An improved 3D shape context registration method for non-rigid surface registration

3D shape context is a method to define matching points between similar shapes as a pre-processing step to non-rigid registration. The main limitation of the approach is point mismatching, which includes long geodesic distance mismatch and neighbors crossing mismatch. In this paper, we propose a topological structure verification method to correct the long geodesic distance mismatch and a correspondence field smoothing method to correct the neighbors crossing mismatch. A robust 3D shape context model is proposed and further combined with thin-plate spline model for non-rigid surface registration. The method was tested on phantoms and rat hind limb skeletons from micro CT images. The results from experiments on mouse hind limb skeletons indicate that the approach is robust

A non-rigid registration method for mouse whole body skeleton registration

Micro-CT/PET imaging scanner provides a powerful tool to study tumor in small rodents in response to therapy. Accurate image registration is a necessary step to quantify the characteristics of images acquired in longitudinal studies. Small animal registration is challenging because of the very deformable body of the animal often resulting in different postures despite physical restraints. In this paper, we propose a non-rigid registration approach for the automatic registration of mouse whole body skeletons, which is based on our improved 3D shape context non-rigid registration method. The whole body skeleton registration approach has been tested on 21 pairs of mouse CT images with variations of individuals and time-instances. The experimental results demonstrated the stability and accuracy of the proposed method for automatic mouse whole body skeleton registration

Modelling human pose and shape based on a database of human 3D scans

Generating realistic human shapes and motion is an important task both in the motion picture industry and in computer games. In feature films, high quality and believability are the most important characteristics. Additionally, when creating virtual doubles the generated charactes have to match as closely as possible to given real persons. In contrast, in computer games the level of realism does not need to be as high but real-time performance is essential. It is desirable to meet all these requirements with a general model of human pose and shape. In addition, many markerless human tracking methods applied, e.g., in biomedicine or sports science can benefit greatly from the availability of such a model because most methods require a 3D model of the tracked subject as input, which can be generated on-the-fly given a suitable shape and pose model. In this thesis, a comprehensive procedure is presented to generate different general models of human pose. A database of 3D scans spanning the space of human pose and shape variations is introduced. Then, four different approaches for transforming the database into a general model of human pose and shape are presented, which improve the current state of the art. Experiments are performed to evaluate and compare the proposed models on real-world problems, i.e., characters are generated given semantic constraints and the underlying shape and pose of humans given 3D scans, multi-view video, or uncalibrated monocular images is estimated.Die Erzeugung realistischer Menschenmodelle ist eine wichtige Anwendung in der Filmindustrie und bei Computerspielen. In Spielen ist Echtzeitsynthese unabdingbar aber der Detailgrad muß nicht so hoch sein wie in Filmen. Für virtuelle Doubles, wie sie z.B. in Filmen eingesetzt werden, muss der generierte Charakter dem gegebenen realen Menschen möglichst ähnlich sein. Mit einem generellen Modell für menschliche Pose und Körperform ist es möglich alle diese Anforderungen zu erfüllen. Zusätzlich können viele Verfahren zur markerlosen Bewegungserfassung, wie sie z.B. in der Biomedizin oder in den Sportwissenschaften eingesetzt werden, von einem generellen Modell für Pose und Körperform profitieren. Da diese ein 3D Modell der erfassten Person benötigen, das jetzt zur Laufzeit generiert werden kann. In dieser Doktorarbeit wird ein umfassender Ansatz vorgestellt, um verschiedene Modelle für Pose und Körperform zu berechnen. Zunächst wird eine Datenbank von 3D Scans aufgebaut, die Pose- und Körperformvariationen von Menschen umfasst. Dann werden vier verschiedene Verfahren eingeführt, die daraus generelle Modelle für Pose und Körperform berechnen und Probleme beim Stand der Technik beheben. Die vorgestellten Modelle werden auf realistischen Problemstellungen getestet. So werden Menschenmodelle aus einigen wenigen Randbedingungen erzeugt und Pose und Körperform von Probanden wird aus 3D Scans, Multi-Kamera Videodaten und Einzelbildern der bekleideten Personen geschätzt

Automated analysis and visualization of preclinical whole-body microCT data

In this thesis, several strategies are presented that aim to facilitate the analysis and visualization of whole-body in vivo data of small animals. Based on the particular challenges for image processing, when dealing with whole-body follow-up data, we addressed several aspects in this thesis. The developed methods are tailored to handle data of subjects with significantly varying posture and address the large tissue heterogeneity of entire animals. In addition, we aim to compensate for lacking tissue contrast by relying on approximation of organs based on an animal atlas. Beyond that, we provide a solution to automate the combination of multimodality, multidimensional data.* Advanced School for Computing and Imaging (ASCI), Delft, NL * Bontius Stichting inz Doelfonds Beeldverwerking, Leiden, NL * Caliper Life Sciences, Hopkinton, USA * Foundation Imago, Oegstgeest, NLUBL - phd migration 201

MONOCULAR POSE ESTIMATION AND SHAPE RECONSTRUCTION OF QUASI-ARTICULATED OBJECTS WITH CONSUMER DEPTH CAMERA

Quasi-articulated objects, such as human beings, are among the most commonly seen objects in our daily lives. Extensive research have been dedicated to 3D shape reconstruction and motion analysis for this type of objects for decades. A major motivation is their wide applications, such as in entertainment, surveillance and health care. Most of existing studies relied on one or more regular video cameras. In recent years, commodity depth sensors have become more and more widely available. The geometric measurements delivered by the depth sensors provide significantly valuable information for these tasks. In this dissertation, we propose three algorithms for monocular pose estimation and shape reconstruction of quasi-articulated objects using a single commodity depth sensor. These three algorithms achieve shape reconstruction with increasing levels of granularity and personalization. We then further develop a method for highly detailed shape reconstruction based on our pose estimation techniques. Our first algorithm takes advantage of a motion database acquired with an active marker-based motion capture system. This method combines pose detection through nearest neighbor search with pose refinement via non-rigid point cloud registration. It is capable of accommodating different body sizes and achieves more than twice higher accuracy compared to a previous state of the art on a publicly available dataset. The above algorithm performs frame by frame estimation and therefore is less prone to tracking failure. Nonetheless, it does not guarantee temporal consistent of the both the skeletal structure and the shape and could be problematic for some applications. To address this problem, we develop a real-time model-based approach for quasi-articulated pose and 3D shape estimation based on Iterative Closest Point (ICP) principal with several novel constraints that are critical for monocular scenario. In this algorithm, we further propose a novel method for automatic body size estimation that enables its capability to accommodate different subjects. Due to the local search nature, the ICP-based method could be trapped to local minima in the case of some complex and fast motions. To address this issue, we explore the potential of using statistical model for soft point correspondences association. Towards this end, we propose a unified framework based on Gaussian Mixture Model for joint pose and shape estimation of quasi-articulated objects. This method achieves state-of-the-art performance on various publicly available datasets. Based on our pose estimation techniques, we then develop a novel framework that achieves highly detailed shape reconstruction by only requiring the user to move naturally in front of a single depth sensor. Our experiments demonstrate reconstructed shapes with rich geometric details for various subjects with different apparels. Last but not the least, we explore the applicability of our method on two real-world applications. First of all, we combine our ICP-base method with cloth simulation techniques for Virtual Try-on. Our system delivers the first promising 3D-based virtual clothing system. Secondly, we explore the possibility to extend our pose estimation algorithms to assist physical therapist to identify their patients’ movement dysfunctions that are related to injuries. Our preliminary experiments have demonstrated promising results by comparison with the gold standard active marker-based commercial system. Throughout the dissertation, we develop various state-of-the-art algorithms for pose estimation and shape reconstruction of quasi-articulated objects by leveraging the geometric information from depth sensors. We also demonstrate their great potentials for different real-world applications

The natverse, a versatile toolbox for combining and analysing neuroanatomical data.

To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation and clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison across many neurons of morphology and connectivity after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community

Brain-shift compensation using intraoperative ultrasound and constraint-based biomechanical simulation

International audiencePurpose. During brain tumor surgery, planning and guidance are based on pre-operative images which do not account for brain-shift. However, this deformation is a major source of error in image-guided neurosurgery and affects the accuracy of the procedure. In this paper, we present a constraint-based biome-chanical simulation method to compensate for craniotomy-induced brain-shift that integrates the deformations of the blood vessels and cortical surface, using a single intraoperative ultrasound acquisition. Methods. Prior to surgery, a patient-specific biomechanical model is built from preoperative images, accounting for the vascular tree in the tumor region and brain soft tissues. Intraoperatively, a navigated ultrasound acquisition is performed directly in contact with the organ. Doppler and B-mode images are recorded simultaneously, enabling the extraction of the blood vessels and probe footprint respectively. A constraint-based simulation is then executed to register the pre-and intraoperative vascular trees as well as the cortical surface with the probe footprint. Finally, preoperative images are updated to provide the surgeon with images corresponding to the current brain shape for navigation. Results. The robustness of our method is first assessed using sparse and noisy synthetic data. In addition, quantitative results for five clinical cases are provided , first using landmarks set on blood vessels, then based on anatomical structures delineated in medical images. The average distances between paired vessels landmarks ranged from 3.51 to 7.32 (in mm) before compensation. With our method, on average 67% of the brain-shift is corrected (range [1.26; 2.33]) against 57% using one of the closest existing works (range [1.71; 2.84]). Finally, our method is proven to be fully compatible with a surgical workflow in terms of execution times and user interactions. Conclusion. In this paper, a new constraint-based biomechanical simulation method is proposed to compensate for craniotomy-induced brain-shift. While being efficient to correct this deformation, the method is fully integrable in a clinical process