JAABA: Getting Started

JAABA is a machine learning-based program that will help you create automatic behavior detectors. To define a behavior and create a behavior detector, you will need to label the behavior of animals in a subset of frames in videos. It is very important to choose these labels carefully. In addition, there are limitations to the types of behaviors for which JAABA can create behavior classifiers. These limitations are not exactly well-defined, and the best way we know for understanding them is to try out JAABA. If you are new to JAABA, please follow the instructions in this document to get a feel for the types of behaviors JAABA can create detectors for, and the effect of different types of labels on JAABA's performance. In general, you will start with a task that we know is within JAABA's capabilities, then iteratively make the task more complicated to test and understand JAABA's abilities and limitations.


Suggested Itinerary

  1. Computer requirements: Check the computer requirements at Minimum Computer Requirements to ensure that you have a sufficiently powerful computer to run JAABA.
  2. Download and install: Please follow the instructions at Installation and Starting JAABA on how to download and install JAABA.
  3. Demonstration: Watch our video tutorial to using JAABA on YouTube. We recommend watching the HD version.
  4. Sample data: Download our sample data from Sourceforge. Follow the instructions at Sample Data.
  5. Train a chase classifier using the sample data, in particular using the included Project Configuration file sampledata/Chase_JAABAProject.mat and the two experiments pBDPGAL4U_TrpA_Rig2Plate17BowlA_20120202T145723 and Chase1_TrpA_Rig1Plate15BowlA_20120404T141155. Read and refer to the rest of the documentation on this site while training, in particular the sections on Training.html and Evaluating a Behavior Classifier. While training, we recommend you start with the most obvious bouts of chases and not chases, then gradually try to get JAABA to work on more difficult examples.
  6. Prepare your data: Follow instructions at Preparing Data for JAABA on how to prepare your own data for use with JAABA.
  7. Train your classifier: Train a behavior classifier for your data that you are interested in, always remembering to try easy things first and hard things later.

Video Tutorial

We have created a video tutorial to using JAABA that we recommend you watch before trying JAABA yourself. This video shows us creating a chase classifier using the Sample Data distributed on out website. We recommend you watch the video in HD, as details will not be visible at lower resolutions. This sample and data and this tutorial are similar to the introduction we gave in our usability study described in our paper.

Sample Data

We have provided a sample JAABA project and two sample videos, available for download at Sourceforge.

The sample data directory contains two experiment directories that can be used with JAABA:

Each experiment directory contains the following files:

SampleChaseJAABAProject.jab is a sample JAABA project. To test JAABA, we recommend:

  1. Setting the project to be SampleChaseJAABAProject.jab.
  2. Adding the two experiment directories in this directory.
  3. Test out JAABA.