Open-source tools for behavioral video analysis: Setup, methods, and best practices

MC-Calib: A generic and robust calibration toolbox for multi-camera systems

(2022) Francois Rameau et al.   COMPUTER VISION AND IMAGE UNDERSTANDING

SLEAP: A deep learning system for multi-animal pose tracking

(2022) Talmo D. Pereira et al.   NATURE METHODS

Identifying behavioral structure from deep variational embeddings of animal motion

(2022) Kevin Luxem et al.   Communications Biology

A rapid whisker-based decision underlying skilled locomotion in mice

(2021) Richard A Warren et al.   eLife

TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields

(2021) Tristan Walter et al.   eLife

DeepLabStream enables closed-loop behavioral experiments using deep learning-based markerless, real-time posture detection

(2021) Jens F. Schweihoff et al.   Communications Biology

Geometric deep learning enables 3D kinematic profiling across species and environments

(2021) Timothy W. Dunn et al.   NATURE METHODS

A review of 28 free animal-tracking software applications: current features and limitations

(2021) Veronica Panadeiro et al.   LAB ANIMAL

LiftPose3D, a deep learning-based approach for transforming two-dimensional to three-dimensional poses in laboratory animals

(2021) Adam Gosztolai et al.   NATURE METHODS

B-SOiD, an open-source unsupervised algorithm for identification and fast prediction of behaviors

(2021) Alexander I. Hsu et al.   Nature Communications

Scanned optogenetic control of mammalian somatosensory input to map input-specific behavioral outputs

(2021) Ara Schorscher-Petcu et al.   eLife

Automated pose estimation in primates

(2021) Benjamin Y. Hayden et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Datasheets for datasets

(2021) Timnit Gebru et al.   COMMUNICATIONS OF THE ACM

A review of uncertainty quantification in deep learning: Techniques, applications and challenges

(2021) Moloud Abdar et al.   Information Fusion

Multisensory coding of angular head velocity in the retrosplenial cortex

(2021) Sepiedeh Keshavarzi et al.   NEURON

The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice

(2021) Cristina Segalin et al.   eLife

A quantitative reward prediction error signal in the ventral pallidum

(2020) David J. Ottenheimer et al.   NATURE NEUROSCIENCE

A Neural Network for Wind-Guided Compass Navigation

(2020) Tatsuo S. Okubo et al.   NEURON

Deep learning-based behavioral analysis reaches human accuracy and is capable of outperforming commercial solutions

(2020) Oliver Sturman et al.   NEUROPSYCHOPHARMACOLOGY

Revealing the structure of pharmacobehavioral space through motion sequencing

(2020) Alexander B. Wiltschko et al.   NATURE NEUROSCIENCE

Automated markerless pose estimation in freely moving macaques with OpenMonkeyStudio

(2020) Praneet C. Bala et al.   Nature Communications

Real-time, low-latency closed-loop feedback using markerless posture tracking

(2020) Gary A Kane et al.   eLife

Adaptive, locally linear models of complex dynamics

(2019) Antonio C. Costa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spontaneous behaviors drive multidimensional, brainwide activity

(2019) Carsen Stringer et al.   SCIENCE

Single-trial neural dynamics are dominated by richly varied movements

(2019) Simon Musall et al.   NATURE NEUROSCIENCE

DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning

(2019) Jacob M Graving et al.   eLife

DeepFly3D, a deep learning-based approach for 3D limb and appendage tracking in tethered, adult Drosophila

(2019) Semih Günel et al.   eLife

ezTrack: An open-source video analysis pipeline for the investigation of animal behavior

(2019) Zachary T. Pennington et al.   Scientific Reports

Measuring behavior across scales

(2018) Gordon J. Berman   BMC BIOLOGY

The Striatum Organizes 3D Behavior via Moment-to-Moment Action Selection

(2018) Jeffrey E. Markowitz et al.   CELL

DeepLabCut: markerless pose estimation of user-defined body parts with deep learning

(2018) Alexander Mathis et al.   NATURE NEUROSCIENCE

Fast animal pose estimation using deep neural networks

(2018) Talmo D. Pereira et al.   NATURE METHODS

Neuroscience Needs Behavior: Correcting a Reductionist Bias

(2017) John W. Krakauer et al.   NEURON

Vicarious trial and error

(2016) A. David Redish   NATURE REVIEWS NEUROSCIENCE

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

ImageNet Large Scale Visual Recognition Challenge

(2015) Olga Russakovsky et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Bonsai: an event-based framework for processing and controlling data streams

(2015) Gonçalo Lopes et al.   Frontiers in Neuroinformatics

BEEtag: A Low-Cost, Image-Based Tracking System for the Study of Animal Behavior and Locomotion

(2015) James D. Crall et al.   PLoS One

Mapping the stereotyped behaviour of freely moving fruit flies

(2014) G. J. Berman et al.   Journal of the Royal Society Interface

Toward a Science of Computational Ethology

(2014) David J. Anderson et al.   NEURON

Automated multi-day tracking of marked mice for the analysis of social behaviour

(2013) Shay Ohayon et al.   JOURNAL OF NEUROSCIENCE METHODS

Anterior cingulate neurons in the rat map anticipated effort and reward to their associated action sequences

(2012) Stephen L. Cowen et al.   JOURNAL OF NEUROPHYSIOLOGY

JAABA: interactive machine learning for automatic annotation of animal behavior

(2012) Mayank Kabra et al.   NATURE METHODS

Beyond the Reward Pathway: Coding Reward Magnitude and Error in the Rat Subthalamic Nucleus

(2009) Sylvie Lardeux et al.   JOURNAL OF NEUROPHYSIOLOGY

Single-Cell and Population Coding of Expected Reward Probability in the Orbitofrontal Cortex of the Rat

(2009) E. van Duuren et al.   JOURNAL OF NEUROSCIENCE