Application of a novel open-source program for measuring the effects of toxicants on the swimming behavior of large groups of unmarked fish

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The aim of this study was to demonstrate a novel method for measuring the effects of toxicants on the behavior of groups of unmarked fish. Ctrax is an open source Python-based machine vision program that was originally designed to track fruit flies (Drosophila). The effects of the fish anaesthetic quinaldine sulfate on the behavior of groups of 10 unmarked Arabian killifish (Aphanias dispar) in a small arena were measured. Ctrax was able to identify and track the X-Y coordinates of the individual fish over 1. min recording periods. The data was analyzed using specifically written Matlab (The Mathworks™) toolboxes and the effects of quinaldine sulfate on absolute swimming velocity, forward swimming velocity, rate of change in orientation and distance to wall were calculated. Additionally the effects of quinaldine sulfate on path tortuosity were also measured. Ctrax has significant benefits over other available technologies for tracking the 2-dimensional coordinates of fish. In particular the software is open source and thus freely available, it is accurate, requires only simple easily available equipment and able to track potentially large groups of fish (possibly >50) while maintaining their individual identities.

Original languageEnglish
Pages (from-to)938-944
Number of pages7
Issue number9
Publication statusPublished - Mar 2012



  • Automation
  • Fish
  • Swimming behavior
  • Tracking

ASJC Scopus subject areas

  • Environmental Chemistry
  • Chemistry(all)

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