@article {45098, title = {Automated image-based tracking and its application in ecology.}, journal = {Trends in Ecology and Evolution}, volume = {29}, year = {2014}, month = {2014 Jul}, pages = {417-428}, abstract = {

The behavior of individuals determines the strength and outcome of ecological interactions, which drive population, community, and ecosystem organization. Bio-logging, such as telemetry and animal-borne imaging, provides essential individual viewpoints, tracks, and life histories, but requires capture of individuals and is often impractical to scale. Recent developments in automated image-based tracking offers opportunities to remotely quantify and understand individual behavior at scales and resolutions not previously possible, providing an essential supplement to other tracking methodologies in ecology. Automated image-based tracking should continue to advance the field of ecology by enabling better understanding of the linkages between individual and higher-level ecological processes, via high-throughput quantitative analysis of complex ecological patterns and processes across scales, including analysis of environmental drivers.

}, issn = {1872-8383}, doi = {10.1016/j.tree.2014.05.004}, author = {Dell, Anthony I and Bender, John A and Branson, Kristin and Couzin, Iain D and de Polavieja, Gonzalo G and Noldus, Lucas P J J and P{\'e}rez-Escudero, Alfonso and Perona, Pietro and Straw, Andrew D and Wikelski, Martin and Brose, Ulrich} } @article {6953, title = {Flying Drosophila stabilize their vision-based velocity controller by sensing wind with their antennae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, year = {2014}, month = {2014 Apr 1}, pages = {E1182-91}, abstract = {

Flies and other insects use vision to regulate their groundspeed in flight, enabling them to fly in varying wind conditions. Compared with mechanosensory modalities, however, vision requires a long processing delay (\ 100 ms) that might introduce instability if operated at high gain. Flies also sense air motion with their antennae, but how this is used in flight control is unknown. We manipulated the antennal function of fruit flies by ablating their aristae, forcing them to rely on vision alone to regulate groundspeed. Arista-ablated flies in flight exhibited significantly greater groundspeed variability than intact flies. We then subjected them to a series of controlled impulsive wind gusts delivered by an air piston and experimentally manipulated antennae and visual feedback. The results show that an antenna-mediated response alters wing motion to cause flies to accelerate in the same direction as the gust. This response opposes flying into a headwind, but flies regularly fly upwind. To resolve this discrepancy, we obtained a dynamic model of the fly{\textquoteright}s velocity regulator by fitting parameters of candidate models to our experimental data. The model suggests that the groundspeed variability of arista-ablated flies is the result of unstable feedback oscillations caused by the delay and high gain of visual feedback. The antenna response drives active damping with a shorter delay (\ 20 ms) to stabilize this regulator, in exchange for increasing the effect of rapid wind disturbances. This provides insight into flies{\textquoteright} multimodal sensory feedback architecture and constitutes a previously unknown role for the antennae.

}, issn = {1091-6490}, doi = {10.1073/pnas.1323529111}, author = {Fuller, Sawyer Buckminster and Straw, Andrew D and Peek, Martin Y and Murray, Richard M and Dickinson, Michael H} } @article {45059, title = {FlyMAD: rapid thermogenetic control of neuronal activity in freely walking Drosophila.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Jul 11}, pages = {756-62}, abstract = {

Rapidly and selectively modulating the activity of defined neurons in unrestrained animals is a powerful approach in investigating the circuit mechanisms that shape behavior. In Drosophila melanogaster, temperature-sensitive silencers and activators are widely used to control the activities of genetically defined neuronal cell types. A limitation of these thermogenetic approaches, however, has been their poor temporal resolution. Here we introduce FlyMAD (the fly mind-altering device), which allows thermogenetic silencing or activation within seconds or even fractions of a second. Using computer vision, FlyMAD targets an infrared laser to freely walking flies. As a proof of principle, we demonstrated the rapid silencing and activation of neurons involved in locomotion, vision and courtship. The spatial resolution of the focused beam enabled preferential targeting of neurons in the brain or ventral nerve cord. Moreover, the high temporal resolution of FlyMAD allowed us to discover distinct timing relationships for two neuronal cell types previously linked to courtship song.

}, issn = {1548-7105}, doi = {10.1038/nmeth.2973}, author = {Bath, Daniel E and Stowers, John R and H{\"o}rmann, Dorothea and Poehlmann, Andreas and Dickson, Barry J and Straw, Andrew D} } @article {2161, title = {Multi-camera real-time three-dimensional tracking of multiple flying animals.}, journal = {Journal of the Royal Society, Interface}, volume = {8}, year = {2011}, month = {2011 Mar 6}, pages = {395-409}, abstract = {

Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time{\textendash}with minimal latency{\textendash}opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as {\textquoteright}virtual reality{\textquoteright}-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.

}, issn = {1742-5662}, doi = {10.1098/rsif.2010.0230}, author = {Straw, Andrew D and Branson, Kristin and Neumann, Titus R and Dickinson, Michael H} }