Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

See the Difference: Direct Pre-Image Reconstruction and Pose Estimation by Differentiating HOG

The Histogram of Oriented Gradient (HOG) descriptor has led to many advances in computer vision over the last decade and is still part of many state of the art approaches. We realize that the associated feature computation is piecewise differentiable and therefore many pipelines which build on HOG can be made differentiable. This lends to advanced introspection as well as opportunities for end-to-end optimization. We present our implementation of $\nabla$HOG based on the auto-differentiation toolbox Chumpy and show applications to pre-image visualization and pose estimation which extends the existing differentiable renderer OpenDR pipeline. Both applications improve on the respective state-of-the-art HOG approaches

Temporally Coherent General Dynamic Scene Reconstruction

Existing techniques for dynamic scene reconstruction from multiple wide-baseline cameras primarily focus on reconstruction in controlled environments, with fixed calibrated cameras and strong prior constraints. This paper introduces a general approach to obtain a 4D representation of complex dynamic scenes from multi-view wide-baseline static or moving cameras without prior knowledge of the scene structure, appearance, or illumination. Contributions of the work are: An automatic method for initial coarse reconstruction to initialize joint estimation; Sparse-to-dense temporal correspondence integrated with joint multi-view segmentation and reconstruction to introduce temporal coherence; and a general robust approach for joint segmentation refinement and dense reconstruction of dynamic scenes by introducing shape constraint. Comparison with state-of-the-art approaches on a variety of complex indoor and outdoor scenes, demonstrates improved accuracy in both multi-view segmentation and dense reconstruction. This paper demonstrates unsupervised reconstruction of complete temporally coherent 4D scene models with improved non-rigid object segmentation and shape reconstruction and its application to free-viewpoint rendering and virtual reality.Comment: Submitted to IJCV 2019. arXiv admin note: substantial text overlap with arXiv:1603.0338

Robust Temporally Coherent Laplacian Protrusion Segmentation of 3D Articulated Bodies

In motion analysis and understanding it is important to be able to fit a suitable model or structure to the temporal series of observed data, in order to describe motion patterns in a compact way, and to discriminate between them. In an unsupervised context, i.e., no prior model of the moving object(s) is available, such a structure has to be learned from the data in a bottom-up fashion. In recent times, volumetric approaches in which the motion is captured from a number of cameras and a voxel-set representation of the body is built from the camera views, have gained ground due to attractive features such as inherent view-invariance and robustness to occlusions. Automatic, unsupervised segmentation of moving bodies along entire sequences, in a temporally-coherent and robust way, has the potential to provide a means of constructing a bottom-up model of the moving body, and track motion cues that may be later exploited for motion classification. Spectral methods such as locally linear embedding (LLE) can be useful in this context, as they preserve "protrusions", i.e., high-curvature regions of the 3D volume, of articulated shapes, while improving their separation in a lower dimensional space, making them in this way easier to cluster. In this paper we therefore propose a spectral approach to unsupervised and temporally-coherent body-protrusion segmentation along time sequences. Volumetric shapes are clustered in an embedding space, clusters are propagated in time to ensure coherence, and merged or split to accommodate changes in the body's topology. Experiments on both synthetic and real sequences of dense voxel-set data are shown. This supports the ability of the proposed method to cluster body-parts consistently over time in a totally unsupervised fashion, its robustness to sampling density and shape quality, and its potential for bottom-up model constructionComment: 31 pages, 26 figure