Welcome to JABS documentation!

JABS (JAX Animal Behavior System) is an integrated rodent phenotyping platform to the community for data acquisition, machine learning based behavior annotation, classifier sharing and automated genetic analysis.

Check out the Set up section for further information, including how to Installation the project.

Note

This project is under active development.

Contents

• Set up
  • Installation
    • Creating the Virtual Environment
    • Activating
    • Deactivating
    • Installing on Apple M1/M2 Silicone
    • Enabling XGBoost Classifier
  • Launching JABS GUI
  • Preparing the JABS Project
• JABS User Guide
  • The JABS Project Directory
    • Example JABS project directory listing:
  • Initializing A JABS Project Directory
  • The Rotta Directory
    • rotta/annotations
    • rotta/archive
    • rotta/cache
    • rotta/classifiers
    • rotta/features
    • rotta/predictions
  • GUI
    • Main Window
    • Classifier Controls
    • Label and Prediction Visualizations
    • Menu
  • Labeling
    • Selecting Frames
    • Applying Labels
    • Keyboard Shortcuts
    • Navigation Keyboard Controls
    • Labeling Controls
    • Identity Gaps
  • All Keyboard Shortcuts
    • File Menu
    • Navigation
    • Labeling
    • Other
  • The Command Line Classifier
  • File Formats
    • Inference File
    • Location
    • Contents
    • predicted_class
    • probabilities
    • identity_to_track
• JABS Video Tutorial
• Advanced JABS usage
  • Active Learning Strategy in JABS
  • Finding new videos
  • Ground Truth Validation
• Introduction to the JABS downstream analysis
• 2022 Short Course on the Application of Machine Learning for Automated Quantification of Behavior
  • Day 4 Workshop - Training Classifiers to Classify Animal Behavior
  • Purpose/Expectations
    • Step 0
    • Step 1
    • Step 2
    • Step 3
      • Question 1
      • Question 2
      • Question 3-4
    • Discussion 1
    • Extra visualizations of the dataset
    • Step 4
    • Experiment 1
    • Label Balancing
      • Question 5
    • Experiment 2
    • Step 5
      • Question 6
    • Step 6
      • Question 7
    • Step 7
    • Experiment 3
    • Experiment 4
    • Step 8
    • Discussion 2
    • Step 9
    • Step 10
    • Discussion 3
    • Step 11
    • Experiment 5