Animal Papers Save

Animal Paper Collection (Ongoing)

[2023.12.14] Here is a workshop involving animals and infants CV4Smalls Workshop! Feel free to check it out!

[2023.11.26] My own paper "MAMMAL" is published online in Nature Communications now!

[2023.06.10] The program of CV4Animals Workshop in CVPR 2023 is available!

[2022.08.08] Here is the Ph.D thesis of SEMIH GÜNEL (https://infoscience.epfl.ch/record/293821), who is the author of well-known DeepFly3D and LiftPose3D.

[2022.06.22] The 2nd CV4Animals Workshop in CVPR 2022 (https://www.cv4animals.com/) presents many excellent works on rodent 3D reconstruction!

[2022.01.02] To make it easy to track, I sort the papers using the timepoint I find them (not publication time), and add label badges to show paper features.

[2021.11.28] I recommend MMPose for 2D animal pose estimation. It has collected various kinds of datasets.

[2021.07.16] I recommend CV4Animal workshop in CVPR 2021 (https://www.cv4animals.com/) because it is a good collection of recent advances in animal pose estimation area!

Recently, markerless animal motion capture and 3D reconstruction attracts more and more attention in computer vision community. Inspired by remarkable techniques for markerless human motion capture, a few excellent literatures appear for animal modeling and reconstruction such as SMAL and DeepLabCut. However, there is still a long way before computer vision methods could capture natural motion of arbitary animals in industrial-grade.

Therefore, I contribute this repository to track every step towards the ultimate goal of high quality animal capture. If you want to add/remove an article, please send an email to Liang An(al17 at mails dot tsinghua dot edu dot cn). Thank all the authors for their contribution and support.

	MarmoPose: A Deep Learning-Based System for Real-time Multi-Marmoset 3D Pose Tracking Chaoqun Cheng, Zijian Huang, Ruiming Zhang, Guozheng Huang, Han Wang, Likai Tang, Xiaoqin Wang In biorxiv 2024
	replicAnt: a pipeline for generating annotated images of animals in complex environments using Unreal Engine Fabian Plum, René Bulla, Hendrik K. Beck, Natalie Imirzian, David Labonte In Nature Communications 2023
	Investigating the use of odour and colour foraging cues by rosy-faced lovebirds (Agapornis roseicollis) using deep-learning based behavioural analysis Winson King Wai Tsang, Emily Shui Kei Poon, Chris Newman, Christina D. Buesching, Simon Yung Wa Sin In biorxiv 2024
	Automated 3D analysis of social head-gaze behaviors in freely moving marmosets Feng Xing, Alec G. Sheffield, Monika P. Jadi, Steve W.C Chang, Anirvan S. Nandy In biorxiv 2024
	A-SOiD, an active learning platform for expert-guided, data efficient discovery of behavior Jens F. Tillmann, Alexander I. Hsu, Martin K. Schwarz, Eric A. Yttri In Nature Methods 2024
	Anti-drift pose tracker (ADPT): A transformer-based network for robust animal pose estimation cross-species Guoling Tang, Yaning Han, Quanying Liu, Pengfei Wei In biorxiv 2024
	vmTracking: Virtual Markers Overcome Occlusion and Crowding in Multi-Animal Pose Tracking Hirotsugu Azechi, Susumu Takahashi In biorxiv 2024
	ARBUR, a machine learning-based analysis system for relating behaviors and ultrasonic vocalizations of rats Zhe Chen, Guanglu Jia, Qijie Zhou, Yulai Zhang, Zhenzhen Quan, Xuechao Chen, Toshio Fukuda, Qiang Huang, Qing Shi In biorxiv 2024
	WILDPOSE: A LONG-RANGE 3D WILDLIFE MOTION CAPTURE SYSTEM Naoya Muramatsu, Sangyun Shin, Qianyi Deng, Andrew Markham, Amir Patel In biorxiv 2024
	Combining Unity with machine vision to create low latency, flexible, and simple virtual realities Yuri Ogawa, Raymond Aoukar, Richard Leibbrandt, Jake S Manger, Zahra M Bagheri, Luke Turnbull, Chris Johnston, Pavan K Kaushik, Jan M Hemmi, Karin Nordström In biorxiv 2024
	MacAction: Realistic 3D macaque body animation based on multi-camera markerless motion capture Lucas M. Martini, Anna Bogn´ar, Rufin Vogels, Martin A. Giese In biorxiv 2024
	DAMM for the detection and tracking of multiple animals within complex social and environmental settings Gaurav Kaul, Jonathan McDevitt, Justin Johnson, Ada Eban-Rothschild In biorxiv 2024
	Computer Vision for Primate Behavior Analysis in the Wild Richard Vogg, Timo Luddecke, Jonathan Henrich, Sharmita Dey, Matthias Nuske, Valentin Hassler, Derek Murphy, Julia Fischer, Julia Ostner, Oliver Schulke, Peter M. Kappeler, Claudia Fichte, Alexander Gail, Stefan Treue, Hansjorg Scherberger, Florentin Worg otter, Alexander S. Ecker In arxiv 2024
	PanAf20K: A Large Video Dataset for Wild Ape Detection and Behaviour Recognition Otto Brookes et.al. In IJCV 2024
	Multi-animal 3D social pose estimation, identification and behaviour embedding with a few-shot learning framework Yaning Han, Ke Chen, Yunke Wang, Wenhao Liu, Zhouwei Wang, Xiaojing Wang, Chuanliang Han, Jiahui Liao, Kang Huang, Shengyuan Cai, Yiting Huang, Nan Wang, Jinxiu Li, Yangwangzi Song, Jing Li, Guodong Wang, Liping Wang, Yaping Zhang, Pengfei Wei In Nature Machine Intelligence 2024
	Facemap: a framework for modeling neural activity based on orofacial tracking Atika Syeda, Lin Zhong, Renee Tung, Will Long, Marius Pachitariu, Carsen Stringer In Nature Neuroscience 2023
	Three-dimensional surface motion capture of multiple freely moving pigs using MAMMAL Liang An, Jilong Ren, Tao Yu, Tang Hai, Yichang Jia, Yebin Liu In Nature Communications 2023
	DeepLabCut-based Behavioural and Posture Analysis in a Cricket Shota Hayakawa, Kosuke Kataoka, Masanobu Yamamoto, Toru Asahi, Takeshi Suzuki In biorxiv 2023
	Distinct developmental trajectories of autonomous behaviors and agency in rodents C Mitelut, M Diez Castro, RE Peterson, M Gonçalves, MM Gamer, SRO Nilsson, TD Pereira, DH Sanes In biorxiv 2023
	BARN: Behavior-Aware Relation Network for multi-label behavior detection in socially housed macaques Sen Yang, Zhi-Yuan Chen, Ke-Wei Liang, Cai-Jie Qin, Yang Yang, Wen-Xuan Fan, Chen-Lu Jie, Xi-Bo Ma In Zoological Research 2023
	CATER: Combined Animal Tracking & Environment Reconstruction Lars Haalck, Michael Mangan, Antoine Wystrach, Leo Clement, Barbara Webb, Benjamin Risse In Science Advances 2023
	SMART-BARN: Scalable multimodal arena for real-time tracking behavior of animals in large numbers Máté Nagy, Hemal Naik, Fumihiro Kano, Nora V. Carlson, Jens C. Koblitz, Martin Wikelski, Iain D. Couzin In Science Advances 2023
	Hierarchical organization of rhesus macaque behavior Benjamin Voloh, Benjamin R. Eisenreich, David J-N. Maisson, R. Becket Ebitz, Hyun Soo Park, Benjamin Y. Hayden, Jan Zimmermann In Oxford Open Neuroscience 2023
	Open-source tools for behavioral video analysis: Setup, methods, and best practices Kevin Luxem, Jennifer J Sun, Sean P Bradley, Keerthi Krishnan, Eric Yttri, Jan Zimmermann, Talmo D Pereira, Mark Laubach In Elife 2023
	Automated measurement of livestock body based on pose normalisation using statistical shape model Xinying Luo, Yihu Hu, Zicheng Gao, Hao Guo, Yang Su In Biosystems Engineering 2023
	Establishing an AI-based evaluation system that quantifies social/pathophysiological behaviors of common marmosets Takaaki Kaneko, Jumpei Matsumoto, Wanyi Lu, Xincheng Zhao, Louie Richard UenoNigh, Takao Oishi, Kei Kimura, Yukiko Otsuka, Andi Zheng, Kensuke Ikenaka, Kousuke Baba, Hideki Mochizuki, Hisao Nishijo, Ken-ichi Inoue, Masahiko Takada In biorxiv 2023
	Long-term tracking of social structure in groups of rats M´at´e Nagy, Jacob D. Davidson, G´abor V´as´arhelyi, D´aniel Abel, Enik˝o Kubinyi, Ahmed El Hady, Tam´as Vicsek In biorxiv 2023
	Automatically annotated motion tracking identifies a distinct social behavioral profile following chronic social defeat stress Joeri Bordes, Lucas Miranda, Maya Reinhardt, Sowmya Narayan, Jakob Hartmann, Emily L. Newman, Lea Maria Brix, Lotte van Doeselaar, Clara Engelhardt, Larissa Dillmann, Shiladitya Mitra, Kerry J. Ressler, Benno Pütz, Felix Agakov, Bertram Müller-Myhsok, Mathias V. Schmidt In Nature Communications 2023
	LoTE-Animal: A Long Time-span Dataset for Endangered Animal Behavior Understanding Dan Liu, Jin Hou, Shaoli Huang, Jing Liu, Yuxin He, Bochuan Zheng, Jifeng Ning, Jindong Zhang In ICCV 2023
	Stimulatory effect of monoacylglycerol lipase inhibitor MJN110 on locomotion and step kinematics demonstrated by high-precision 3D motion capture in mice Bogna M. Ignatowska-Jankowska, Aysen Gurkan Ozer, Alexander Kuck, Micah J. Niphakis, Daisuke Ogasawara, Benjamin F. Cravatt, Marylka Y. Uusisaari In biorxiv 2023
	NeuroMechFly 2.0, a framework for simulating embodied sensorimotor control in adult Drosophila Sibo Wang-Chen, Victor Alfred Stimpfling, Pembe Gizem Ozdil, Louise Genoud, Femke Hurtak, Pavan Ramdya In biorxiv 2023
	Simultaneous recording of ultrasonic vocalizations and sniffing from socially interacting individual rats using a miniature microphone Shanah Rachel John, Rishika Tiwari, Yizhaq Goussha, Rotem Amar, Alex Bizer, Shai Netser, Shlomo Wagner In biorxiv 2023
	Automated Maternal Behavior during Early life in Rodents (AMBER) pipeline Hannah E. Lapp, Melissa G. Salazar, Frances A. Champagne In biorxiv 2023
	Three-dimensional markerless motion capture of multiple freely behaving monkeys for automated characterization of social behavior Jumpei Matsumoto, Takaaki Kaneko, Kei Kimura, Salvador Blanco Negrete, Jia Guo, Naoko Suda-Hashimoto, Akihisa Kaneko, Mayumi Morimoto, Hiroshi Nishimaru, Tsuyoshi Setogawa, Yasuhiro Go, Tomohiro Shibata, Hisao Nishijo, Masahiko Takada, Ken-ichi Inoue In biorxiv 2023
	3D mouse pose from single‑view video and a new dataset Bo Hu, Bryan Seybold, Shan Yang, Avneesh Sud, Yi Liu, Karla Barron, Paulyn Cha, Marcelo Cosino, Ellie Karlsson, Janessa Kite, Ganesh Kolumam, Joseph Preciado, José Zavala‑Solorio, Chunlian Zhang, Xiaomeng Zhang, Martin Voorbach, Ann E.Tovcimak, J.Graham Ruby, David A. Ross In Scientific Reports 2023
	Animal3D: A Comprehensive Dataset of 3D Animal Pose and Shape Jiacong Xu, Yi Zhang, Jiawei Peng, Wufei Ma, Artur Jesslen, Pengliang Ji, Qixin Hu, Jiehua Zhang, Qihao Liu, Jiahao Wang, Wei Ji, Chen Wang, Xiaoding Yuan, Prakhar Kaushik, Guofeng Zhang, Jie Liu, Yushan Xie, Yawen Cui, Alan Yuille, Adam Kortylewski In ICCV 2023
	PPR: Physically Plausible Reconstruction from Monocular Videos Gengshan Yang, Shuo Yang, John Z. Zhang, Zachary Manchester, Deva Ramanan In ICCV 2023
	AmadeusGPT: a natural language interface for interactive animal behavioral analysis Shaokai Ye, Jessy Lauer, Mu Zhou, Alexander Mathis, Mackenzie Weygandt Mathis In NeurIPS 2023
	ARTIC3D: Learning Robust Articulated 3D Shapes from Noisy Web Image Collections Chun-Han Yao, Amit Raj, Wei-Chih Hung, Yuanzhen Li, Michael Rubinstein, Ming-Hsuan Yang, Varun Jampani In arxiv 2023
	Behavioral decomposition reveals rich encoding structure employed across neocortex in rats Bartul Mimica, Tuçe Tombaz, Claudia Battistin, Jingyi Guo Fuglstad, Benjamin A. Dunn, Jonathan R. Whitlock In Nature Communications 2023
	MABe22: A Multi-Species Multi-Task Benchmark for Learned Representations of Behavior Jennifer J. Sun, Markus Marks, Andrew W. Ulmer, Dipam Chakraborty, Brian Geuther, Edward Hayes, Heng Jia, Vivek Kumar, Sebastian Oleszko, Zachary Partridge, Milan Peelman, Alice Robie, Catherine E. Schretter, Keith Sheppard, Chao Sun, Param Uttarwar, Julian M. Wagner, Erik Werner, Joseph Parker, Pietro Perona, Yisong Yue, Kristin Branson, Ann Kennedy In ICML 2023
	3D-POP - An automated annotation approach to facilitate markerless 2D-3D tracking of freely moving birds with marker-based motion capture Hemal Naik, Alex Hoi Hang Chan, Junran Yang, Mathilde Delacoux, Iain D. Couzin, Fumihiro Kano, Mate Nagy In CVPR 2023
	SuperAnimal models pretrained for plug-and-play analysis of animal behavior Shaokai Ye, Anastasiia Filippova, Jessy Lauer, Maxime Vidal, Steffen Schneider, Tian Qiu, Alexander Mathis, Mackenzie Weygandt Mathis In arxiv 2023
	CatFLW: Cat Facial Landmarks in the Wild Dataset George Martvel, Nareed Farhat, Ilan Shimshoni, Anna Zamansky In CV4Animals Workshop in CVPR 2023
	Decompose to Generalize: Species-Generalized Animal Pose Estimation Guangrui Li, Yifan Sun, Zongxin Yang, Yi Yang In ICLR 2023
	MammalNet: A Large-scale Video Benchmark for Mammal Recognition and Behavior Understanding Jun Chen, Ming Hu, Darren J. Coker, Michael L. Berumen, Blair Costelloe, Sara Beery, Anna Rohrbach, Mohamed Elhoseiny In CVPR 2023
	Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics Caleb Weinreb, Mohammed Abdal Monium Osman, Libby Zhang, Sherry Lin, Jonah Pearl, Sidharth Annapragada, Eli Conlin, Winthrop F. Gillis, Maya Jay, Ye Shaokai, Alexander Mathis, Mackenzie Weygandt Mathis, Talmo Pereira, Scott W. Linderman, Sandeep Robert Datta In biorxiv 2023
	BITE: Beyond Priors for Improved Three-D Dog Pose Estimation Nadine Rüegg, Shashank Tripathi, Konrad Schindler, Michael J. Black, Silvia Zuffi In CVPR 2023
	MagicPony: Learning Articulated 3D Animals in the Wild Shangzhe Wu, Ruining Li, Tomas Jakab, Christian Rupprecht, Andrea Vedaldi In CVPR 2023
	CLAMP: Prompt-based Contrastive Learning for Connecting Language and Animal Pose Xu Zhang, Wen Wang, Zhe Chen, Yufei Xu, Jing Zhang, Dacheng Tao In CVPR 2023
	3D shape reconstruction of semi-transparent worms Thomas P. Ilett, Omer Yuval, Thomas Ranner, Netta Cohen, David C. Hogg In CVPR 2023
	A robust and flexible deep-learning workflow for animal tracking Abhishek Dutta, Natalia Pérez-Campanero, Graham K. Taylor, Andrew Zisserman, Cait Newport In biorxiv 2023
	Analysis of antennal responses to motion stimuli in the honey bee by automated tracking using DeepLabCut Hiroki Kohno, Shuichi Kamata, Takeo Kubo In biorxiv 2023
	Learning Articulated Shape with Keypoint Pseudo-labels from Web Images Anastasis Stathopoulos, Georgios Pavlakos, Ligong Han, Dimitris Metaxas In CVPR 2023
	Farm3D: Learning Articulated 3D Animals by Distilling 2D Diffusion Tomas Jakab, Ruining Li, Shangzhe Wu, Christian Rupprecht, Andrea Vedaldi In arxiv 2023
	Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second Kevin C. Zhou, Mark Harfouche, Colin L. Cooke, Jaehee Park, Pavan C. Konda, Lucas Kreiss, Kanghyun Kim, Joakim Jönsson, Thomas Doman, Paul Reamey, Veton Saliu, Clare B. Cook, Maxwell Zheng, John P. Bechtel, Aurélien Bègue, Matthew McCarroll, Jennifer Bagwell, Gregor Horstmeyer, Michel Bagnat, Roarke Horstmeyer In Nature Photonics 2023
	Scalable Apparatus to Measure Posture and Locomotion (SAMPL): a high-throughput solution to study unconstrained vertical behavior in small animals Yunlu Zhu, Franziska Auer, Hannah Gelnaw, Samantha N. Davis, Kyla R. Hamling, Christina E. May, Hassan Ahamed, Niels Ringstad, Katherine I. Nagel, David Schoppik In biorxiv 2023
	ScarceNet: Animal Pose Estimation with Scarce Annotations Chen Li, Gim Hee Lee In CVPR 2023
	Lights, Camera, Mirrors, Action! Toolbox for 3D Analysis of High-rate Maneuvers Using a Single Camera and Planar Mirrors Wajahat Hussain, Mahum Naveed, Asad Khan, Taimoor Hasan Khan, Muhammad Latif Anjum, Shahzad Rasool, Adnan Maqsood In biorxiv 2023
	Unsupervised decomposition of natural monkey behavior into a sequence of motion motifs Koki Mimura, Jumpei Matsumoto, Daichi Mochihashi, Tomoaki Nakamura, Toshiyuki Hirabayashi, Makoto Higuchi, Takafumi Minamimoto In biorxiv 2023
	ArMo: An Articulated Mesh Approach for Mouse 3D Reconstruction James P. Bohnslav, Mohammed Abdal Monium Osman, Akshay Jaggi, Sofia Soares, Caleb Weinreb, Sandeep Robert Datta, Christopher D. Harvey In biorxiv 2023
	Predicting long-term collective animal behavior with deep learning Vaios Papaspyros, Ram´on Escobedo, Alexandre Alahi, Guy Theraulaz, Cl´ement Sire, Francesco Mondada In biorxiv 2023
	Three‑dimensional unsupervised probabilistic pose reconstruction (3D‑UPPER) for freely moving animals Aghileh S. Ebrahimi, Patrycja Orlowska‑Feuer, Qian Huang, AntonioG. Zippo, Franck P. Martial, Rasmus S. Petersen, Riccardo Storchi In Scientific Reports 2023
	A review of 28 free animal-tracking software applications: current features and limitations Veronica Panadeiro, Alvaro Rodriguez, Jason Henry, Donald Wlodkowic, Magnus Andersson In Lab Animal 2021
	JAX Animal Behavior System (JABS): A video-based phenotyping platform for the laboratory mouse Glen Beane, Brian Q. Geuther, Thomas J. Sproule, Anshul Choudhary, Jarek Trapszo, Leinani Hession, Vivek Kohar, Vivek Kumar In biorxiv 2023
	An 8-cage imaging system for automated analyses of mouse behavior Thaís Del Rosario Hernández, Narendra R. Joshi, Sayali V. Gore, Jill A. Kreiling, Robbert Creton In biorxiv 2023
	Quantifying the movement, behavior, and environmental context of group-living animals using drones and computer vision Benjamin Koger, Adwait Deshpande, Jeffrey T. Kerby, Jacob M. Graving, Blair R. Costelloe, Iain D. Couzin In Journal of Animal Ecology 2023
	Gait-level analysis of mouse open field behavior using deep learning-based pose estimation Keith Sheppard, Justin Gardin, Gautam Sabnis, Asaf Peer, Megan Darrell, Sean Deats, Brian Geuther, Cathleen M. Lutz, Vivek Kumar In Cell Reports 2022
	Markerless tracking of an entire honey bee colony Katarzyna Bozek, Laetitia Hebert, Yoann Portugal, Alexander S. Mikheyev, Greg J. Stephens In Nature Communications 2021
	Capturing the continuous complexity of behaviour in Caenorhabditis elegans Tosif Ahamed, Antonio C. Costa, Greg J. Stephens In Nature Physics 2020
	ConstrastivePose: A contrastive learning approach for self-supervised feature engineering for pose estimation and behavorial classification of interacting animals Tianxun Zhou, Calvin Chee Hoe Cheah, Eunice Wei Mun Chin, Jie Chen, Hui Jia Farm, Eyleen Lay Keow Goh, Keng Hwee Chiam In biorxiv 2022
	Common Pets in 3D: Dynamic New-View Synthesis of Real-Life Deformable Categories Samarth Sinha, Roman Shapovalov, Jeremy Reizenstein, Ignacio Rocco, Natalia Neverova, Andrea Vedaldi, David Novotny In arxiv 2022
	B-SOiD, an open-source unsupervised algorithm for identification and fast prediction of behaviors Alexander I. Hsu, Eric A. Yttri In Nature Communications 2022
	Estimation of skeletal kinematics in freely moving rodents Arne Monsees, Kay-Michael Voit, Damian J. Wallace, Juergen Sawinski, Edyta Charyasz, Klaus Scheffler, Jakob H. Macke, Jason N. D. Kerr In Nature Methods 2022
	OpenLabCluster: Active Learning Based Clustering and Classification of Animal Behaviors in Videos Based on Automatically Extracted Kinematic Body Keypoints Jingyuan Li, Moishe Keselman, Eli Shlizerman In biorxiv 2022
	LASSIE: Learning Articulated Shapes from Sparse Image Ensemble via 3D Part Discovery Chun-Han Yao, Wei-Chih Hung, Yuanzhen Li, Michael Rubinstein, Ming-Hsuan Yang, Varun Jampani In NeurIPS 2022
	Evaluation of mouse behavioral responses to nutritive versus nonnutritive sugar using a deep learning-based 3D real-time pose estimation system Jineun Kim, Dae-gun Kim, Wongyo Jung, Greg S. B. Suh In biorxiv 2022
	Development of a new 3D tracking system for multiple marmosets under free-moving conditions Terumi Yurimoto, Wakako Kumita, Kenya Sato, Rika Kikuchi, Yusuke Shibuki, Rino Hashimoto, Michiko Kamioka, Yumi Hayasegawa, Eiko Yamazaki, Yoko Kurotaki, Norio Goda, Junichi Kitakami, Tatsuya Fujita, Takashi Inoue, Erika Sasaki In biorxiv 2022
	LabGym: quantification of user-defined animal behaviors using learning-based holistic assessment Yujia Hu, Carrie R. Ferrario, Alexander D. Maitland, Rita B. Ionides, Anjesh Ghimire, Brendon Watson, Kenichi Iwasaki, Hope White, Yitao Xi, Jie Zhou, Bing Ye In Cell Reports Methods 2022
	BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking Christopher J Gabriel, Zachary Zeidler, Benita Jin, Changliang Guo, Caitlin M Goodpaster, Adrienne Q Kashay, Anna Wu, Molly Delaney, Jovian Cheung, Lauren E DiFazio, Melissa J Sharpe, Daniel Aharoni, Scott A Wilke, Laura A DeNardo In eLife 2022
	Cross-Skeleton Interaction Graph Aggregation Network for Representation Learning of Mouse Social Behaviour Feixiang Zhou, Xinyu Yang, Fang Chen, Long Chen, Zheheng Jiang, Hui Zhu, Reiko Heckel, Haikuan Wang, Minrui Fei, Huiyu Zhou In arxiv 2022
	Animal pose estimation: A closer look at the state-of-the-art, existing gaps and opportunities Le Jiang, Caleb Lee, Divyang Teotia, Sarah Ostadabbas In Computer Vision and Image Understanding (CVIU) 2022
	3D pose estimation enables virtual head fixation in freely moving rats Artur Schneider, Christian Zimmermann, Mansour Alyahyay, Florian Steenbergen, Thomas Brox, Ilka Diester In Neuron 2022
	Natural behavior is the language of the brain Cory T. Miller, David Gire, Kim Hoke, Alexander C. Huk, Darcy Kelley, David A. Leopold, Matthew C. Smear, Frederic Theunissen, Michael Yartsev, Cristopher M. Niell In Current Biology 2022
	Deep-learning based identification, tracking, pose estimation, and behavior classification of interacting primates and mice in complex environments Markus Marks, Jin Qiuhan, Oliver Sturman, Lukas von Ziegler, Sepp Kollmorgen, Wolfger von der Behrens, Valerio Mante, Johannes Bohacek, Mehmet Fatih Yanik In Nature Machine Intelligence 2022
	EXPLORE: A novel deep learning-based analysis method for exploration behaviour in object recognition tests Victor Iba˜nez, Laurens Bohlen, Francesca Manuell, Isabelle Mansuy, Fritjof Helmchen, Anna-Sophia Wahl In biorxiv 2022
	TRex, a fast multi-animal tracking system with markerless identification, 2D body posture estimation and visual field reconstruction Tristan Walter, Iain D Couzin In eLife 2021
	Unsupervised behaviour analysis and magnification (uBAM) using deep learning Biagio Brattoli, Uta Büchler, Michael Dorkenwald, Philipp Reiser, Linard Filli, Fritjof Helmchen, Anna-Sophia Wahl, Björn Ommer In Nature Machine Intelligence 2021
	Leaving Flatland: Advances in 3D behavioral measurement Jesse D. Marshall, Tianqing Li, Joshua H. Wu, Timothy W. Dunn In Current Opinion in Neurobiology 2022
	Improved Markerless 3D Animal Pose Estimation Using Temporal Semi-Supervision Tianqing Li, Kyle S. Severson, Fan Wang, Timothy W. Dunn In CV4Animal workshop at CVPR 2022
	A whole-body musculoskeletal model of the mouse Shravan Tata Ramalingasetty, Simon M. Danner, Jonathan Arreguit, Sergey N. Markin, Dimitri Rodarie, Claudia Kathe, Grégoire Courtine, Ilya A. Rybak, Auke Ijspeert In IEEE Access 2021
	AVATAR: AI Vision Analysis for Three-dimensional Action in Real-time Dae-Gun Kim, Anna Shin, Yong-Cheol Jeong, Seahyung Park, Daesoo Kim In biorxiv 2022
	TAVA: Template-free Animatable Volumetric Actors Ruilong Li, Julian Tanke, Minh Vo, Michael Zollhoefer, Jurgen Gall, Angjoo Kanazawa, Christoph Lassner In ECCV 2022
	Selfee, Self-supervised Features Extraction of animal behaviors Yinjun Jia, Shuaishuai Li, Xuan Guo, Bo Lei, Junqiang Hu, Xiao-Hong Xu, Wei Zhang In Elife 2022
	NeuroMechFly, a neuromechanical model of adult Drosophila melanogaster Victor Lobato Rios, Pembe Gizem Ozdil, Shravan Tata Ramalingasetty, Jonathan Arreguit, Auke Jan Ijspeert, Pavan Ramdya In Nature Methods 2022
	SemiMultiPose: A Semi-supervised Multi-animal Pose Estimation Framework Ari Blau, Christoph Gebhardt, Andres Bendesky, Liam Paninski, Anqi Wu In arxiv 2022
	Animal Kingdom: A Large and Diverse Dataset for Animal Behavior Understanding Xun Long Ng, Kian Eng Ong, Qichen Zheng, Yun Ni, Si Yong Yeo, Jun Liu In CVPR 2022 (oral)
	Multi-animal pose estimation, identification and tracking with DeepLabCut Jessy Lauer, Mu Zhou, Shaokai Ye, William Menegas, Steffen Schneider, Tanmay Nath, Mohammed Mostafizur Rahman, Valentina Di Santo, Daniel Soberanes, Guoping Feng, Venkatesh N. Murthy, George Lauder, Catherine Dulac, Mackenzie Weygandt Mathis, Alexander Mathis In Nature Methods 2022
	SLEAP: A deep learning system for multi-animal pose tracking Talmo D. Pereira, Nathaniel Tabris, Arie Matsliah, David M. Turner, Junyu Li, Shruthi Ravindranath, Eleni S. Papadoyannis, Edna Normand, David S. Deutsch, Z. Yan Wang, Grace McKenzie-Smith, Catalin C. Mitelut, Marielisa Diez Castro, John D'Uva, Mikhail Kislin, Dan H. Sanes, Sarah D. Kocher, Samuel S.-H. Wang, Annegret L. Falkner, Joshua W. Shaevitz, Mala Murthy In Nature Methods 2022
	BARC: Learning to Regress 3D Dog Shape from Images by Exploiting Breed Information Nadine Ruegg, Silvia Zuffi, Konrad Schindler, Michael J. Black In CVPR 2022
	Artemis: Articulated Neural Pets with Appearance and Motion Synthesis Haimin Luo, Teng Xu, Yuheng Jiang, Chenglin Zhou, Qiwei Qiu, Yingliang Zhang, Wei Yang, Lan Xu, Jingyi Yu In TOG (Siggraph) 2022
	Automatic mapping of multiplexed social receptive fields by deep learning and GPU-accelerated 3D videography Christian L. Ebbesen, Robert C. Froemke In Nature Communications 2022
	BANMo: Building Animatable 3D Neural Models from Many Casual Videos Gengshan Yang, Minh Vo, Natalia Neverova, Deva Ramanan, Andrea Vedaldi, Hanbyul Joo In CVPR 2022
	Overcoming the Domain Gap in Neural Action Representations Semih Gunel, Florian Aymanns, Sina Honari, Pavan Ramdya, Pascal Fua In arxiv 2021
	Incremental Learning for Animal Pose Estimation using RBF k-DPP Gaurav Kumar Nayak, Het Shah, Anirban Chakraborty In BMVC 2021
	Muti-view Mouse Social Behaviour Recognition with Deep Graphic Model Zheheng Jiang, Feixiang Zhou, Aite Zhao, Xin Li, Ling Li, Dacheng Tao, Xuelong Li, Huiyu Zhou In TIP 2021
	MouseVenue3D: A Markerless Three-Dimension Behavioral Tracking System for Matching Two-Photon Brain Imaging in Free-Moving Mice Yaning Han, Kang Huang, Ke Chen, Hongli Pan, Furong Ju, Yueyue Long, Gao Gao, Runlong Wu, Aimin Wang, Liping Wang, Pengfei Wei In Neuroscience Bulletin 2021
	Multi-camera real-time threedimensional tracking of multiple flying animals Andrew D. Straw, Kristin Branson, Titus R. Neumann, Michael H. Dickinson In J. R. Soc. Interface 2011
	The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice Cristina Segalin, Jalani Williams, Tomomi Karigo, May Hui, Moriel Zelikowsky, Jennifer J Sun, Pietro Perona, David J Anderson, Ann Kennedy In eLife 2021
	Self-Supervised Keypoint Discovery in Behavioral Videos Jennifer J. Sun, Serim Ryou, Roni Goldshmid, Brandon Weissbourd, John Dabiri, David J. Anderson, Ann Kennedy, Yisong Yue, Pietro Perona In arxiv 2021
	The Multi-Agent Behavior Dataset: Mouse Dyadic Social Interactions Jennifer J. Sun, Tomomi Karigo, Dipam Chakraborty, Sharada P. Mohanty, David J. Anderson, Pietro Perona, Yisong Yue, Ann Kennedy In NeurIPS (Dataset & Benchmarks) 2021
	Task Programming: Learning Data Efficient Behavior Representations Jennifer J. Sun, Ann Kennedy, Eric Zhan, David J. Anderson, Yisong Yue, Pietro Perona In CVPR 2021 (Best Student Paper Award)
	Coarse-to-fine Animal Pose and Shape Estimation Chen Li, Gim Hee Lee In NeurIPS 2021
	Unified 3D Mesh Recovery of Humans and Animals by Learning Animal Exercise Kim Youwang, Kim Ji-Yeon, Kyungdon Joo, Tae-Hyun Oh In BMVC 2021
	Anipose: a toolkit for robust markerless 3D pose estimation Pierre Karashchuk, Katie L. Rupp, Evyn S. Dickinson, SarahWalling-Bell, Elischa Sanders, Eiman Azim, Bingni W. Brunton, John C. Tuthill In Cell Reports (Resource) 2021
	Multimodal-based Scene-Aware Framework for Aquatic Animal Segmentation Minh-Quan Le, Trung-Nghia Le, Tam V. Nguyen, Isao Echizen, Minh-Triet Tran In arxiv 2021
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	Facial expressions of emotion states and their neuronal correlates in mice Nejc Dolensek, Daniel A. Gehrlach, Alexandra S. Klein, Nadine Gogolla In Science 2020
	ZooBuilder: 2D and 3D Pose Estimation for Quadrupeds Using Synthetic Data Abassin Sourou Fangbemi, Yi Fei Lu, Mao Yuan Xu, Xiao Wu Luo, Alexis Rolland, Chedy Raissi In SCA (ACM Siggraph/Eurographics Symposium on Computer Animation) 2020
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	EthoLoop: automated closed-loop neuroethology in naturalistic environments Ali Nourizonoz, Robert Zimmermann, Chun Lum Andy Ho, Sebastien Pellat, Yannick Ormen, Clément Prévost-Solié, Gilles Reymond, Fabien Pifferi, Fabienne Aujard, Anthony Herrel, Daniel Huber In Nature Methods 2020 (cover)
	Automated Markerless Pose Estimation in Freely Moving Macaques using OpenMonkeyStudio Praneet C. Bala, Benjamin R. Eisenreich, Seng Bum Michael Yoo, Benjamin Y. Hayden, Hyun Soo Park, Jan Zimmermann In Nature Communications 2020
	3D Bird Reconstruction: a Dataset, Model, and Shape Recovery from a Single View Marc Badger, Yufu Wang, Adarsh Modh, Ammon Perkes, Nikos Kolotouros, Bernd Pfrommer, Marc F. Schmidt, Kostas Daniilidis In ECCV 2020
	Who Left the Dogs Out? 3D Animal Reconstruction with Expectation Maximization in the Loop Benjamin Biggs, Oliver Boyne, James Charles, Andrew Fitzgibbon, Roberto Cipolla In ECCV 2020
	Shape and Viewpoint without Keypoints Shubham Goel, Angjoo Kanazawa, Jitendra Malik In ECCV 2020
	Deep Cross-species Feature Learning for Animal Face Recognition via Residual Interspecies Equivariant Network Xiao Shi, Chenxue Yang, Xue Xia, Xiujuan Chai In ECCV 2020
	RGBD-Dog: Predicting Canine Pose from RGBD Sensors Sinead Kearney, Wenbin Li, Martin Parsons, Kwang In Kim, Darren Cosker In CVPR 2020
	AnimalWeb: A Large-Scale Hierarchical Dataset of Annotated Animal Faces Muhammad Haris Khan, John McDonagh, Salman Khan, Muhammad Shahabuddin, Aditya Arora, Fahad Shahbaz Khan, Ling Shao, Georgios Tzimiropoulos In CVPR 2020
	Articulation Aware Canonical Surface Mapping Nilesh Kulkarni, Abhinav Gupta, David F. Fouhey, Shubham Tulsiani In CVPR 2020
	Deformation-aware Unpaired Image Translation for Pose Estimation on Laboratory Animals Siyuan Li, Semih Gunel, Mirela Ostrek, Pavan Ramdya, Pascal Fua, Helge Rhodin In CVPR 2020
	Learning from Synthetic Animals Jiteng Mu, Weichao Qiu, Gregory Hager, Alan Yuille In CVPR 2020 (oral)
	3D-ZeF: A 3D Zebrafish Tracking Benchmark Dataset Malte Pedersen, Joakim Bruslund Haurum, Stefan Hein Bengtson, Thomas B. Moeslund In CVPR 2020
	Transferring Dense Pose to Proximal Animal Classes Artsiom Sanakoyeu, Vasil Khalidov, Maureen S. McCarthy, Andrea Vedaldi, Natalia Neverova In CVPR 2020
	Unsupervised Learning of Probably Symmetric Deformable 3D Objects from Images in the Wild Shangzhe Wu, Christian Rupprecht, Andrea Vedaldi In CVPR 2020 (Best Paper Award)
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	Using DeepLabCut for 3D markerless pose estimation across species and behaviors Tanmay Nath, Alexander Mathis, An Chi Chen, Amir Patel, Matthias Bethge, Mackenzie Weygandt Mathis In Nature Protocols 2019 (cover)
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	Real-time analysis of the behaviour of groups of mice via a depth-sensing camera and machine learning Fabrice de Chaumont, Elodie Ey, Nicolas Torquet, Thibault Lagache, Stéphane Dallongeville, Albane Imbert, Thierry Legou, Anne-Marie Le Sourd, Philippe Faure, Thomas Bourgeron, Jean-Christophe Olivo-Marin In Nature Biomedical Engineering 2019
	Cross-Domain Adaptation for Animal Pose Estimation Jinkun Cao, Hongyang Tang, Hao-Shu Fang, Xiaoyong Shen, Cewu Lu, Yu-Wing Tai In ICCV 2019 (oral)
	Canonical Surface Mapping via Geometric Cycle Consistency Nilesh Kulkarni, Abhinav Gupta, Shubham Tulsiani In ICCV 2019
	MONET: Multiview Semi-supervised Keypoint Detection via Epipolar Divergence Yuan Yao, Yasamin Jafarian, Hyun Soo Park In ICCV 2019
	Three-D Safari: Learning to Estimate Zebra Pose, Shape, and Texture from Images "In the Wild" Silvia Zuffi, Angjoo Kanazawa, Tanya Berger-Wolf, Michael J. Black In ICCV 2019
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	Learning Category-Specific Mesh Reconstruction from Image Collections Angjoo Kanazawa, Shubham Tulsiani, Alexei A. Efros, Jitendra Malik In ECCV 2018
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	Single-View 3D Reconstruction of Animals Angjoo Kanazawa In Ph.D Thesis 2017
	3D Menagerie: Modeling the 3D shape and pose of animals Silvia Zuffi, Angjoo Kanazawa, David W. Jacobs, Michael J. Black In CVPR 2017 (spotlight)
	3D Pose Estimation of Flying Animals in Multi-view Video Datasets Mikhail Breslav In Ph.D Thesis 2016
	Learning 3D Deformation of Animals from 2D Images Angjoo Kanazawa, Shahar Kovalsky, Ronen Basri, David W. Jacobs In Eurographics 2016 (Günter Enderle Best Paper Award)
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Last updated in Mar 2024

This repository is inspired by Cat Papers with some code borrowed from it. Paper and project signs are taken from http://kesen.realtimerendering.com/.