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

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
Behavior Classification
Behavior Classification of multiple videos
Metrics in mice
Neural Data example

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.

De Almeida et al, 2022: https://doi.org/10.3389/fnins.2022.779106
De Almeida et al, 2021: 10.5281/zenodo.5883277

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, TÃºlio and
                  Spinelli, Bruno and
                  Gonzalez, Maria Carolina and
                  Lima, RamÃ³n 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:

Tulio Almeida - GitHub - Google Scholar - Site
Bruno Spinelli - GitHub - Google Scholar
Ramon Hypolito - GitHub - Google Scholar
Maria Carolina Gonzalez - GitHub - Google Scholar
Abner Rodrigues - GitHub - Google Scholar

Metadata

Release files for pyratlib 0.7.7

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pyratlib 0.7.7
File	Size	Uploaded
pyratlib-0.7.7.tar.gz	22.7 kB	Feb 18, 2023	Details

Release files / pyratlib-0.7.7.tar.gz

Download URL	pyratlib-0.7.7.tar.gz
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