jabs-behavior-classifier 0.44.2

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JAX Animal Behavior System (JABS)

An open-source platform for standardized mouse behavioral phenotyping.

Documentation · User Guide · Sample Data · Contact Us

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Features

• Interactive GUI for behavior annotation and classifier training
• Machine learning-powered automatic behavior classification
• XGBoost support for high-performance classification
• Command-line tools for batch processing and HPC integration
• Singularity containers for reproducible deployments

Quick Start

Installation (Recommended)

# Using pipx (recommended)
pipx install jabs-behavior-classifier

# OR using uv
uv tool install jabs-behavior-classifier

Run Without Installing

uvx --from jabs-behavior-classifier jabs

Launch JABS

jabs              # Launch the GUI
jabs-init --help  # View project initialization options

Note: The first launch may take a few minutes to initialize. Subsequent launches will be much faster.

Installation Options

Install from PyPI

pip install jabs-behavior-classifier

To include optional extras, use bracket notation. For example, to install with NWB export support:

pip install "jabs-behavior-classifier[nwb]"

Available extras:

Extra	Description
nwb	NWB export support (pynwb, ndx-pose)

Install from Source

# From GitHub
pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git

# Specific branch or commit
pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git@branch-name

# From local clone
git clone https://github.com/KumarLabJax/JABS-behavior-classifier.git
cd JABS-behavior-classifier
pip install .

Virtual Environment Setup

python -m venv jabs.venv

# Linux/macOS
source jabs.venv/bin/activate

# Windows
jabs.venv\Scripts\activate.bat

pip install jabs-behavior-classifier

macOS: Enable XGBoost

XGBoost requires the OpenMP library, which doesn't ship with macOS:

brew install libomp

Command Line Tools

Command	Description
jabs	Launch the JABS GUI
jabs-init	Initialize a new project or recompute features
jabs-classify	Run a trained classifier
jabs-export-training	Export training data from a project
jabs-cli	Collection of utility commands

Run <command> --help for detailed usage information.

Prerequisites

JABS requires pose files generated from the Kumar Lab's mouse pose estimation neural networks:

• Single mouse: deep-hrnet-mouse
• Multi-mouse: Under development — contact us for more information

Singularity/Apptainer (Linux)

We provide Singularity/Apptainer definition files and SLURM batch scripts for running JABS on Linux compute clusters. See vm/README.md for build instructions and usage details.

Project Portability

JABS uses four version numbers to track compatibility:

Version	Description
Package version	Bumped every release
Feature version	Bumped when feature values or storage format changes
Classifier version	Bumped when classifier characteristics change
Prediction version	Bumped when prediction storage format changes

Artifact Compatibility

Artifact	Portability	Best For
Project folders	Cross-version compatible	Long-term storage, upgrades
Exported training data	Same JABS version	Sharing, archiving, HPC workflows
Classifier pickle files	Same machine only	Large-scale pipeline predictions

Detailed Portability Information

Project folders are the most compatible for upgrades. The vast majority of JABS upgrades allow transparent upgrades (e.g., re-generation of features) within the project folder without user interaction. We will provide instructions for changes that are not automatically compatible. Project folders are large but are almost always compatible across JABS versions.

Exported training data is compatible across computers but should generally not be considered compatible across JABS package versions. Once we add the appropriate version checks, error messages should be clearer about when and why these aren't compatible across versions. A common use case is to export training data from a project folder, transfer it to an HPC cluster, and then train and run a classifier using the jabs-classify command from the same version of JABS that was used to export the training file.

Classifier pickle files are the serialized trained classifiers. They load very fast and are tiny and efficient, but are only compatible within a specific install of the package (e.g., macOS will not be compatible with Windows). These should not be considered portable beyond the computer and specific JABS install that created them. We use these for large-scale predictions in pipelines—for example, using exported training data to train a classifier saved as a .pickle file, which can then be used to classify many videos as part of a pipeline.

Documentation

• ReadTheDocs Tutorial — Complete user guide and tutorials
• User Guide — Markdown documentation
• Sample Data — Test datasets for demonstration

Contributing

Interested in contributing? Check out our:

• Contributing Guide
• Development Guide

Citation

If you use JABS in your research, please cite:

Choudhary, A., Geuther, B. Q., Sproule, T. J., Beane, G., Kohar, V., Trapszo, J., & Kumar, V. (2025). JAX Animal Behavior System (JABS): A genetics informed, end-to-end advanced behavioral phenotyping platform for the laboratory mouse. eLife, 14:RP107259. https://doi.org/10.7554/eLife.107259.2

License

Copyright 2023 The Jackson Laboratory — All rights reserved.

JABS is licensed under a non-commercial use license. See LICENSE for details.

For commercial licensing inquiries, contact us.

Acknowledgements

JABS was influenced by JAABA (Janelia Automatic Animal Behavior Annotator) developed by the Branson lab at Janelia Research Campus of the Howard Hughes Medical Institute. We are grateful for their pioneering work in automated behavior classification.

Kabra, M., Robie, A., Rivera-Alba, M. et al. JAABA: interactive machine learning for automatic annotation of animal behavior. Nature Methods 10, 64–67 (2013). https://doi.org/10.1038/nmeth.2281

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The Jackson Laboratory · Kumar Lab

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