ToxTrac: A fast and robust software for tracking organisms

Abstract

Behavioural analysis based on video recording is becoming increasingly popular within research fields such as; ecology, medicine, ecotoxicology and toxicology. However, the programs available to analyse the data, which are free of cost, user‐friendly, versatile, robust, fast and provide reliable statistics for different organisms (invertebrates, vertebrates and mammals) are significantly limited. We present an automated open‐source executable software (ToxTrac) for image‐based tracking that can simultaneously handle several organisms monitored in a laboratory environment. We compare the performance of ToxTrac with current accessible programs on the web. The main advantages of ToxTrac are as follows: (i) no specific knowledge of the geometry of the tracked bodies is needed; (ii) processing speed, ToxTrac can operate at a rate >25 frames per second in HD videos using modern computers; (iii) simultaneous tracking of multiple organisms in multiple arenas; (iv) integrated distortion correction and camera calibration; (v) robust against false positives; (vi) preservation of individual identification; (vii) useful statistics and heat maps in real scale are exported in image, text and excel formats. ToxTrac can be used for high speed tracking of insects, fish, rodents or other species, and provides useful locomotor information in animal behavior experiments. Download ToxTrac here: https://toxtrac.sourceforge.io (Current version v2.61).

Towards Sustainable Environmental Quality: Priority Research Questions for the Australasian Region of Oceania

“…These have screened thousands of chemicals with hundreds of in vitro assays, largely adapted from drug discovery and safety testing programs, to identify likely MIEs associated with many untested chemicals. More recent applications include employing these in vitro systems for prioritizing environmental assessments and performing cross-species extrapolation (LaLone et al 2018), or tracking movements of multiple individuals simultaneously using ToxTrac (Rodriguez et al 2018). For example, identification of diverse MIEs associated with chemical properties is supporting development of next-generation computational toxicology models to identify problematic (and useful) substances and to sustainably design less hazardous chemicals.…”

“…For example, identification of diverse MIEs associated with chemical properties is supporting development of next-generation computational toxicology models to identify problematic (and useful) substances and to sustainably design less hazardous chemicals. More recent applications include employing these in vitro systems for prioritizing environmental assessments and performing cross-species extrapolation (LaLone et al 2018), or tracking movements of multiple individuals simultaneously using ToxTrac (Rodriguez et al 2018). Such efforts promise to continue to further advance environmental risk assessment practices (Villeneuve et al 2019).…”

pathtrackr: An r package for video tracking and analysing animal movement

“…Labelled fields identify attributes of selected animal tracking software packages. 1: Mouselabtracker 0.2.9 (Tort et al, 2006); 2: Ctrax 0.5.18 (Branson, Robie, Bender, Perona, & Dickinson, 2009); 3: EthoVision XT 13.0 (Noldus, 2018); 4: ToxTrac 2.75 (Rodriguez et al, 2017), idTracker 2.1 (Pérez-Escudero et al, 2014); 5: SwisTrack 4.0.1 (Correll et al, 2006); 6: pathtrackr 1.2.3 (this study) the tracked object list as input, extract summary statistics and plot the tracking data.…”

“…Hays, Scott, & Higham, 2013;Ramot, Johnson, Berry, Carnell, & Goodman, 2008), and addressing questions about health (e.g. Rodriguez et al, 2017;Samson et al, 2015), ecology (e.g. Birgiolas, Jernigan, Smith, & Crook, 2017;Klaassen et al, 2013), environmental change (e.g.…”

“…Kissling, Pattemore David, & Hagen, 2013;Mattern, Ellenberg, Houston, & Davis, 2007), and non-contact technologies gather tracking data from estimates of animal position (e.g. Pérez-Escudero, Vicente-Page, Hinz, Arganda, & Polavieja, 2014;Rodriguez et al, 2017).…”