/pyrat

PyRat is a user friendly library in python to analyze data from the DeepLabCut. Developed to help researchers unfamiliar with programming can perform animal behavior analysis more simpler.

Primary LanguageJupyter NotebookMIT LicenseMIT

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PyRat - Python in Rodent Analysis and Tracking

PyRat is a user friendly library in python to analyze data from the DeepLabCut. Developed to help researchers unfamiliar with programming can perform animal behavior analysis more simpler.

Installation

The latest stable release is available on PyPi, and you can install it by saying

pip install pyratlib

Anaconda users can install using conda-forge:

conda install -c conda-forge pyratlib

To build PyRat from source, say python setup.py build. Then, to install PyRat, say python setup.py install. If all went well, you should be able to execute the demo scripts under examples/ (OS X users should follow the installation guide given below).

Alternatively, you can download or clone the repository and use pip to handle dependencies:

unzip pyratlib.zip
pip install -e pyratlib

or

git clone https://github.com/pyratlib/pyrat.git
pip install -e pyratlib

By calling pip list you should see pyrat now as an installed package:

pyrat (0.x.x, /path/to/pyratlib)

Data

The data is available on Zenodo

Examples

  • Basic Usage Open In Colab
  • Behavior Classification Open In Colab
  • Behavior Classification of multiple videos Open In Colab
  • Metrics in mice Open In Colab
  • Neural Data example Open In Colab

References:

If you use our code we kindly as that you please cite De Almeida et al, 2022 and, if you use the dataset please also cite De Almeida et al, 2021.

Please check out the following references for more details:

@article{deAlmeida2022,
  title        = {PyRAT: An open source-python library for fast and robust animal behavior analysis and neural data synchronization},
  author       = {De Almeida, Tulio Fernandes and 
                  Spinelli, Bruno Guedes and 
                  Hypolito Lima, Ram{\'o}n and 
                  Gonzalez, Maria Carolina and 
                  Rodrigues, Abner Cardoso},
  journal      = {Frontiers in Neuroscience},
  pages        = {505},
  publisher    = {Frontiers}
}

@dataset{deAlmeida2021,
  title        = {PyRAT-data-example},
  author       = {Almeida, Túlio and
                  Spinelli, Bruno and
                  Gonzalez, Maria Carolina and
                  Lima, Ramón and
                  Rodrigues, Abner},
  month        = sep,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {1.0.0},
  doi          = {10.5281/zenodo.5883277},
  url          = {https://doi.org/10.5281/zenodo.5883277}
}

Development Team: