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Today appeared our two companion papers on tracking individual fruit flies or their larvae in PLoS ONE. While our colleagues Alex Gomez-Marin and Matthieu Louis in Spain described work on larval locomotion, our paper was about tracking adult flies in Buridan's paradigm:



What I particularly like about our two papers is that they're moving us a step closer to making science more open. All the code used in this work is completely open and accessible to anybody. We also made the raw data available for download, so anybody can use the software and check our results or come up with clever new ways to analyze it.

Currently, we're working on the technology to make the data publicly available at the time of analysis, rather than publication and to have that data stored in semantic databases, taking advantage of semantic web technology. The first and corresponding author of our paper, Julien Colomb is the person behind this project. He is currently collaborating with Mark Hahnel from FigShare to work on the technicalities on hooking up our R-Scripts, which do all the analysis with the database at FigShare. We've also started thinking about an ontology for (fly) behavior, but this work hasn't really taken off, yet.
Read the press release here.
Below are the two abstracts and links to the full publications:

Gomez-Marin A. Partoune N; Stephens G, Louis M (2012) Automated tracking of animal posture and movement during exploration and sensory orientation behaviors
http://dx.plos.org/10.1371/journal.pone.0041642
The nervous functions of an organism are primarily reflected in the behavior it is capable of. Measuring behavior quantitatively, at high-resolution and in an automated fashion provides valuable information about the underlying neural circuit computation. Accordingly, computer-vision applications for animal tracking are becoming a key complementary toolkit to genetic, molecular and electrophysiological characterization in systems neuroscience.We present Sensory Orientation Software (SOS) to measure behavior and infer sensory experience correlates. SOS is a simple and versatile system to track body posture and motion of single animals in two-dimensional environments. In the presence of a sensory landscape, tracking the trajectory of the animal’s sensors and its postural evolution provides a quantitative framework to study sensorimotor integration. To illustrate the utility of SOS, we examine the orientation behavior of fruit fly larvae in response to odor, temperature and light gradients. We show that SOS is suitable to carry out high-resolution behavioral tracking for a wide range of organisms including flatworms, fishes and mice.Our work contributes to the growing repertoire of behavioral analysis tools for collecting rich and fine-grained data to draw and test hypothesis about the functioning of the nervous system. By providing open-access to our code and documenting the software design, we aim to encourage the adaptation of SOS by a wide community of non-specialists to their particular model organism and questions of interest.

Colomb J, Reiter L, Blaszkiewicz J, Wessnitzer J, Brembs B (2012) Open source tracking and analysis of adult Drosophila locomotion in Buridan's paradigm with and without visual targets
http://dx.plos.org/10.1371/journal.pone.0042247
Insects have been among the most widely used model systems for studying the control of locomotion by nervous systems. In Drosophila, we implemented a simple test for locomotion: in Buridan's paradigm, flies walk back and forth between two inaccessible visual targets [1]. Until today, the lack of easily accessible tools for tracking the fly position and analyzing its trajectory has probably contributed to the slow acceptance of Buridan's paradigm.We present here a package of open source software designed to track a single animal walking in a homogeneous environment (Buritrack) and to analyze its trajectory. The Centroid Trajectory Analysis (CeTrAn) software is coded in the open source statistics project R. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. We demonstrate the capabilities of our package by measuring the locomotor behavior of adult Drosophila melanogaster (whose wings were clipped), either in the presence or in the absence of visual targets, and comparing the latter to different computer-generated data. The analysis of the trajectories confirms that flies are centrophobic and shows that inaccessible visual targets can alter the orientation of the flies without changing their overall patterns of activity.Using computer generated data, the analysis software was tested, and chance values for some metrics (as well as chance value for their correlation) were set. Our results prompt the hypothesis that fixation behavior is observed only if negative phototaxis can overcome the propensity of the flies to avoid the center of the platform. Together with our companion paper, we provide new tools to promote Open Science as well as the collection and analysis of digital behavioral data.
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Posted on Thursday 09 August 2012 - 22:59:45 comment: 0
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