Appendix C — References

Anderson, David J., and Pietro Perona. 2014. “Toward a Science of Computational Ethology.” Neuron 84 (1): 18–31. https://doi.org/10.1016/j.neuron.2014.09.005.

Beane, Glen, Brian Q. Geuther, Thomas J. Sproule, et al. 2023. JAX Animal Behavior System (JABS): A Video-Based Phenotyping Platform for the Laboratory Mouse. bioRxiv. https://doi.org/10.1101/2022.01.13.476229.

Berman, Gordon J., Daniel M. Choi, William Bialek, and Joshua W. Shaevitz. 2014. “Mapping the Stereotyped Behaviour of Freely Moving Fruit Flies.” Journal of The Royal Society Interface 11 (99): 20140672. https://doi.org/10.1098/rsif.2014.0672.

Biderman, Dan, Matthew R. Whiteway, Cole Hurwitz, et al. 2024. “Lightning Pose: Improved Animal Pose Estimation via Semi-Supervised Learning, Bayesian Ensembling and Cloud-Native Open-Source Tools.” Nature Methods 21 (7): 1316–28. https://doi.org/10.1038/s41592-024-02319-1.

Blau, Ari, Evan S. Schaffer, Neeli Mishra, et al. 2024. “A Study of Animal Action Segmentation Algorithms Across Supervised, Unsupervised, and Semi-Supervised Learning Paradigms.” Neurons, Behavior, Data Analysis, and Theory, December, 1–46. https://doi.org/10.51628/001c.127770.

Bohnslav, James P, Nivanthika K Wimalasena, Kelsey J Clausing, et al. 2021. “DeepEthogram, a Machine Learning Pipeline for Supervised Behavior Classification from Raw Pixels.” eLife 10 (September): e63377. https://doi.org/10.7554/eLife.63377.

Bradski, G. 2000. “The OpenCV Library.” Dr. Dobb’s Journal of Software Tools.

Chindemi, Giuseppe, Benoit Girard, and Camilla Bellone. 2023. LISBET: A Machine Learning Model for the Automatic Segmentation of Social Behavior Motifs. https://arxiv.org/abs/2311.04069.

“CRISPR Ants Lose Ability to Smell.” 2017. Nature 548 (7667): 263–63. https://doi.org/10.1038/d41586-017-02337-4.

Datta, Sandeep Robert, David J. Anderson, Kristin Branson, Pietro Perona, and Andrew Leifer. 2019. “Computational Neuroethology: A Call to Action.” Neuron 104 (1): 11–24. https://doi.org/10.1016/j.neuron.2019.09.038.

De Almeida, Tulio Fernandes, Bruno Guedes Spinelli, Ramón Hypolito Lima, Maria Carolina Gonzalez, and Abner Cardoso Rodrigues. 2022. “PyRAT: An Open-Source Python Library for Animal Behavior Analysis.” Frontiers in Neuroscience 16. https://www.frontiersin.org/articles/10.3389/fnins.2022.779106.

Dunn, Timothy W., Jesse D. Marshall, Kyle S. Severson, et al. 2021. “Geometric Deep Learning Enables 3D Kinematic Profiling Across Species and Environments.” Nature Methods 18 (5): 564–73. https://doi.org/10.1038/s41592-021-01106-6.

Duporge, Isla, Sofia Minano, Nikoloz Sirmpilatze, et al. 2025. Tracking the Flight: Exploring a Computational Framework for Analyzing Escape Responses in Plains Zebra (Equus Quagga). arXiv. https://doi.org/10.48550/arXiv.2505.16882.

Friard, Olivier, and Marco Gamba. 2016. “BORIS: A Free, Versatile Open-Source Event-Logging Software for Video/Audio Coding and Live Observations.” Methods in Ecology and Evolution 7 (11): 1325–30. https://doi.org/10.1111/2041-210X.12584.

Gallois, Benjamin, and Raphaël Candelier. 2021. “FastTrack: An Open-Source Software for Tracking Varying Numbers of Deformable Objects.” PLOS Computational Biology 17 (2): e1008697. https://doi.org/10.1371/journal.pcbi.1008697.

Goodwin, Nastacia L., Jia J. Choong, Sophia Hwang, et al. 2024. “Simple Behavioral Analysis (SimBA) as a Platform for Explainable Machine Learning in Behavioral Neuroscience.” Nature Neuroscience, May, 1–14. https://doi.org/10.1038/s41593-024-01649-9.

Graser, Anita. 2019. “MovingPandas: Efficient Structures for Movement Data in Python.” GI_Forum 2019, Volume 7, (June): 54–68. https://doi.org/10.1553/giscience2019_01_s54.

Graving, Jacob M, Daniel Chae, Hemal Naik, et al. 2019. “DeepPoseKit, a Software Toolkit for Fast and Robust Animal Pose Estimation Using Deep Learning.” eLife 8 (October): e47994. https://doi.org/10.7554/eLife.47994.

Günel, Semih, Helge Rhodin, Daniel Morales, João Campagnolo, Pavan Ramdya, and Pascal Fua. 2019. “DeepFly3D, a Deep Learning-Based Approach for 3D Limb and Appendage Tracking in Tethered, Adult Drosophila.” eLife 8 (October): e48571. https://doi.org/10.7554/eLife.48571.

Ho, Hinze, Nejc Kejzar, Hiroki Sasaguri, et al. 2023. “A Fully Automated Home Cage for Long-Term Continuous Phenotyping of Mouse Cognition and Behavior.” Cell Reports Methods 3 (7): 100532. https://doi.org/10.1016/j.crmeth.2023.100532.

Hsu, Alexander I., and Eric A. Yttri. 2021. “B-SOiD, an Open-Source Unsupervised Algorithm for Identification and Fast Prediction of Behaviors.” Nature Communications 12 (1): 5188. https://doi.org/10.1038/s41467-021-25420-x.

Hu, Yujia, Carrie R. Ferrario, Alexander D. Maitland, et al. 2023. “LabGym: Quantification of User-Defined Animal Behaviors Using Learning-Based Holistic Assessment.” Cell Reports Methods 0 (0). https://doi.org/10.1016/j.crmeth.2023.100415.

Kabra, Mayank, Alice A. Robie, Marta Rivera-Alba, Steven Branson, and Kristin Branson. 2013. “JAABA: Interactive Machine Learning for Automatic Annotation of Animal Behavior.” Nature Methods 10 (1): 64–67. https://doi.org/10.1038/nmeth.2281.

Karashchuk, Pierre, Katie L. Rupp, Evyn S. Dickinson, et al. 2021. “Anipose: A Toolkit for Robust Markerless 3D Pose Estimation.” Cell Reports 36 (13): 109730. https://doi.org/10.1016/j.celrep.2021.109730.

Koolhaas Jaap M., de Boer Sietse F., Coppens Caroline M. 2013. “The Resident-Intruder Paradigm: A Standardized Test for Aggression, Violence and Social Stress.” JoVE, no. 77: e4367. https://doi.org/doi:10.3791/4367.

Krakauer, John W., Asif A. Ghazanfar, Alex Gomez-Marin, Malcolm A. MacIver, and David Poeppel. 2017. “Neuroscience Needs Behavior: Correcting a Reductionist Bias.” Neuron 93 (3): 480–90. https://doi.org/10.1016/j.neuron.2016.12.041.

Lauer, Jessy, Mu Zhou, Shaokai Ye, et al. 2022. “Multi-Animal Pose Estimation, Identification and Tracking with DeepLabCut.” Nature Methods 19 (4): 496–504. https://doi.org/10.1038/s41592-022-01443-0.

Levitis, Daniel A., William Z. Lidicker, and Glenn Freund. 2009. “Behavioural Biologists Don’t Agree on What Constitutes Behaviour.” Animal Behaviour 78 (1): 103–10. https://doi.org/10.1016/j.anbehav.2009.03.018.

Lopes, Gonçalo, Niccolò Bonacchi, João Frazão, et al. 2015. “Bonsai: An Event-Based Framework for Processing and Controlling Data Streams.” Frontiers in Neuroinformatics 9. https://www.frontiersin.org/articles/10.3389/fninf.2015.00007.

Luxem, Kevin, Petra Mocellin, Falko Fuhrmann, et al. 2022. “Identifying Behavioral Structure from Deep Variational Embeddings of Animal Motion.” Communications Biology 5 (1): 1–15. https://doi.org/10.1038/s42003-022-04080-7.

Luxem, Kevin, Jennifer J Sun, Sean P Bradley, et al. 2023. “Open-Source Tools for Behavioral Video Analysis: Setup, Methods, and Best Practices.” eLife 12 (March): e79305. https://doi.org/10.7554/eLife.79305.

Martinez, Romain, Benjamin Michaud, and Mickael Begon. 2020. “‘Pyomeca‘: An Open-Source Framework for Biomechanical Analysis.” Journal of Open Source Software 5 (53): 2431. https://doi.org/10.21105/joss.02431.

Mathis, Alexander, Pranav Mamidanna, Kevin M. Cury, et al. 2018. “DeepLabCut: Markerless Pose Estimation of User-Defined Body Parts with Deep Learning.” Nature Neuroscience 21 (9): 1281–89. https://doi.org/10.1038/s41593-018-0209-y.

Mathis, Alexander, Steffen Schneider, Jessy Lauer, and Mackenzie Weygandt Mathis. 2020. “A Primer on Motion Capture with Deep Learning: Principles, Pitfalls, and Perspectives.” Neuron 108 (1): 44–65. https://doi.org/10.1016/j.neuron.2020.09.017.

Miranda, Lucas, Joeri Bordes, Benno Pütz, Mathias V. Schmidt, and Bertram Müller-Myhsok. 2023. “DeepOF: A Python Package for Supervised and Unsupervised Pattern Recognition in Mice Motion Tracking Data.” Journal of Open Source Software 8 (86): 5394. https://doi.org/10.21105/joss.05394.

Overall, Rupert W. 2024. ColonyTrack: Analysis of Multi-Subject Tracking Data from Interconnected Cage Networks.

Overall, Rupert W, Sara Zocher, Alexander Garthe, and Gerd Kempermann. 2020. “Rtrack: A Software Package for Reproducible Automated Water Maze Analysis.” bioRxiv 2020.02.27.967372. https://doi.org/10.1101/2020.02.27.967372.

Pappalardo, Luca, Filippo Simini, Gianni Barlacchi, and Roberto Pellungrini. 2022. “Scikit-Mobility: A Python Library for the Analysis, Generation, and Risk Assessment of Mobility Data.” Journal of Statistical Software 103 (1): 1–38. https://doi.org/10.18637/jss.v103.i04.

Pereira, Talmo D., Joshua W. Shaevitz, and Mala Murthy. 2020. “Quantifying Behavior to Understand the Brain.” Nature Neuroscience 23 (12): 1537–49. https://doi.org/10.1038/s41593-020-00734-z.

Pereira, Talmo D., Nathaniel Tabris, Arie Matsliah, et al. 2022. “SLEAP: A Deep Learning System for Multi-Animal Pose Tracking.” Nature Methods 19 (4): 486–95. https://doi.org/10.1038/s41592-022-01426-1.

Roald-Arbøl, Mikkel. 2024. Animovement: An r Toolbox for Analysing Animal Movement Across Space and Time. Version 0.2.0. http://www.roald-arboel.com/animovement/.

Romero-Ferrero, Francisco, Mattia G. Bergomi, Robert C. Hinz, Francisco J. H. Heras, and Gonzalo G. de Polavieja. 2019. “Idtracker.ai: Tracking All Individuals in Small or Large Collectives of Unmarked Animals.” Nature Methods 16 (2): 179–82. https://doi.org/10.1038/s41592-018-0295-5.

Schweihoff, Jens F., Alexander I. Hsu, Martin K. Schwarz, and Eric A. Yttri. 2022. A-SOiD, an Active Learning Platform for Expert-Guided, Data Efficient Discovery of Behavior. bioRxiv. https://doi.org/10.1101/2022.11.04.515138.

Segalin, Cristina, Jalani Williams, Tomomi Karigo, et al. 2021. “The Mouse Action Recognition System (MARS) Software Pipeline for Automated Analysis of Social Behaviors in Mice.” eLife 10 (November): e63720. https://doi.org/10.7554/eLife.63720.

Sirmpilatze, Niko, Sofía Miñano, Chang Huan Lo, et al. 2025. Neuroinformatics-Unit/Movement: V0.9.0. Zenodo. https://doi.org/10.5281/zenodo.16754905.

Sun, Jennifer J., Tomomi Karigo, David J. Anderson, Pietro Perona, Yisong Yue, and Ann Kennedy. 2021. Caltech Mouse Social Interactions (CalMS21) Dataset. CaltechDATA. https://doi.org/10.22002/D1.1991.

Tinbergen, Niko. 1951. The Study of Instinct. Clarendon Press.

Tomar, Suramya. 2006. “Converting Video Formats with FFmpeg.” Linux Journal 2006 (146): 10.

Walter, Tristan, and Iain D Couzin. 2021. “TRex, a Fast Multi-Animal Tracking System with Markerless Identification, and 2D Estimation of Posture and Visual Fields.” eLife 10 (February): e64000. https://doi.org/10.7554/eLife.64000.

Weinreb, Caleb. 2024. “Keypoint-MoSeq: Parsing Behavior by Linking Point Tracking to Pose Dynamics.” Nature Methods 21.

Wiltschko, Alexander B., Matthew J. Johnson, Giuliano Iurilli, et al. 2015. “Mapping Sub-Second Structure in Mouse Behavior.” Neuron 88 (6): 1121–35. https://doi.org/10.1016/j.neuron.2015.11.031.