Noninvasive behavioral tracking of animals during experiments is crucial to many scientific pursuits. Extracting the poses of animals without using markers is often essential for measuring behavioral effects in biomechanics, genetics, ethology & neuroscience. Yet, 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 using limited training data to precisely track user-defined features that matches human labeling accuracy. Here, with this paper we provide an updated toolbox that is self contained within a Python package that includes new features such as graphical user interfaces and active-learning based network refinement. Lastly, we provide a step-by-step guide for using DeepLabCut.>> deeplabcut.create_labeled_video(config_path,['/analysis/project /videos/reachingvideo1.avi','/analysis/project/videos/reachingvideo2.avi'])This function has various parameters, in particular the user can set the colormap, the dotsize, and alphavalue of the labels in config.yaml file.

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Noninvasive behavioral tracking of animals during experiments is crucial to many scientific pursuits. Extracting the poses of animals without using markers is often essential for measuring behavioral effects in biomechanics, genetics, ethology & neuroscience. Yet, 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 using limited training data to precisely track user-defined features that matches human labeling accuracy. Here, with this paper we provide an updated toolbox that is self contained within a Python package that includes new features such as graphical user interfaces and active-learning based network refinement. Lastly, we provide a step-by-step guide for using DeepLabCut.

In this paper we propose a method to improve the accuracy of trajectory optimization for dynamic robots with intermittent contact by using orthogonal collocation. Until recently, most trajectory optimization methods for systems with contacts employ mode-scheduling, which requires an a priori knowledge of the contact order and thus cannot produce complex or non-intuitive behaviors. Contact-implicit trajectory optimization methods offer a solution to this by allowing the optimization to make or break contacts as needed, but thus far have suffered from poor accuracy. Here, we combine methods from direct collocation using higher order orthogonal polynomials with contact-implicit optimization to generate trajectories with significantly improved accuracy. The key insight is to increase the order of the polynomial representation while maintaining the assumption that impact occurs over the duration of one finite element.

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