Investigation of Parallel Data Processing Using Hybrid High Performance CPU + GPU Systems and CUDA Streams

The paper investigates parallel data processing in a hybrid CPU+GPU(s) system using multiple CUDA streams for overlapping communication and computations. This is crucial for efficient processing of data, in particular incoming data stream processing that would naturally be forwarded using multiple CUDA streams to GPUs. Performance is evaluated for various compute time to host-device communication time ratios, numbers of CUDA streams, for various numbers of threads managing computations on GPUs. Tests also reveal benefits of using CUDA MPS for overlapping communication and computations when using multiple processes. Furthermore, using standard memory allocation on a GPU and Unified Memory versions are compared, the latter including programmer added prefetching. Performance of a hybrid CPU+GPU version as well as scaling across multiple GPUs are demonstrated showing good speed-ups of the approach. Finally, the performance per power consumption of selected configurations are presented for various numbers of streams and various relative performances of GPUs and CPUs

ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Resolution enhancement for topography measurement of high-dynamic-range surfaces via image fusion

In this paper, we introduce a method and algorithm for resolution enhancement of low-resolution surface topography data by fusing it with corresponding high-resolution intensity images. This fusion is carried out by linking the three-dimensional topographical map to its intensity image via an intrinsic image-based shape-from-shading algorithm. Through computational simulation and physical experiments, the effectiveness of the proposed method and the repeatability have been evaluated, and the computational cost has been shown to be less than other state-of-the-art algorithms. This proposed method can be easily integrated with high-speed in-line measurements of high-dynamic-range surfaces

Large-scale physically accurate modelling of real proton exchange membrane fuel cell with deep learning

Proton exchange membrane fuel cells, consuming hydrogen and oxygen to generate clean electricity and water, suffer acute liquid water challenges. Accurate liquid water modelling is inherently challenging due to the multi-phase, multi-component, reactive dynamics within multi-scale, multi-layered porous media. In addition, currently inadequate imaging and modelling capabilities are limiting simulations to small areas (<1 mm2) or simplified architectures. Herein, an advancement in water modelling is achieved using X-ray micro-computed tomography, deep learned super-resolution, multi-label segmentation, and direct multi-phase simulation. The resulting image is the most resolved domain (16 mm2 with 700 nm voxel resolution) and the largest direct multi-phase flow simulation of a fuel cell. This generalisable approach unveils multi-scale water clustering and transport mechanisms over large dry and flooded areas in the gas diffusion layer and flow fields, paving the way for next generation proton exchange membrane fuel cells with optimised structures and wettabilities

Model-Based Design for High-Performance Signal Processing Applications

Developing high-performance signal processing applications requires not only effective signal processing algorithms but also efficient software design methods that can take full advantage of the available processing resources. An increasingly important type of hardware platform for high-performance signal processing is a multicore central processing unit (CPU) combined with a graphics processing unit (GPU) accelerator. Efficiently coordinating computations on both the host (CPU) and device (GPU), and managing host-device data transfers are critical to utilizing CPU-GPU platforms effectively. However, such coordination is challenging for system designers, given the complexity of modern signal processing applications and the stringent constraints under which they must operate. Dataflow models of computation provide a useful framework for addressing this challenge. In such a modeling approach, signal processing applications are represented as directed graphs that can be viewed intuitively as high-level signal flow diagrams. The formal, high-level abstraction provided by dataflow principles provides a useful foundation to investigate model-based analysis and optimization for new challenges in design and implementation of signal processing systems. This thesis presents a new model-based design methodology and an evolution of three novel design tools. These contributions provide an automated design flow for high performance signal processing. The design flow takes high-level dataflow representations as input and systematically derives optimized implementations on CPU-GPU platforms. The proposed design flow and associated design methodology are inspired by a previously-developed application programming interface (API) called the Hybrid Task Graph Scheduler (HTGS). HTGS was developed for implementing scalable workflows for high-performance computing applications on compute nodes that have large numbers of processing cores, and that may be equipped with multiple GPUs. However, HTGS has a limitation due to its relatively loose use of dataflow techniques (or other forms of model-based design), which results in a significant designer effort being required to apply the provided APIs effectively. The main contributions of the thesis are summarized as follows: (1) Development of a companion tool to HTGS that is called the HTGS Model-based Engine (HMBE). HMBE introduces novel capabilities to automatically analyze application dataflow graphs and generate efficient schedules for these graphs through hybrid compile-time and runtime analysis. The systematic, model-based approaches provided by HMBE enable the automation of complex tasks that must be performed manually when using HTGS alone. We have demonstrated the effectiveness of HMBE and the associated model-based design methodology through extensive experiments involving two case studies: an image stitching application for large scale microscopy images, and a background subtraction application for multispectral video streams. (2) Integration of HMBE with HTGS to develop a new design tool for the design and implementation of high-performance signal processing systems. This tool, called HMBE-Integrated-HTGS (HI-HTGS), provides novel capabilities for model-based system design, memory management, and scheduling targeted to multicore platforms. HMBE takes as input a single- or multi-dimensional dataflow model of the given signal processing application. The tool then expands the dataflow model into an expanded representation that exposes more parallelism and provides significantly more detail on the interactions between different application tasks (dataflow actors). This expanded representation is derived by HI-HTGS at compile-time and provided as input to the HI-HTGS runtime system. The runtime system in turn applies the expanded representation to guide dynamic scheduling decisions throughout system execution. (3) Extension of HMBE to the class of CPU-GPU platforms motivated above. We call this new model-based design tool the CPU-GPU Model-Based Engine (CGMBE). CGMBE uses an unfolded dataflow graph representation of the application along with thread-pool-based executors, which are optimized for efficient operation on the targeted CPU-GPU platform. This approach automates complex aspects of the design and implementation process for signal processing system designers while maximizing the utilization of computational power, reducing the memory footprint for both the CPU and GPU, and facilitating experimentation for tuning performance-oriented designs

Comparison of Multiscale Imaging Methods for Brain Research

A major challenge in neuroscience is how to study structural alterations in the brain. Even small changes in synaptic composition could have severe outcomes for body functions. Many neuropathological diseases are attributable to disorganization of particular synaptic proteins. Yet, to detect and comprehensively describe and evaluate such often rather subtle deviations from the normal physiological status in a detailed and quantitative manner is very challenging. Here, we have compared side-by-side several commercially available light microscopes for their suitability in visualizing synaptic components in larger parts of the brain at low resolution, at extended resolution as well as at super-resolution. Microscopic technologies included stereo, widefield, deconvolution, confocal, and super-resolution set-ups. We also analyzed the impact of adaptive optics, a motorized objective correction collar and CUDA graphics card technology on imaging quality and acquisition speed. Our observations evaluate a basic set of techniques, which allow for multi-color brain imaging from centimeter to nanometer scales. The comparative multi-modal strategy we established can be used as a guide for researchers to select the most appropriate light microscopy method in addressing specific questions in brain research, and we also give insights into recent developments such as optical aberration corrections

Optical projection tomography for rapid whole mouse brain imaging

In recent years, three-dimensional mesoscopic imaging has gained significant importance in life sciences for fundamental studies at the whole-organ level. In this manuscript, we present an optical projection tomography (OPT) method designed for imaging of the intact mouse brain. The system features an isotropic resolution of ~50 μm and an acquisition time of four to eight minutes, using a 3-day optimized clearing protocol. Imaging of the brain autofluorescence in 3D reveals details of the neuroanatomy, while the use of fluorescent labels displays the vascular network and amyloid deposition in 5xFAD mice, an important model of Alzheimer’s disease (AD). Finally, the OPT images are compared with histological slices

Forum Bildverarbeitung 2022

Bildverarbeitung verknüpft das Fachgebiet die Sensorik von Kameras – bildgebender Sensorik – mit der Verarbeitung der Sensordaten – den Bildern. Daraus resultiert der besondere Reiz dieser Disziplin. Der vorliegende Tagungsband des „Forums Bildverarbeitung“, das am 24. und 25.11.2022 in Karlsruhe als Veranstaltung des Karlsruher Instituts für Technologie und des Fraunhofer-Instituts für Optronik, Systemtechnik und Bildauswertung stattfand, enthält die Aufsätze der eingegangenen Beiträge

Optimization of the holographic process for imaging and lithography

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 272-297).Since their invention in 1948 by Dennis Gabor, holograms have demonstrated to be important components of a variety of optical systems and their implementation in new fields and methods is expected to continue growing. Their ability to encode 3D optical fields on a 2D plane opened the possibility of novel applications for imaging and lithography. In the traditional form, holograms are produced by the interference of a reference and object waves recording the phase and amplitude of the complex field. The holographic process has been extended to include different recording materials and methods. The increasing demand for holographic-based systems is followed by a need for efficient optimization tools designed for maximizing the performance of the optical system. In this thesis, a variety of multi-domain optimization tools designed to improve the performance of holographic optical systems are proposed. These tools are designed to be robust, computationally efficient and sufficiently general to be applied when designing various holographic systems. All the major forms of holographic elements are studied: computer generated holograms, thin and thick conventional holograms, numerically simulated holograms and digital holograms. Novel holographic optical systems for imaging and lithography are proposed. In the case of lithography, a high-resolution system based on Fresnel domain computer generated holograms (CGHs) is presented. The holograms are numerically designed using a reduced complexity hybrid optimization algorithm (HOA) based on genetic algorithms (GAs) and the modified error reduction (MER) method. The algorithm is efficiently implemented on a graphic processing unit. Simulations as well as experimental results for CGHs fabricated using electron-beam lithography are presented. A method for extending the system's depth of focus is proposed. The HOA is extended for the design and optimization of multispectral CGHs applied for high efficiency solar concentration and spectral splitting. A second lithographic system based on optically recorded total internal reflection (TIR) holograms is studied. A comparative analysis between scalar and (cont.) vector diffraction theories for the modeling and simulation of the system is performed.A complete numerical model of the system is conducted including the photoresist response and first order models for shrinkage of the holographic emulsion. A novel block-stitching algorithm is introduced for the calculation of large diffraction patterns that allows overcoming current computational limitations of memory and processing time. The numerical model is implemented for optimizing the system's performance as well as redesigning the mask to account for potential fabrication errors. The simulation results are compared to experimentally measured data. In the case of imaging, a segmented aperture thin imager based on holographically corrected gradient index lenses (GRIN) is proposed. The compound system is constrained to a maximum thickness of 5mm and utilizes an optically recorded hologram for correcting high-order optical aberrations of the GRIN lens array. The imager is analyzed using system and information theories. A multi-domain optimization approach is implemented based on GAs for maximizing the system's channel capacity and hence improving the information extraction or encoding process. A decoding or reconstruction strategy is implemented using the superresolution algorithm. Experimental results for the optimization of the hologram's recording process and the tomographic measurement of the system's space-variant point spread function are presented. A second imaging system for the measurement of complex fluid flows by tracking micron sized particles using digital holography is studied. A stochastic theoretical model based on a stability metric similar to the channel capacity for a Gaussian channel is presented and used to optimize the system. The theoretical model is first derived for the extreme case of point source particles using Rayleigh scattering and scalar diffraction theory formulations. The model is then extended to account for particles of variable sizes using Mie theory for the scattering of homogeneous dielectric spherical particles. The influence and statistics of the particle density dependent cross-talk noise are studied. Simulation and experimental results for finding the optimum particle density based on the stability metric are presented. For all the studied systems, a sensitivity analysis is performed to predict and assist in the correction of potential fabrication or calibration errors.by José Antonio Domínguez-Caballero.Ph.D