JAABA: The Janelia Automatic Animal Behavior Annotator
JAABA is a machine learning-based system that enables researchers to automatically compute interpretable, quantitative statistics describing video of behaving animals. Through our system, users encode their intuition about the structure of behavior by labeling the behavior of the animal, e.g. walking, grooming, or following, in a small set of video frames. JAABA uses machine learning techniques to convert these manual labels into behavior detectors that can then be used to automatically classify the behaviors of animals in large data sets with high throughput. Our system combines an intuitive graphical user interface, a fast and powerful machine learning algorithm, and visualizations of the classifier into an interactive, usable system for creating automatic behavior detectors. JAABA is complementary to video-based tracking methods, and we envision that it will facilitate extraction of detailed, scientifically meaningful measurements of the behavioral effects in large experiments.
JAABA is an open-source, freely available program developed by members of the Branson lab. It is available for download at: http://jaaba.sourceforge.net/.
Ctrax is an open-source, freely available, machine vision program for estimating the positions and orientations of many walking flies, maintaining their individual identities over long periods of time.
Ctrax was designed to allow high-throughput, quantitative analysis of behavior in freely moving flies. Our primary goal in this project is to provide quantitative behavior analysis tools to the neuroethology community; thus, we've endeavored to make the system adaptable to other labs' setups. We have assessed the quality of the tracking results for our setup, and found that it can maintain fly identities indefinitely with minimal supervision, and on average for 1.5 fly-hours automatically.
To further compensate for identity and other tracking errors, we provide the FixErrors Matlab GUI that identifies suspicious sequences of frames and allows a user to correct any tracking errors. We also distribute the BehavioralMicroarray Matlab Toolbox for defining and detecting a broad palette of individual and social behaviors. This software inputs the trajectories output by Ctrax and computes descriptive statistics of the behavior of each individual fly. We provide software for three proof-of-concept experiments to show the potential of the Ctrax software and our behavior detectors.
Ctrax is available for download at http://ctrax.sourceforge.net/.