The animal_papers from limzh00

Animal Paper Collection (Ongoing)

[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.

	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 biorxiv 2021 [Paper]
	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 biorxiv 2021 [Paper] [Project]
	OpenMonkeyChallenge: Dataset and Benchmark Challenges for Pose Tracking of Non-human Primates Yuan Yao, Abhiraj Mohan, Eliza Bliss-Moreau, Kristine Coleman, Sienna M. Freeman, Christopher J. Machado, Jessica Raper, Jan Zimmermann, Benjamin Y. Hayden, Hyun Soo Park In biorxiv 2021 [Paper] [Project]
	ThruTracker: Open-Source Software for 2-D and 3-D Animal Video Tracking Aaron J. Corcoran, Michael R. Schirmacher, Eric Black, Tyson L. Hedrick In biorxiv 2021 [Paper]
	A Novel Dataset for Keypoint Detection of Quadruped Animals from Images Prianka Banik, Lin Li, Xishuang Dong In arxiv 2021 [Paper]
	Big behavior: challenges and opportunities in a new era of deep behavior profiling Lukas von Ziegler, Oliver Sturman, Johannes Bohacek In Neuropsychopharmacology 2021 [Paper]
	AP-10K: A Benchmark for Animal Pose Estimation in the Wild Hang Yu, Yufei Xu, Jing Zhang, Wei Zhao, Ziyu Guan, Dacheng Tao In NeurIPS 2021 [Paper] [Project]
	Across-animal odor decoding by probabilistic manifold alignment Pedro Herrero-Vidal, Dmitry Rinberg, Cristina Savin In NeurIPS 2021 [Paper]
	Coarse-to-fine Animal Pose and Shape Estimation Chen Li, Gim Hee Lee In NeurIPS 2021 [Paper]
	Learning interaction rules from multi-animal trajectories via augmented behavioral models Keisuke Fujii, Naoya Takeishi, Kazushi Tsutsui, Emyo Fujioka, Nozomi Nishiumi, Ryoya Tanaka, Mika Fukushiro, Kaoru Ide, Hiroyoshi Kohno, Ken Yoda, Susumu Takahashi, Shizuko Hiryu, Yoshinobu Kawahara In NeurIPS 2021 [Paper]
	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 2021 [Paper] [Project]
	The PAIR-R24M Dataset for Multi-animal 3D Pose Estimation Jesse Marshall, Ugne Klibaite, Amanda Gellis, Diego Aldarondo, Bence O¨lveczky, Tim Dunn In NeurIPS 2021 [Paper] [Project]
	DeepImageJ: A user-friendly environment to run deep learning models in ImageJ Estibaliz Gómez-de-Mariscal, Carlos García-López-de-Haro, Wei Ouyang, Laurène Donati, Emma Lundberg, Michael Unser, Arrate Muñoz-Barrutia, Daniel Sage In Nature Methods (brief communication) 2021 [Paper] [Project]
	A three-dimensional virtual mouse generates synthetic training data for behavioral analysis Luis A. Bolaños, Dongsheng Xiao, Nancy L. Ford, Jeff M. LeDue, Pankaj K. Gupta, Carlos Doebeli, Hao Hu, Helge Rhodin, Timothy H. Murphy In Nature Methods (Brief Communication) 2021 (cover) [Paper] [Project]
	Geometric deep learning enables 3D kinematic profiling across species and environments Timothy W. Dunn, Jesse D. Marshall, Kyle S. Severson, Diego E. Aldarondo, David G. C. Hildebrand, Selmaan N. Chettih, William L. Wang, Amanda J. Gellis, David E. Carlson, Dmitriy Aronov, Winrich A. Freiwald, Fan Wang, Bence P. Ölveczky In Nature Methods 2021 [Paper] [Project]
	LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals Adam Gosztolai, Semih Gunel, Marco Pietro Abrate, Daniel Morales, Victor Lobato Rios, Helge Rhodin, Pascal Fua, Pavan Ramdya In Nature Methods 2021 [Paper] [Project]
	A Hierarchical 3D-motion Learning Framework for Animal Spontaneous Behavior Mapping Kang Huang, Yaning Han, Ke Chen, Hongli Pan, Wenling Yi, Xiaoxi Li, Siyuan Liu, Liping Wang, Pengfei Wei In Nature Communications 2021 [Paper] [Project]
	4DComplete: Non-Rigid Motion Estimation Beyond the Observable Surface Yang Li, Hikari Takehara, Takafumi Taketomi, Bo Zheng, Matthias Nießner In ICCV 2021 [Paper] [Project]
	DensePose 3D: Lifting Canonical Surface Maps of Articulated Objects to the Third Dimension Roman Shapovalov, David Novotny, Benjamin Graham, Patrick Labatut, Andrea Vedaldi In ICCV 2021 [Paper]
	Body language signals for rodent social communication Christian L. Ebbesen, Robert C. Froemke In Current Opinion in Neurobiology 2021 [Paper]
	DeepLabStream enables closed-loop behavioral experiments using deep learning-based markerless, real-time posture detection Jens F. Schweihoff, Matvey Loshakov, Irina Pavlova, Laura Kück, Laura A. Ewell, Martin K. Schwarz In Communications Biology 2021 [Paper] [Project]
	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 [Paper] [Project]
	Birds of a Feather: Capturing Avian Shape Models from Images Yufu Wang, Nikos Kolotouros, Kostas Daniilidis, Marc Badger In CVPR 2021 [Paper] [Project]
	Discovering Relationships between Object Categories via Universal Canonical Maps Natalia Neverova, Artsiom Sanakoyeu, Patrick Labatut, David Novotny, Andrea Vedaldi In CVPR 2021 [Paper]
	From Synthetic to Real: Unsupervised Domain Adaptation for Animal Pose Estimation Chen Li, Gim Hee Lee In CVPR 2021 (oral) [Paper] [Project]
	LASR: Learning Articulated Shape Reconstruction from a Monocular Video Gengshan Yang, Deqing Sun, Varun Jampani, Daniel Vlasic, Forrester Cole, Huiwen Chang, Deva Ramanan, William T. Freeman, Ce Liu In CVPR 2021 [Paper] [Project]
	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 Paper Candidate) [Paper] [Project]
	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 [Paper]
	Dynamics of gaze control during prey capture in freely moving mice Angie M Michaiel, Elliott TT Abe, Cristopher M Niell In eLife 2020 [Paper]
	Real-time, low-latency closed-loop feedback using markerless posture tracking Gary Kane, Gonçalo Lopes, Jonny L. Saunders, Alexander Mathis, Mackenzie W. Mathis In eLife 2020 (Featured by Nature Methods) [Paper] [Project]
	AlphaTracker: A Multi-Animal Tracking and Behavioral Analysis Tool Zexin Chen, Ruihan Zhang, Yu Eva Zhang, Haowen Zhou, Hao-Shu Fang, Rachel R. Rock, Aneesh Bal, Nancy Padilla-Coreano, Laurel Keyes, Kay M. Tye, Cewu Lu In biorxiv 2020 [Paper] [Project]
	Automatic mapping of multiplexed social receptive fields by deep learning and GPU-accelerated 3D videography Christian L. Ebbesen, Robert C. Froemke In biorxiv 2020 [Paper]
	FreiPose: A Deep Learning Framework for Precise Animal Motion Capture in 3D Spaces Christian Zimmermann, Artur Schneider, Mansour Alyahyay, Thomas Brox, Ilka Diester In biorxiv 2020 [Paper] [Project]
	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 biorxiv 2020 [Paper]
	SLEAP: Multi-animal pose tracking Talmo D. Pereira, Nathaniel Tabris, Junyu Li, Shruthi Ravindranath, Eleni S. Papadoyannis, Z. Yan Wang, David M. Turner, Grace McKenzie-Smith, Sarah D. Kocher, Annegret L. Falkner, Joshua W. Shaevitz, Mala Murthy In biorxiv 2020 [Paper] [Project]
	Simple Behavioral Analysis (SimBA)-an open source toolkit for computer classification of complex social behaviors in experimental animals Simon RO Nilsson, Nastacia L. Goodwin, Jia Jie Choong, Sophia Hwang, Hayden R Wright, Zane C Norville, Xiaoyu Tong, Dayu Lin, Brandon S. Bentzley, Neir Eshel, Ryan J McLaughlin, Sam A. Golden In biorxiv 2020 [Paper]
	TRex, a fast multi-animal tracking system with markerless identification, 2D body posture estimation and visual field reconstruction Tristan Walter, Iain D Couzin In biorxiv 2020 [Paper]
	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 arxiv 2020 [Paper]
	Multiview Supervision By Registration Yilun Zhang, Hyun Soo Park In WACV 2020 [Paper]
	Facial expressions of emotion states and their neuronal correlates in mice Nejc Dolensek, Daniel A. Gehrlach, Alexandra S. Klein, Nadine Gogolla In Science 2020 [Paper]
	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 [Paper]
	A Primer on Motion Capture with Deep Learning: Principles, Pitfalls and Perspectives Alexander Mathis, Steffen Schneider, Jessy Lauer, Mackenzie W. Mathis In Neuron 2020 [Paper]
	Continuous Whole-Body 3D Kinematic Recordings across the Rodent Behavioral Repertoire Jesse D. Marshall, Diego E. Aldarondo, Timothy W. Dunn, William L. Wang, Gordon J. Berman, Bence P. O¨lveczky In Neuron 2020 [Paper]
	Deep Graph Pose: a semi-supervised deep graphical model for improved animal pose tracking Anqi Wu, E. Kelly Buchanan, Matthew Whiteway, Michael Schartner, Guido Meijer, Jean-Paul Noel, Erica Rodriguez, Claire Everett, Amy Norovich, Evan Schaffer, Neeli Mishra, C. Daniel Salzman, Dora Angelaki, Andrés Bendesky, The International Brain Laboratory, John Cunningham, Liam Paninski In NeurIPS 2020 [Paper] [Project]
	Quantifying behavior to understand the brain Talmo D. Pereira, Joshua W. Shaevitz, Mala Murthy In Nature Neuroscience 2020 (review article) [Paper]
	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) [Paper]
	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 [Paper] [Project]
	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 [Paper] [Project]
	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 [Paper]
	Shape and Viewpoint without Keypoints Shubham Goel, Angjoo Kanazawa, Jitendra Malik In ECCV 2020 [Paper] [Project]
	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 [Paper]
	3D-ZeF: A 3D Zebrafish Tracking Benchmark Dataset Malte Pedersen, Joakim Bruslund Haurum, Stefan Hein Bengtson, Thomas B. Moeslund In CVPR 2020 [Paper] [Project]
	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 [Paper] [Project]
	Articulation Aware Canonical Surface Mapping Nilesh Kulkarni, Abhinav Gupta, David F. Fouhey, Shubham Tulsiani In CVPR 2020 [Paper] [Project]
	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 [Paper] [Project]
	Learning from Synthetic Animals Jiteng Mu, Weichao Qiu, Gregory Hager, Alan Yuille In CVPR 2020 (oral) [Paper] [Project]
	RGBD-Dog: Predicting Canine Pose from RGBD Sensors Sinead Kearney, Wenbin Li, Martin Parsons, Kwang In Kim, Darren Cosker In CVPR 2020 [Paper] [Project]
	Transferring Dense Pose to Proximal Animal Classes Artsiom Sanakoyeu, Vasil Khalidov, Maureen S. McCarthy, Andrea Vedaldi, Natalia Neverova In CVPR 2020 [Paper] [Project]
	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) [Paper] [Project]
	DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning Jacob M. Graving, Daniel Chae, Hemal Naik, Liang Li, Benjamin Koger, Blair R. Costelloe, Iain D. Couzin In eLife 2019 [Paper] [Project]
	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) [Paper] [Project]
	idtracker.ai: tracking all individuals in small or large collectives of unmarked animals Francisco Romero-Ferrero, Mattia G. Bergomi, Robert C. Hinz, Francisco J. H. Heras, Gonzalo G. de Polavieja In Nature Methods (Brief Communication) 2019 [Paper] [Project]
	Fast animal pose estimation using deep neural networks Talmo D. Pereira, Diego E. Aldarondo, Lindsay Willmore, Mikhail Kislin, Samuel S.-H. Wang, Mala Murthy, Joshua W. Shaevitz In Nature Methods 2019 [Paper] [Project]
	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 [Paper] [Project]
	Canonical Surface Mapping via Geometric Cycle Consistency Nilesh Kulkarni, Abhinav Gupta, Shubham Tulsiani In ICCV 2019 [Paper] [Project]
	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) [Paper] [Project]
	MONET: Multiview Semi-supervised Keypoint Detection via Epipolar Divergence Yuan Yao, Yasamin Jafarian, Hyun Soo Park In ICCV 2019 [Paper]
	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 [Paper] [Project]
	Robust mouse tracking in complex environments using neural networks Brian Q. Geuther, Sean P. Deats, Kai J. Fox, Steve A. Murray, Robert E. Braun, Jacqueline K. White, Elissa J. Chesler, Cathleen M. Lutz, Vivek Kumar In Communications Biology 2019 [Paper]
	DeepLabCut: markerless pose estimation of user-defined body parts with deep learning Alexander Mathis, Pranav Mamidanna, Kevin M. Cury, Taiga Abe, Venkatesh N. Murthy, Mackenzie Weygandt Mathis, Matthias Bethge In Nature Neuroscience 2018 [Paper] [Project]
	Learning Category-Specific Mesh Reconstruction from Image Collections Angjoo Kanazawa, Shubham Tulsiani, Alexei A. Efros, Jitendra Malik In ECCV 2018 [Paper] [Project]
	Lions and Tigers and Bears: Capturing Non-Rigid, 3D, Articulated Shape from Images Silvia Zuffi, Angjoo Kanazawa, Michael J. Black In CVPR 2018 (spotlight) [Paper] [Project]
	Creatures great and SMAL: Recovering the shape and motion of animals from video Benjamin Biggs, Thomas Roddick, Andrew Fitzgibbon, Roberto Cipolla In ACCV 2018 (oral) [Paper]
	An unsupervised method for quantifying the behavior of paired animals Ugne Klibaite, Gordon J Berman, Jessica Cande, David L Stern, Joshua W Shaevitz In Physical Biology 2017 [Paper]
	Single-View 3D Reconstruction of Animals Angjoo Kanazawa In Ph.D Thesis 2017 [Paper]
	3D Menagerie: Modeling the 3D shape and pose of animals Silvia Zuffi, Angjoo Kanazawa, David W. Jacobs, Michael J. Black In CVPR 2017 (spotlight) [Paper] [Project]
	3D Pose Estimation of Flying Animals in Multi-view Video Datasets Mikhail Breslav In Ph.D Thesis 2016 [Paper]
	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) [Paper] [Project]
	idTracker: Tracking individuals in a group by automatic identification of unmarked animals Alfonso Pérez-Escudero, Julián Vicente-Page, Robert C Hinz, Sara Arganda, Gonzalo G de Polavieja1 In Nature Methods 2014 [Paper] [Project]
	coding of facial expressions of pain in the laboratory mouse Dale J Langford, Andrea L Bailey, Mona Lisa Chanda, Sarah E Clarke, Tanya E Drummond, Stephanie Echols, Sarah Glick, Joelle Ingrao, Tammy Klassen-Ross, Michael L LaCroix-Fralish, Lynn Matsumiya, Robert E Sorge, Susana G Sotocinal, John M Tabaka, David Wong, Arn M J M van den Maagdenberg, Michel D Ferrari, Kenneth D Craig, Jeffrey S Mogil In Nature Methods (brief communications) 2010 [Paper]