GPU-accelerated ray-casting for 3D fiber orientation analysis

Orientation analysis of fibers is widely applied in the fields of medical, material and life sciences. The orientation information allows predicting properties and behavior of materials to validate and guide a fabrication process of materials with controlled fiber orientation. Meanwhile, development of detector systems for high-resolution non-invasive 3D imaging techniques led to a significant increase in the amount of generated data per a sample up to dozens of gigabytes. Though plenty of 3D orientation estimation algorithms were developed in recent years, neither of them can process large datasets in a reasonable amount of time. This fact complicates the further analysis and makes impossible fast feedback to adjust fabrication parameters. In this work, we present a new method for quantifying the 3D orientation of fibers. The GPU implementation of the proposed method surpasses another popular method for 3D orientation analysis regarding accuracy and speed. The validation of both methods was performed on a synthetic dataset with varying parameters of fibers. Moreover, the proposed method was applied to perform orientation analysis of scaffolds with different fibrous micro-architecture studied with the synchrotron μCT imaging setup. Each acquired dataset of size 600x600x450 voxels was analyzed in less 2 minutes using standard PC equipped with a single GPU

Novel system of pavement cracking detection algorithms using 1mm 3D surface data

Pavement cracking is one of the major concerns for pavement design and management. There have been rapid developments of automated pavement cracking detection in recent years. However, none of them has been widely accepted so far due to lack of capability of maintaining consistently high detection accuracy for various pavement surfaces. Using 1mm 3D data collected by WayLink Digital Highway Data Vehicle (DHDV), an entire system of algorithms, which consists of Fully Automated Cracking Detection Subsystem, Interactive Cracking Detection Subsystem and Noisy Pattern Detection Subsystem, is proposed in this study for improvements in adaptability, reliability and interactivity of pavement cracking detection.The Fully Automated Cracking Detection Subsystem utilizes 3D Shadow Simulation to find lower areas in local neighborhood, and then eliminates noises by subsequent noise suppressing procedures. The assumption behind 3D Shadow Simulation is that local lower areas will be shadowed under light with a certain projection angle. According to the Precision-Recall Analysis on two real pavement segments, the fully automated subsystem can achieve a high level of Precision and Recall on both pavement segments.The Interactive Cracking Detection Subsystem implements an interactive algorithm proposed in this study, which is capable of improving its detection accuracy by adjustments based on the operator's feedback, to provide a slower but more flexible as well as confident approach to pavement cracking detection. It is demonstrated in the case study that the interactive subsystem can retrieve almost 100 percent of cracks with nearly no noises.The Noisy Pattern Detection Subsystem is proposed to exclude pavement joints and grooves from cracking detection so that false-positive errors on rigid pavements can be reduced significantly. This subsystem applies Support Vector Machines (SVM) to train the classifiers for the recognition of transverse groove, transverse joint, longitudinal groove and longitudinal joint respectively. Based on the trained classifiers, pattern extraction procedures are developed to find the exact locations of pavement joints and grooves.Non-dominated Sorting Genetic Algorithm II (NSGA-II), which is one of multi objective genetic algorithms, is employed in this study to optimize parameters of the fully automated subsystem for the pursuing of high Precision and high Recall simultaneously. In addition to NSGA-II, an Auxiliary Prediction Model (APM) is proposed in this study to assist NSGA-II for faster convergence and better diversity.Finally, CPU-based and GPU-based Parallel Computing Techniques, including MultiGPU, GPU streaming, Multi-Core and Multi-Threading are combined in this study to increase the processing speed for all computational tasks that can be synchronous

FPGA Acceleration of Communication-Bound Streaming Applications: Architecture Modeling and a 3D Image Compositing Case Study

Reconfigurable computers usually provide a limited number of different memory resources, such as host memory, external memory, and on-chip memory with different capacities and communication characteristics. A key challenge for achieving high-performance with reconfigurable accelerators is the efficient utilization of the available memory resources. A detailed knowledge of the memories' parameters is key for generating an optimized communication layout. In this paper, we discuss a benchmarking environment for generating such a characterization. The environment is built on IMORC, our architectural template and on-chip network for creating reconfigurable accelerators. We provide a characterization of the memory resources available on the XtremeData XD1000 reconfigurable computer. Based on this data, we present as a case study the implementation of a 3D image compositing accelerator that is able to double the frame rate of a parallel renderer

Fast extraction of neuron morphologies from large-scale SBFSEM image stacks

Neuron morphology is frequently used to classify cell-types in the mammalian cortex. Apart from the shape of the soma and the axonal projections, morphological classification is largely defined by the dendrites of a neuron and their subcellular compartments, referred to as dendritic spines. The dimensions of a neuron’s dendritic compartment, including its spines, is also a major determinant of the passive and active electrical excitability of dendrites. Furthermore, the dimensions of dendritic branches and spines change during postnatal development and, possibly, following some types of neuronal activity patterns, changes depending on the activity of a neuron. Due to their small size, accurate quantitation of spine number and structure is difficult to achieve (Larkman, J Comp Neurol 306:332, 1991). Here we follow an analysis approach using high-resolution EM techniques. Serial block-face scanning electron microscopy (SBFSEM) enables automated imaging of large specimen volumes at high resolution. The large data sets generated by this technique make manual reconstruction of neuronal structure laborious. Here we present NeuroStruct, a reconstruction environment developed for fast and automated analysis of large SBFSEM data sets containing individual stained neurons using optimized algorithms for CPU and GPU hardware. NeuroStruct is based on 3D operators and integrates image information from image stacks of individual neurons filled with biocytin and stained with osmium tetroxide. The focus of the presented work is the reconstruction of dendritic branches with detailed representation of spines. NeuroStruct delivers both a 3D surface model of the reconstructed structures and a 1D geometrical model corresponding to the skeleton of the reconstructed structures. Both representations are a prerequisite for analysis of morphological characteristics and simulation signalling within a neuron that capture the influence of spines

Time of flight PET reconstruction using nonuniform update for regional recovery uniformity

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147742/1/mp13321.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147742/2/mp13321_am.pd

Illustrative interactive stipple rendering

Journal ArticleAbstract-Simulating hand-drawn illustration can succinctly express information in a manner that is communicative and informative. We present a framework for an interactive direct stipple rendering of volume and surface-based objects. By combining the principles of artistic and scientific illustration, we explore several feature enhancement techniques to create effective, interactive visualizations of scientific and medical data sets. We also introduce a rendering mechanism that generates appropriate point lists at all resolutions during an automatic preprocess and modifies rendering styles through different combinations of these feature enhancements. The new system is an effective way to interactively preview large, complex volume and surface data sets in a concise, meaningful, and illustrative manner. Stippling is effective for many applications and provides a quick and efficient method to investigate both volume and surface models

Bayesian log-Gaussian Cox process regression: applications to meta-analysis of neuroimaging working memory studies

Working memory (WM) was one of the first cognitive processes studied with functional magnetic resonance imaging. With now over 20 years of studies on WM, each study with tiny sample sizes, there is a need for meta-analysis to identify the brain regions that are consistently activated by WM tasks, and to understand the interstudy variation in those activations. However, current methods in the field cannot fully account for the spatial nature of neuroimaging meta-analysis data or the heterogeneity observed among WM studies. In this work, we propose a fully Bayesian random-effects metaregression model based on log-Gaussian Cox processes, which can be used for meta-analysis of neuroimaging studies. An efficient Markov chain Monte Carlo scheme for posterior simulations is presented which makes use of some recent advances in parallel computing using graphics processing units. Application of the proposed model to a real data set provides valuable insights regarding the function of the WM

Diffusion MRI analysis:robust and efficient microstructure modeling

Diffusion MRI (dMRI) allows for investigating the structure of the human brain. This is useful for both scientific brain research as well as medical diagnosis. Since the raw dMRI data is not directly interpretable by humans, we use mathematical models to convert the raw dMRI data into something interpretable. These models can be computed using multiple different computational methods, each having a different trade-off in accuracy, robustness and efficiency. In this thesis we studied multiple different computational models for their usability and efficiency for dMRI modeling. In the end we provide the reader with methodological recommendations for dMRI modeling and provide a high performance GPU enabled dMRI computing platform containing all recommendations