3D pose estimation of flying animals in multi-view video datasets

Flying animals such as bats, birds, and moths are actively studied by researchers wanting to better understand these animals’ behavior and flight characteristics. Towards this goal, multi-view videos of flying animals have been recorded both in lab- oratory conditions and natural habitats. The analysis of these videos has shifted over time from manual inspection by scientists to more automated and quantitative approaches based on computer vision algorithms. This thesis describes a study on the largely unexplored problem of 3D pose estimation of flying animals in multi-view video data. This problem has received little attention in the computer vision community where few flying animal datasets exist. Additionally, published solutions from researchers in the natural sciences have not taken full advantage of advancements in computer vision research. This thesis addresses this gap by proposing three different approaches for 3D pose estimation of flying animals in multi-view video datasets, which evolve from successful pose estimation paradigms used in computer vision. The first approach models the appearance of a flying animal with a synthetic 3D graphics model and then uses a Markov Random Field to model 3D pose estimation over time as a single optimization problem. The second approach builds on the success of Pictorial Structures models and further improves them for the case where only a sparse set of landmarks are annotated in training data. The proposed approach first discovers parts from regions of the training images that are not annotated. The discovered parts are then used to generate more accurate appearance likelihood terms which in turn produce more accurate landmark localizations. The third approach takes advantage of the success of deep learning models and adapts existing deep architectures to perform landmark localization. Both the second and third approaches perform 3D pose estimation by first obtaining accurate localization of key landmarks in individual views, and then using calibrated cameras and camera geometry to reconstruct the 3D position of key landmarks. This thesis shows that the proposed algorithms generate first-of-a-kind and leading results on real world datasets of bats and moths, respectively. Furthermore, a variety of resources are made freely available to the public to further strengthen the connection between research communities

Discovering useful parts for pose estimation in sparsely annotated datasets

Our work introduces a novel way to increase pose estimation accuracy by discovering parts from unannotated regions of training images. Discovered parts are used to generate more accurate appearance likelihoods for traditional part-based models like Pictorial Structures and its derivatives. Our experiments on images of a hawkmoth in flight show that our proposed approach significantly improves over existing work for this application, while also being more generally applicable. Our proposed approach localizes landmarks at least twice as accurately as a baseline based on a Mixture of Pictorial Structures (MPS) model. Our unique High-Resolution Moth Flight (HRMF) dataset is made publicly available with annotations.https://arxiv.org/abs/1605.00707Accepted manuscrip

Automating image analysis by annotating landmarks with deep neural networks

Image and video analysis is often a crucial step in the study of animal behavior and kinematics. Often these analyses require that the position of one or more animal landmarks are annotated (marked) in numerous images. The process of annotating landmarks can require a significant amount of time and tedious labor, which motivates the need for algorithms that can automatically annotate landmarks. In the community of scientists that use image and video analysis to study the 3D flight of animals, there has been a trend of developing more automated approaches for annotating landmarks, yet they fall short of being generally applicable. Inspired by the success of Deep Neural Networks (DNNs) on many problems in the field of computer vision, we investigate how suitable DNNs are for accurate and automatic annotation of landmarks in video datasets representative of those collected by scientists studying animals. Our work shows, through extensive experimentation on videos of hawkmoths, that DNNs are suitable for automatic and accurate landmark localization. In particular, we show that one of our proposed DNNs is more accurate than the current best algorithm for automatic localization of landmarks on hawkmoth videos. Moreover, we demonstrate how these annotations can be used to quantitatively analyze the 3D flight of a hawkmoth. To facilitate the use of DNNs by scientists from many different fields, we provide a self contained explanation of what DNNs are, how they work, and how to apply them to other datasets using the freely available library Caffe and supplemental code that we provide.https://arxiv.org/abs/1702.00583Published versio