biologists Ltd
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