https://jabs-tutorial.readthedocs.io/en/latest/index.html
Copyright 2023 The Jackson Laboratory -- All rights reserved.
email us at jabs@jax.org
JABS is licensed under a non-commercial use license, see LICENSE for more information. Contact us for information about licensing for commercial use.
This is beta software. Changes, including incompatible changes to exported training data and prediction output, are forthcoming.
JABS requires pose files generated from the Kumar Lab's mouse pose estimation neural networks. Single mouse pose files are generated from this repository. Multi-mouse is still under development. Contact us for more information.
Developed and tested on Python 3.10. See the requirements.txt
for a list of required Python packages. These packages are available from the
Python Package Index (PyPI)
The following instructions are for Linux or MacOS Users. Windows users can follow the instructions in the "Windows" section below.
You will need to create the virtual environment before you can run the labeler
for the first time. The following commands will create a new Python3 virtual
environment, activate it, and install the required packages. Note, your python
executable may be named python or python3 depending on your installation.
python -m venv jabs.venv
source jabs.venv/bin/activate
pip install -r requirements.txt
The virtual environment must be activated before you can run the labeling interface. To activate, run the following command:
source jabs.venv/bin/activate
The virtual environment can be deactivated if you no longer need it:
deactivate
The XGBoost Classifier has a dependency on the OpenMP library. This does
not ship with MacOS. XGBoost should work "out of the box" on other platforms.
On MacOS, you can install libomp with Homebrew (preferred) with the following
command brew install libomp. You can also install libomp from source if you
can't use Homebrew, but this is beyond the scope of this Readme.
Make sure that a compatible version of Python is installed (3.10).
There are two convenience scripts included with JABS, setup_windows.bat and
jabs.bat, that allow a user to set up the Python environment and launch
JABS without using the command prompt.
The setup_windows.bat script will create a Python virtual
environment in the JABS directory called jabs.venv and then install all
the required packages from PyPi. This script can be executed by double-clicking
on it in the Windows Explorer. This script only needs to be executed once.
The jabs.bat script will activate the jabs.venv virtual environment and
launch the JABS application. This can be executed by double-clicking on it in
the Windows Explorer.
You can also set up the Python virtual environment and execute JABS from the Windows Command Prompt (cmd.exe).
To configure the Python virtual environment manually, Open a Command Prompt in the JABS directory and run the following commands:
python -m venv jabs.venv
jabs.venv\Scripts\activate.bat
pip install -r requirements.txt
To launch JABS from the command prompt, open a command prompt in the JABS directory and run the following commands:
jabs.venv\Scripts\activate.bat
python app.py
We supply a tested pair of singularity definition files. The first vm is indended for command-line use on compute clusters when scaling inferences. The second vm is designed for interacting with the GUI in a portable environment. Please inspect the definition files for related linux packages to run the software.