Multi-camera Realtime 3D Tracking of Multiple Flying Animals

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 realtime - with minimal latency - opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behavior. Here we describe a new system capable of tracking the position and body orientation of animals such as flies and birds. The system operates with less than 40 msec 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 Neighbor Standard Filter data association algorithm. In one implementation, an eleven 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 behavior of freely flying animals. If combined with other techniques, such as `virtual reality'-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.Comment: pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6), 18 pages with 9 figure

Path-tracing Monte Carlo Library for 3D Radiative Transfer in Highly Resolved Cloudy Atmospheres

Interactions between clouds and radiation are at the root of many difficulties in numerically predicting future weather and climate and in retrieving the state of the atmosphere from remote sensing observations. The large range of issues related to these interactions, and in particular to three-dimensional interactions, motivated the development of accurate radiative tools able to compute all types of radiative metrics, from monochromatic, local and directional observables, to integrated energetic quantities. In the continuity of this community effort, we propose here an open-source library for general use in Monte Carlo algorithms. This library is devoted to the acceleration of path-tracing in complex data, typically high-resolution large-domain grounds and clouds. The main algorithmic advances embedded in the library are those related to the construction and traversal of hierarchical grids accelerating the tracing of paths through heterogeneous fields in null-collision (maximum cross-section) algorithms. We show that with these hierarchical grids, the computing time is only weakly sensitivive to the refinement of the volumetric data. The library is tested with a rendering algorithm that produces synthetic images of cloud radiances. Two other examples are given as illustrations, that are respectively used to analyse the transmission of solar radiation under a cloud together with its sensitivity to an optical parameter, and to assess a parametrization of 3D radiative effects of clouds.Comment: Submitted to JAMES, revised and submitted again (this is v2