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).
Contents
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:
- Branson, K., Robie, A. A., Bender, J., Perona, P. & Dickinson, M. H. (2009). High-throughput ethomics in large groups of Drosophila. Nature Methods 6:451-457. DOI:10.1038/nmeth.1328
- Simon, J. C. & Dickinson, M. H. (2010). A new chamber for studying the behavior of Drosophila. PLoS ONE 5(1):e8793. DOI:10.1371/journal.pone.0008793
- White, K. E., Humphrey, D. M. & Hirth, F. (2010). The dopaminergic system in the aging brain of Drosophila. Front Neurosci 4:205. DOI:10.3389/fnins.2010.00205
- Reid, C. R., Sumpter, D. J. T. & Beekman, M. (2011). Optimisation in a natural system: Argentine ants solve the Towers of Hanoi. J Exp Biol 214(1):50-58. DOI:10.1242/jeb.048173
- Bender, J. A., Simpson, E. M., Tietz, B. R., Daltorio, K. A., Quinn, R. D. & Ritzmann, R. E. (2011). Kinematic and behavioral evidence for a distinction between trotting and ambling gaits in the cockroach, Blaberus discoidalis. J Exp Biol 214(12):2057-2064. DOI:10.1242/jeb.056481
- Ofstad, T. A., Zuker, C. S. & Reiser, M. B. (2011). Visual place learning in Drosophila melanogaster. Nature, 474(7350):204-207. DOI:10.1038/nature10131
- Herbert-Read, J. E., Perna, A., Mann, R. P., Schaerfa, T. M., Sumpter, D. J. T. & Ward, A. J. W. (2011). Inferring the rules of interaction of shoaling fish. Proc Nat Acad Sci USA 108(46):18726-18731. DOI:10.1073/pnas.1109355108
- Barry, M. J. (2012). Application of a novel open-source program for measuring the effects of toxicants on the swimming behavior of large groups of unmarked fish. Chemosphere, 86(9):938-944. DOI:10.1016/j.chemosphere.2011.11.011
- Humphrey, D. M., Parsons, R. B., Ludlow, Z. N., Riemensperger, T., Esposito, G., Verstreken, P., Jacobs, H. T., Birman, S. & Hirth, F. (2012). Alternative oxidase rescues mitochondria-mediated dopaminergic cell loss in Drosophila. Hum Mol Genet, 21(12):2698-2712. DOI: 10.1093/hmg/dds096
- Daltorio, K. A., Tietz, B. R., Bender, J. A., Webster, V. A., Szczecinski, N. S., Branicky, M. S., Ritzmann, R. E. & Quinn, R. D. (2012). A stochastic algorithm for explorative goal seeking extracted from cockroach walking data. Proceedings of the IEEE ICRA conference, St. Paul, MN (pp. 2261-2268). DOI:10.1109/ICRA.2012.6225020
- Schneider, J., Dickinson, M. H. & Levine, J. D. (2012). Social structures depend on innate determinants and chemosensory processing in Drosophila. Proc Nat Acad Sci USA 109(Supplement 2):17174-17179. DOI:10.1073/pnas.1121252109
- Lambert, A. M., Bonkowsky, J. L. & Masino, M. A. (2012). The conserved dopaminergic diencephalospinal tract mediates vertebrate locomotor development in zebrafish larvae. J Neurosci, 32(39):13488-13500. DOI:10.1523/JNEUROSCI.1638-12.2012
- Ramdya, P., Schaffter, T., Floreano, D., & Benton, R. (2012). Fluorescence Behavioral Imaging (FBI) tracks identity in heterogeneous groups of Drosophila. PLoS ONE 7(11):e48381. DOI:10.1371/journal.pone.0048381
- Kabra, M., Robie, A. A., Rivera-Alba, M., Branson, S. & Branson, K. (2012). JAABA: interactive machine learning for automatic annotation of animal behavior. Nature Methods 10:64–67. DOI:10.1038/nmeth.2281
- Diaper, D. C., Adachi, Y., Sutcliffe, B., Humphrey, D. M., Elliot, C. J. H., Stepto, A., Ludlow, Z. N., Vanden Broeck, L., Callaerts, P., Dermaut, B., Al-Chalabi, A., Shaw, C. E., Robinson, I. M., & Hirth, F. (2013). Loss and gain of Drosophila TDP-43 impair synaptic efficacy and motor control leading to age-related neurodegeneration by loss-of-function phenotypes. Hum Mol Genet 22(8):1539-1557. DOI:10.1093/hmg/ddt005
- Barry, M. J. (2013). Effects of fluoxetine on the swimming and behavioural responses of the Arabian killifish. Ecotoxicology, 22(2):425-432. DOI:10.1007/s10646-012-1036-7
- Diaper, D. C., Adachi, Y., Lazarou, L., Greenstein, M., Simoes, F. A., Di Domenico, A., Solomon, D. A., Lowe, S., Alsubaie, R., Cheng, D., Buckley, S., Humphrey, D. M., Shaw, C. E. & Hirth, F (2013). Drosophila TDP-43 dysfunction in glia and muscle cells cause cytological and behavioral phenotypes that characterize ALS and FTLD. Hum Mol Genet 22(19):3883-3893. DOI:10.1093/hmg/ddt243
- Ingebretson, J. J. & Masino, M. A. (2013). Quantification of locomotor activity in larval zebrafish: considerations for the design of high-throughput behavioral studies. Front Neural Circuits 7:109. DOI:10.3389/fncir.2013.00109
- Daltorio, K. A., Tietz, B. R., Bender, J. A., Webster, V. A., Szczecinski, N. S., Branicky, M. S., Ritzmann, R. E. & Quinn, R. D. (2013). A model of exploration and goal-searching in the cockroach, Blaberus discoidalis. Adapt Behav 21(5):404-420. DOI:10.1177/1059712313491615
- Mann, K., Gordon, M. D. & Scott, K. (2013). A pair of interneurons influences the choice between feeding and locomotion in Drosophila. Neuron 79(4):754-765. DOI:10.1016/j.neuron.2013.06.018
- Nath, T., Liu, G., Weyn, B., Hassan, B., Ramaekers, A., De Backer, S. & Scheunders, P. (2013). Tracking for quantifying social network of Drosophila melanogaster. Proceedings of the CAIP conference, York, U.K. (pp. 539-545). DOI:10.1007/978-3-642-40246-3_67
- Decker, A. R., McNeill, M. S., Lambert, A. M., Overton, J. D., Chen, Y.-C., Lorca, R. A., Johnson, N. A., Brockerhoff, S. E., Mohapatra, D. P., MacArthur, H., Panula, P., Masino, M. A., Runnels, L. W. & Cornell, R. A. (2014). Abnormal differentiation of dopaminergic neurons in zebrafish trpm7 mutant larvae impairs development of the motor pattern. Dev Biol 386(2):428-439. DOI:10.1016/j.ydbio.2013.11.015
- Lacin, L., Rusch, J., Yeh, R. T., Fujioka, M., Wilson, B. A., Zhu, Y., Robie, A. A., Mistry, H., Wang, T., Jaynes, J. B. & Skeath, J. B. (2014). Genome-wide identification of Drosophila Hb9 targets reveals a pivotal role in directing the transcriptome within eight neuronal lineages, including activation of Nitric oxide synthase and Fd59a/Fox-D. Dev Biol 388(1):117-133. DOI:10.1016/j.ydbio.2014.01.029
- Ruhl, T., Prinz, N., Oellers, N. Seidel, N. I., Jonas, A. Albayram, Ö, Bilkei-Gorzo, A. & von der Emde, G. (2014). Acute administration of THC impairs spatial but not associative memory function in zebrafish. Psychopharmacology 231(19):3829-3842. DOI:10.1007/s00213-014-3522-5
- Bussell, J. J., Yapici, N., Zhang, S. X., Dickson, B. J. & Vosshall, L. B. (2014). Abdominal-B neurons control Drosophila virgin female receptivity. Curr Biol 24(14):1584-1595. DOI:10.1016/j.cub.2014.06.011
- Ott, B. M., Cruciger, M., Dacks, A. M. & Rio, R. V. M. (2014). Hitchhiking of host biology by beneficial symbionts enhances transmission. Sci Rep 4:5825. DOI:10.1038/srep05825
- Barry, M. J. (2014). Fluoxetine inhibits predator avoidance behavior in tadpoles. Tox Env Chem, 96(4):641-649. DOI:10.1080/02772248.2014.966713
- Gou, B., Liu, Y., Guntur, A. R., Stern, U. & Yang, C-H. (2014). Mechanosensitive neurons on the internal reproductive tract contribute to egg-laying-induced acetic acid attraction in Drosophila. Cell Rep 9(2):522-530. DOI:10.1016/j.celrep.2014.09.033
- Yang, C-H., He, R. & Stern, U. (2015). Behavioral and circuit basis of sucrose rejection by Drosophila females in a simple decision-making task. J Neurosci 35(4):1396-1410. DOI:10.1523/JNEUROSCI.0992-14.2015
- Schneider, J. & Levine, J. D. (2014). Automated identification of social interaction criteria in Drosophila melanogaster. Biol Lett 10(10). DOI:10.1098/rsbl.2014.0749
- Ramdya, P., Lichocki, P., Cruchet, S., Frisch, L., Tse, W., Floreano, D. & Benton, R. (2015). Mechanosensory interactions drive collective behaviour in Drosophila. Nature, 519(7542):233-236. DOI:10.1038/nature14024
- Zhu, E. Y., Guntur, A. R., He, R., Stern, U. & Yang, C-H. (2014). Egg-laying demand induces aversion of UV light in Drosophila females. Curr Biol, 24(23):2797-2804. DOI:10.1016/j.cub.2014.09.076
- Battesti, M., Pasquaretta, P., Moreno, C., Teseo, S., Joly, D., Klensch, E., Petit, O., Sueur, C. & Mery, F. (2014). Ecology of information: social transmission dynamics within groups of non-social insects. Proc Roy Soc Lond B, 282(1801). DOI:10.1098/rspb.2014.2480
- Barnes, A. D., Spey, I.-K., Rohde, L., Brose, U. & Dell, A. I. (2015). Individual behaviour mediates effects of warming on movement across a fragmented landscape. Func Ecol, 29(12):1543-1552. DOI:10.1111/1365-2435.12474
- van der Bijl, W., Thyselius, M., Kotrschal, A., & Kolm, N. (2015). Brain size affects the behavioural response to predators in female guppies (Poecilia reticulata). Proc Roy Soc Lond B, 282:20151132. DOI:10.1098/rspb.2015.1132
- Chan, J. D., Agbedanu, P. N., Grab, T., Zamanian, M., Dosa, P. I., Day, T. A. & Marchant, J. S. (2015). Ergot alkaloids (re)generate new leads as antiparasitics. PLoS Negl Trop Dis, 9(9):e0004063. DOI:10.1371/journal.pntd.0004063
- Martin, J. P., Guo, P., Mu, M., Harley, C. M. & Ritzmann, R. E. (2015). Central-complex control of movement in the freely walking cockroach. Curr Biol, 25(21):2795–2803. DOI:10.1016/j.cub.2015.09.044
- Daltorio, K. A., Mirletz, B. T., Sterenstein, A., Cheng, J. C., Watson, A., Kesavan, M., Bender, J., Martin, J., Ritzmann, R. E. & Quinn, R. D. (2015). How cockroaches exploit tactile boundaries to find new shelters. Bioinspir Biomimem, 10:065002. DOI:10.1088/1748-3190/10/6/065002
- Maesani, M., Ramdya, P., Cruchet, S., Gustafson, K., Benton, R. &Floreano, D. (2015). Fluctuation-driven neural dynamics reproduce Drosophila locomotor patterns. PLoS Comp Biol, 11(11):e1004577. DOI:10.1371/journal.pcbi.1004577
- Stanley Jr., C. E. & Kulathinal, R. J. (2016). Genomic signatures of domestication on neurogenetic genes in Drosophila melanogaster. BMC Evol Biol 16(1):1-14. DOI:10.1186/s12862-015-0580-1
- Mora-Zamorano, F. X., Klingler, R., Murphy, C. A., Basu, N., Head, J. & Carvan III, M. J. (2016). Parental whole life cycle exposure to dietary methylmercury in zebrafish (Danio rerio) affects the behavior of offspring. Environ Sci Technol, 50(9):4808–4816. DOI:10.1021/acs.est.6b00223
- Pasquaretta, C., Klenschi, E., Pansanel, J., Battesti, M., Mery, F. & Sueur, C. (2016). Understanding dynamics of information transmission in Drosophila melanogaster using a statistical modeling framework for longitudinal network data (the RSiena Package). Front Psychol 7:539. DOI:10.3389/fpsyg.2016.00539
- Mora-Zamorano, F. X., Svoboda, K. R. & Carvan III, M. J. (2016). The nicotine-evoked locomotor response: a behavioral paradigm for toxicity screening in zebrafish (Danio rerio) embryos and eleutheroembryos exposed to methylmercury. PLoS ONE, 11(4):e0154570. DOI:10.1371/journal.pone.0154570
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
