PyRAT: An Open-Source Python Library for Animal Behavior Analysis

Here we developed an open-source Python-based library called Python rodent Analysis and Tracking (PyRAT). Our library analyzes tracking data to classify distinct behaviors, estimate traveled distance, speed and area occupancy. To classify and cluster behaviors, we used two unsupervised algorithms: h...

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Bibliographic Details
Published in:Frontiers in neuroscience 2022-05, Vol.16, p.779106-779106
Main Authors: De Almeida, Tulio Fernandes, Spinelli, Bruno Guedes, Hypolito Lima, Ramón, Gonzalez, Maria Carolina, Rodrigues, Abner Cardoso
Format: Article
Language:English
Subjects:
animal tracking
behavioral analysis
deep learning
electrophysiology
Neuroscience
neuroscience method
unsupervised learning
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Summary:Here we developed an open-source Python-based library called Python rodent Analysis and Tracking (PyRAT). Our library analyzes tracking data to classify distinct behaviors, estimate traveled distance, speed and area occupancy. To classify and cluster behaviors, we used two unsupervised algorithms: hierarchical agglomerative clustering and t-distributed stochastic neighbor embedding (t-SNE). Finally, we built algorithms that associate the detected behaviors with synchronized neural data and facilitate the visualization of this association in the pixel space. PyRAT is fully available on GitHub: https://github.com/pyratlib/pyrat.
ISSN:1662-4548
1662-453X
1662-453X
DOI:10.3389/fnins.2022.779106