FreeClimber: Automated quantification of climbing performance in Drosophila, with examples from mitonuclear genotypes

Abstract

Negative geotaxis (climbing) performance is a useful metric for quantifying Drosophila health and vigor. Manual methods to quantify climbing performance are slow, tedious, and may be systematically biased, while available computational methods have inflexible hardware or software requirements. We present an alternative: FreeClimber. This open source, Python-based pipeline subtracts a video’s static background to improve spot detection for moving flies in heterogeneous backgrounds. FreeClimber calculates a cohort’s velocity as the slope of the most linear portion of a mean-vertical position vs. time plot. It can run from a graphical user interface for parameter optimization or a command line interface for high-throughput and automated batch processing. It outputs calculated slopes, spot locations for follow up analyses such as tracking, and several visualizations and diagnostic plots. We demonstrate FreeClimber’s utility in a longitudinal study for endurance exercise performance in Drosophila using six distinct mitochondrial haplotypes paired with a common w1118 nuclear background.Summary statement FreeClimber quantifies the climbing velocity for a group of flies, eliminating systematic biases associated with traditional manual methods in a high throughput and automated (graphical and/or command line-based) platform.List of Symbols and AbbreviationsecceccentricityGUIGraphical User Interfacemito-nuclearMitochondrial-nuclearmitotypesMitochondrial haplotypeOreROregon RROIRegion of InterestyakyakubaZimZimbabwe53View Full Text