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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Neuroscience |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fnins.2022.779106/full |
| _version_ | 1818200697999458304 |
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| author | Tulio Fernandes De Almeida Bruno Guedes Spinelli Ramón Hypolito Lima Maria Carolina Gonzalez Abner Cardoso Rodrigues |
| author_facet | Tulio Fernandes De Almeida Bruno Guedes Spinelli Ramón Hypolito Lima Maria Carolina Gonzalez Abner Cardoso Rodrigues |
| author_sort | Tulio Fernandes De Almeida |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T02:41:47Z |
| format | Article |
| id | doaj.art-05b5dc2302ee49b9984bd172b93b1b57 |
| institution | Directory Open Access Journal |
| issn | 1662-453X |
| language | English |
| last_indexed | 2024-12-12T02:41:47Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroscience |
| spelling | doaj.art-05b5dc2302ee49b9984bd172b93b1b572022-12-22T00:41:08ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2022-05-011610.3389/fnins.2022.779106779106PyRAT: An Open-Source Python Library for Animal Behavior AnalysisTulio Fernandes De AlmeidaBruno Guedes SpinelliRamón Hypolito LimaMaria Carolina GonzalezAbner Cardoso RodriguesHere 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.https://www.frontiersin.org/articles/10.3389/fnins.2022.779106/fulldeep learningunsupervised learningbehavioral analysisanimal trackingelectrophysiologyneuroscience method |
| spellingShingle | Tulio Fernandes De Almeida Bruno Guedes Spinelli Ramón Hypolito Lima Maria Carolina Gonzalez Abner Cardoso Rodrigues PyRAT: An Open-Source Python Library for Animal Behavior Analysis Frontiers in Neuroscience deep learning unsupervised learning behavioral analysis animal tracking electrophysiology neuroscience method |
| title | PyRAT: An Open-Source Python Library for Animal Behavior Analysis |
| title_full | PyRAT: An Open-Source Python Library for Animal Behavior Analysis |
| title_fullStr | PyRAT: An Open-Source Python Library for Animal Behavior Analysis |
| title_full_unstemmed | PyRAT: An Open-Source Python Library for Animal Behavior Analysis |
| title_short | PyRAT: An Open-Source Python Library for Animal Behavior Analysis |
| title_sort | pyrat an open source python library for animal behavior analysis |
| topic | deep learning unsupervised learning behavioral analysis animal tracking electrophysiology neuroscience method |
| url | https://www.frontiersin.org/articles/10.3389/fnins.2022.779106/full |
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