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Ctrax: The Caltech Multiple Walking Fly Tracker

Ctrax is an open-source, freely available, machine vision program for estimating the positions and orientations of many walking flies, maintaining their individual identities over long periods of time. It was designed to allow high-throughput, quantitative analysis of behavior in freely moving flies. Our primary goal in this project is to provide quantitative behavior analysis tools to the neuroethology community; thus, we've endeavored to make the system adaptable to other labs' setups. We have assessed the quality of the tracking results for our setup, and found that it can maintain fly identities indefinitely with minimal supervision, and on average for 1.5 fly-hours automatically.

To further compensate for identity and other tracking errors, we provide the FixErrors Matlab GUI that identifies suspicious sequences of frames and allows a user to correct any tracking errors. We also distribute the BehavioralMicroarray Matlab Toolbox for defining and detecting a broad palette of individual and social behaviors. This software inputs the trajectories output by Ctrax and computes descriptive statistics of the behavior of each individual fly. We provide software for three proof-of-concept experiments to show the potential of the Ctrax software and our behavior detectors.

This package and its algorithms are described in detail in the article "High-Throughput Ethomics in Large Groups of Drosophila," Branson et al., Nature Methods, 2009 (DOI:10.1038/nmeth.1328); reprints are available from the authors by request (see below).



For questions or suggestions about the Ctrax software suite, please post to the Ctrax Google Group. For other inquiries, contact corresponding author Kristin Branson.

See also:


Ctrax has been used for data collection in the following publications, that we know of:

If you know of (or produce) another publication which made use of Ctrax and/or the associated Matlab toolboxes, please let us know!

See also the full reverse-lookup results of citing articles on Google Scholar.


Current version: 0.5.13 (released 12 February 2017)
Active users: 1229 (Sourceforge + Launchpad downloads of version 0.5.8)
Cumulative downloads: 12982 (Sourceforge since June 2011, Launchpad since February 2012)
Citations: 329 (Google Scholar)
Forum posts/month: 18 (average over the past 3 full months)
Forum subscribers: 218
Statistics last updated 22 December 2016