Brain Tumor Vascular Network Segmentation from Micro-Tomography

Micro-tomography produces high resolution images of bio- logical structures such as vascular networks. In this paper, we present a new approach for segmenting vascular network into pathological and normal regions from considering their micro-vessel 3D structure only. We define and use a condi- tional random field for segmenting the output of a watershed algorithm. The tumoral and normal classes are thus character- ized by their respective distribution of watershed region size interpreted as local vascular territories

A Relaxation Scheme for Mesh Locality in Computer Vision.

Parallel processing has been considered as the key to build computer systems of the future and has become a mainstream subject in Computer Science. Computer Vision applications are computationally intensive that require parallel approaches to exploit the intrinsic parallelism. This research addresses this problem for low-level and intermediate-level vision problems. The contributions of this dissertation are a unified scheme based on probabilistic relaxation labeling that captures localities of image data and the ability of using this scheme to develop efficient parallel algorithms for Computer Vision problems. We begin with investigating the problem of skeletonization. The technique of pattern match that exhausts all the possible interaction patterns between a pixel and its neighboring pixels captures the locality of this problem, and leads to an efficient One-pass Parallel Asymmetric Thinning Algorithm (OPATA\sb8). The use of 8-distance in this algorithm, or chessboard distance, not only improves the quality of the resulting skeletons, but also improves the efficiency of the computation. This new algorithm plays an important role in a hierarchical route planning system to extract high level typological information of cross-country mobility maps which greatly speeds up the route searching over large areas. We generalize the neighborhood interaction description method to include more complicated applications such as edge detection and image restoration. The proposed probabilistic relaxation labeling scheme exploit parallelism by discovering local interactions in neighboring areas and by describing them effectively. The proposed scheme consists of a transformation function and a dictionary construction method. The non-linear transformation function is derived from Markov Random Field theory. It efficiently combines evidences from neighborhood interactions. The dictionary construction method provides an efficient way to encode these localities. A case study applies the scheme to the problem of edge detection. The relaxation step of this edge-detection algorithm greatly reduces noise effects, gets better edge localization such as line ends and corners, and plays a crucial rule in refining edge outputs. The experiments on both synthetic and natural images show that our algorithm converges quickly, and is robust in noisy environment

Gap Filling of 3-D Microvascular Networks by Tensor Voting

We present a new algorithm which merges discontinuities in 3-D images of tubular structures presenting undesirable gaps. The application of the proposed method is mainly associated to large 3-D images of microvascular networks. In order to recover the real network topology, we need to fill the gaps between the closest discontinuous vessels. The algorithm presented in this paper aims at achieving this goal. This algorithm is based on the skeletonization of the segmented network followed by a tensor voting method. It permits to merge the most common kinds of discontinuities found in microvascular networks. It is robust, easy to use, and relatively fast. The microvascular network images were obtained using synchrotron tomography imaging at the European Synchrotron Radiation Facility. These images exhibit samples of intracortical networks. Representative results are illustrated

A comprehensive study on pathfinding techniques for robotics and video games

This survey provides an overview of popular pathfinding algorithms and techniques based on graph generation problems. We focus on recent developments and improvements in existing techniques and examine their impact on robotics and the video games industry. We have categorized pathfinding algorithms based on a 2D/3D environment search. The aim of this paper is to provide researchers with a thorough background on the progress made in the last 10 years in this field, summarize the principal techniques, and describe their results. We also give our expectations for future trends in this field and discuss the possibility of using pathfinding techniques in more extensive areas

Spatial Reconstruction of Biological Trees from Point Cloud

Trees are complex systems in nature whose topology and geometry ar

Deep Neural Ensemble for Retinal Vessel Segmentation in Fundus Images towards Achieving Label-free Angiography

Automated segmentation of retinal blood vessels in label-free fundus images entails a pivotal role in computed aided diagnosis of ophthalmic pathologies, viz., diabetic retinopathy, hypertensive disorders and cardiovascular diseases. The challenge remains active in medical image analysis research due to varied distribution of blood vessels, which manifest variations in their dimensions of physical appearance against a noisy background. In this paper we formulate the segmentation challenge as a classification task. Specifically, we employ unsupervised hierarchical feature learning using ensemble of two level of sparsely trained denoised stacked autoencoder. First level training with bootstrap samples ensures decoupling and second level ensemble formed by different network architectures ensures architectural revision. We show that ensemble training of auto-encoders fosters diversity in learning dictionary of visual kernels for vessel segmentation. SoftMax classifier is used for fine tuning each member auto-encoder and multiple strategies are explored for 2-level fusion of ensemble members. On DRIVE dataset, we achieve maximum average accuracy of 95.33\% with an impressively low standard deviation of 0.003 and Kappa agreement coefficient of 0.708 . Comparison with other major algorithms substantiates the high efficacy of our model.Comment: Accepted as a conference paper at IEEE EMBC, 201

Data-Augmented Structure-Property Mapping for Accelerating Computational Design of Advanced Material Systems

abstract: Advanced material systems refer to materials that are comprised of multiple traditional constituents but complex microstructure morphologies, which lead to their superior properties over conventional materials. This dissertation is motivated by the grand challenge in accelerating the design of advanced material systems through systematic optimization with respect to material microstructures or processing settings. While optimization techniques have mature applications to a large range of engineering systems, their application to material design meets unique challenges due to the high dimensionality of microstructures and the high costs in computing process-structure-property (PSP) mappings. The key to addressing these challenges is the learning of material representations and predictive PSP mappings while managing a small data acquisition budget. This dissertation thus focuses on developing learning mechanisms that leverage context-specific meta-data and physics-based theories. Two research tasks will be conducted: In the first, we develop a statistical generative model that learns to characterize high-dimensional microstructure samples using low-dimensional features. We improve the data efficiency of a variational autoencoder by introducing a morphology loss to the training. We demonstrate that the resultant microstructure generator is morphology-aware when trained on a small set of material samples, and can effectively constrain the microstructure space during material design. In the second task, we investigate an active learning mechanism where new samples are acquired based on their violation to a theory-driven constraint on the physics-based model. We demonstrate using a topology optimization case that while data acquisition through the physics-based model is often expensive (e.g., obtaining microstructures through simulation or optimization processes), the evaluation of the constraint can be far more affordable (e.g., checking whether a solution is optimal or equilibrium). We show that this theory-driven learning algorithm can lead to much improved learning efficiency and generalization performance when such constraints can be derived. The outcomes of this research is a better understanding of how physics knowledge about material systems can be integrated into machine learning frameworks, in order to achieve more cost-effective and reliable learning of material representations and predictive models, which are essential to accelerate computational material design.Dissertation/ThesisDoctoral Dissertation Mechanical Engineering 201