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

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
Main Authors: Tulio Fernandes De Almeida, Bruno Guedes Spinelli, Ramón Hypolito Lima, Maria Carolina Gonzalez, Abner Cardoso Rodrigues
Format: Article
Language:English
Published: Frontiers Media S.A. 2022-05-01
Series:Frontiers in Neuroscience
Subjects:
deep learning
unsupervised learning
behavioral analysis
animal tracking
electrophysiology
neuroscience method
Online Access:https://www.frontiersin.org/articles/10.3389/fnins.2022.779106/full
Description
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:1662-453X

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