Usage#

This section provides instructions on how to obtain zebrafish tracking data and how to install and set up the Megabouts package for locomotion analysis.

Obtaining Zebrafish Tracking Data#

There are several tools and methods available for tracking zebrafish. Below are some popular options:

If you are working with video recordings of zebrafish larvae, you can also track them using deep learning-based methods:

Once you have your zebrafish tracking data, you’re ready to analyze it with Megabouts!

Installing Megabouts#

Megabouts is an open-source Python toolbox designed for zebrafish locomotion analysis. To install Megabouts, follow the steps below:

  1. Create a Virtual Environment (using conda): First, create a virtual environment with Python 3.11 using conda:

    conda create --name megabouts python=3.11

    Then activate the environment:

    conda activate megabouts

  2. Install PyTorch [for GPU setup]: Megabouts depends on PyTorch. To enable GPU support, follow the instructions on the PyTorch website to install the appropriate version for your system.

    Example installation command:

    conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia

    Make sure to adjust the command based on your system’s GPU or CPU configuration.

  3. Once PyTorch is installed, you can install Megabouts: Choose one of the following installation methods:

    From PyPI (stable version):

    pip install megabouts

    From GitHub (latest development version):

    pip install git+https://github.com/orger-lab/megabouts.git

  4. Verify the Installation: After installation, you can verify that Megabouts is properly installed by checking its version:

    python -c "import megabouts; print(megabouts.__version__)"

If you see the version number printed without errors, Megabouts has been successfully installed.

Usage Guide#

Now that you’ve installed Megabouts, you can begin analyzing zebrafish locomotion data. Please refer to the Tutorials for detailed instructions and examples.