flydra_analysis - analysis component of flydra

flydra - multi-camera tracking system

⚠️⚠️Please consider our updated software, called Braid.⚠️⚠️ Braid is a modern and maintained derivative of flydra. Braid performs the same tasks as flydra, only better. Flydra is not very actively maintained and substantial updates from the Straw Lab are not anticipated.

Flydra is a markerless, multi-camera tracking 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. Fundamentally, the multi-target tracking algorithm is based on an extended Kalman filter and the nearest neighbour standard filter data association algorithm.

Discussion

For questions or discussion, please use the "multicams" Google Group.

Installation

For installation, we recommend using our Ansible playbooks. In particular, the ros-kinetic-flydra role or the ros-kinetic-freemovr install on Ubuntu 16.04 with ROS Kinetic, either flydra alone or within a full FreemoVR system.

History

This software was originally develped by Andrew Straw in the Dickinson Lab at Caltech from 2004-2010. Ongoing development continued, coordinated by the Straw Lab, from 2010. The software was open sourced in 2017.

Funding

We gratefully acknowledge support from from the Packard Foundation, AFOSR (FA9550-06-1-0079), ARO (DAAD 19-03-D-0004), NIH (R01 DA022777), NSF (0923802), and Caltech to Michael H. Dickinson, and AFOSR (FA9550-10-1-0086), ERC (Starting Grant 281884 FlyVisualCircuits), WWTF (CS11-029), Boehringer Ingelheim, Research Institute of Molecular Pathology (IMP), and the University of Freiburg to Andrew D. Straw.

Directory organization

• docs - documentation
• flydra_analysis - calibration and analysis routines
• flydra_camnode - camera node program
• flydra_core - realtime 3D tracking
• packaging - making Debian/Ubuntu packages

Publications

Flydra is described in the following papers:

Straw AD✎, Branson K, Neumann TR, Dickinson MH. Multicamera Realtime 3D Tracking of Multiple Flying Animals. Journal of The Royal Society Interface 8(11), 395-409 (2011) doi:10.1098/rsif.2010.0230.

Stowers JR*, Hofbauer M*, Bastien R, Griessner J⁑, Higgins P⁑, Farooqui S⁑, Fischer RM, Nowikovsky K, Haubensak W, Couzin ID, Tessmar-Raible K✎, Straw AD✎. Virtual Reality for Freely Moving Animals. Nature Methods (2017) doi:10.1038/nmeth.4399.

Please cite these if you use Flydra.

License

With the exception of third party software, the software, documentation and other resouces are licensed under either of

• Apache License, Version 2.0, (./LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
• MIT license (./LICENSE-MIT or http://opensource.org/licenses/MIT) at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

Code of conduct

Anyone who interacts with flydra in any space including but not limited to this GitHub repository is expected to follow our code of conduct.