February 20, 2019
Francisco Romero Ferrero and colleagues have developed idtracker.ai, an algorithm and software for tracking individuals in large collectives of unmarked animals, recently described in Nature Methods.
Tracking individual animals in large collective groups can give interesting insights to behavior, but has proven to be a challenge for analysis. With advances in artificial intelligence and tracking software, it has become increasingly easier to collect such information from video data. Ferrero et al. have developed an algorithm and tracking software that features two deep networks. The first tracks animal identification and the second tracks when animals touch or cross paths in front of one another. The software has been validated to track individuals with high accuracy in cohorts of up to 100 animals with diverse species from rodents to zebrafish to ants. This software is free, fully-documented and available online with additional jupyter notebooks for data analysis.
Check out their website with full documentation, the recent Nature Methods article, BioRXiv preprint, and a great video of idtracker.ai tracking 100 zebrafish!
Romero-Ferrero, F., Bergomi, M. G., Hinz, R. C., Heras, F. J., & Polavieja, G. G. (2019). Idtracker.ai: Tracking all individuals in small or large collectives of unmarked animals. Nature Methods, 16(2), 179-182. doi:10.1038/s41592-018-0295-5
November 14, 2018
John Stowers and colleagues from the Straw Lab at the University of Frieburg have developed and shared FreemoVR, a virtual reality set-up for unrestrained animals.
Virtual reality (VR) systems can help to mimic nature in behavioral paradigms, which help us to understand behavior and brain function. Typical VR systems require that animals are movement restricted, which limits natural responses. The FreemoVR system was developed to address these issues and allows for virtual reality to be integrated with freely moving behavior. This system can be used with a number of different species including mice, zebrafish, and Drosophila. FreemoVR has been validated to investigate several behavior in tests of height-aversion, social interaction, and visuomotor responses in unrestrained animals.
Read more on the Straw Lab site, Nature Methods paper, or access the software on Github.
Stowers, J. R., Hofbauer, M., Bastien, R., Griessner, J., Higgins, P., Farooqui, S., . . . Straw, A. D. (2017). Virtual reality for freely moving animals. Nature Methods, 14(10), 995-1002. doi:10.1038/nmeth.4399