Open Source for Open Science

international fly tracking collaboration paves way for citizen science

Online fly tracking and open data

Researchers at the Freie Universität Berlin, Germany and the Center for Genomic Regulation in Barcelona, Spain have designed open source software that allows tracking the position of Drosophila fruit flies as well as their larvae during behavioral experiments. The research appeared in two joint publications in the open access journal PLoS ONE. Dr. Matthieu Louis, the head of the Spanish team explains: "Until we developed these tools, many researchers relied on expensive commercial hardware and software to study the behavior of larvae and adult flies. Now, virtually anybody can do this kind of research. The value of the software we are proposing is that it is written in a simple programming language, which facilitates their adaptation to new experimental paradigms" Inexpensive, ubiquitous digital cameras, such as webcams are sufficient to capture the movements of the animals and the open source software packages both for the evaluation of the video feeds for tracking as well as for later data analysis are available for free at and

Buridan's Paradigm

The experiment used in Berlin was a simple assay to study locomotor behavior in flies, Buridan's paradigm. This short video clip explains the basic idea behind the experiment:

Towards citizen science

"Apart from ruining your glass of red wine, Drosophila is a central model organism to study, amongst other problems, how brains work. By carefully watching whether flies turn left or right, we aim at understanding how humans make decisions." explained Dr. Alejandro Gomez-Marin, first author in the Spanish team. The data and tools provided with their publications will allow researchers to not only improve the accuracy of the research results, but also to develop new analysis methods, "maybe someone will come up with an analysis we would have never thought of" hopes Dr. Gomez-Marin. "We are already communicating with several people who are using our software packages even before they were officially published" says Dr. Julien Colomb, first author in the German team, "it's exciting to see other colleagues adopting the tools we developed, because they're easy to access and free". The work presented in the two publications is part of a growing movement pushing for 'Open Science' where publicly funded research data become freely accessible. "Opening up some of the research tools is only a first step", says Dr. Colomb, "the next step in our efforts to promote open science is to make the data available online, not only at publication, but automatically while they are analyzed. And we are working on it.". Ultimately, the blueprints for the various experimental containers in which these experiments take place will be translated into a computer-readable format such that 3D printers can re-create the exact experimental conditions anywhere in the world. "Eventually, I'd like to get everything to be so simple and cheap that anybody would have the chance to do these experiments, even the high school student with fruit flies in the kitchen." said Dr. Björn Brembs, head of the German team.

Please find below the two abstracts and the 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

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

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.