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

Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other animals are often marked with reflective markers to assist with computer-based tracking, but markers are intrusive, and the number and location of the markers must be determined a priori. Here we present an efficient method for markerless pose estimation based on transfer learning with deep neural networks that achieves excellent results with minimal training data. We demonstrate the versatility of this framework by tracking various body parts in multiple species across a broad collection of behaviors. Remarkably, even when only a small number of frames are labeled (~200), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.

Markerless tracking of user-defined features with deep learning

Pranav Mamidanna, Mackenzie Mathis, Alexander Mathis

Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other animals are often marked with reflective markers to assist with computer-based tracking, yet markers are intrusive (especially for smaller animals), and the number and location of the markers must be determined a priori. Here, we present a highly efficient method for markerless tracking based on transfer learning with deep neural networks that achieves excellent results with minimal training data. We demonstrate the versatility of this framework by tracking various body parts in a broad collection of experimental settings: mice odor trail-tracking, egg-laying behavior in drosophila, and mouse hand articulation in a skilled forelimb task. For example, during the skilled reaching behavior, individual joints can be automatically tracked (and a confidence score is reported). Remarkably, even when a small number of frames are labeled (

\approx 200

), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.

2018

Pretraining boosts out-of-domain robustness for pose estimation

Mackenzie Mathis, Alexander Mathis, Mert Yüksekgönül

Deep neural networks are highly effective tools for human and animal pose estimation. However, robustness to out-of-domain data remains a challenge. Here, we probe the transfer and generalization ability for pose estimation with two architecture classes (MobileNetV2s and ResNets) pretrained on ImageNet. We generated a novel dataset of 30 horses that allowed for both within-domain and out-of-domain (unseen horse) testing. We find that pretraining on ImageNet strongly improves out-of-domain performance. Moreover, we show that for both pretrained and networks trained from scratch, better ImageNet-performing architectures perform better for pose estimation, with a substantial improvement on out-of-domain data when pretrained. Collectively, our results demonstrate that transfer learning is particularly beneficial for out-of-domain robustness.

2019

Using DeepLabCut for 3D markerless pose estimation across species and behaviors

An Chi Chen, Mackenzie Mathis, Alexander Mathis, Tanmay Nath

Noninvasive behavioral tracking of animals during experiments is critical to many scientific pursuits. Extracting the poses of animals without using markers is often essential to measuring behavioral effects in biomechanics, genetics, ethology, and neuroscience. However, extracting detailed poses without markers in dynamically changing backgrounds has been challenging. We recently introduced an open-source toolbox called DeepLabCut that builds on a state-of-the-art human pose-estimation algorithm to allow a user to train a deep neural network with limited training data to precisely track user-defined features that match human labeling accuracy. Here, we provide an updated toolbox, developed as a Python package, that includes new features such as graphical user interfaces (GUIs), performance improvements, and active-learning-based network refinement. We provide a step-by-step procedure for using DeepLabCut that guides the user in creating a tailored, reusable analysis pipeline with a graphical processing unit (GPU) in 1–12 h (depending on frame size). Additionally, we provide Docker environments and Jupyter Notebooks that can be run on cloud resources such as Google Colaboratory.

2019

Markerless tracking of user-defined features with deep learning

Pranav Mamidanna, Mackenzie Mathis, Alexander Mathis

Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other animals are often marked with reflective markers to assist with computer-based tracking, yet markers are intrusive (especially for smaller animals), and the number and location of the markers must be determined a priori. Here, we present a highly efficient method for markerless tracking based on transfer learning with deep neural networks that achieves excellent results with minimal training data. We demonstrate the versatility of this framework by tracking various body parts in a broad collection of experimental settings: mice odor trail-tracking, egg-laying behavior in drosophila, and mouse hand articulation in a skilled forelimb task. For example, during the skilled reaching behavior, individual joints can be automatically tracked (and a confidence score is reported). Remarkably, even when a small number of frames are labeled (

\approx 200

), the algorithm achieves excellent tracking performance on test frames that is comparable to human accuracy.

2018