3D Medical Image Lossless Compressor Using Deep Learning Approaches

The ever-increasing importance of accelerated information processing, communica-tion, and storing are major requirements within the big-data era revolution. With the extensive rise in data availability, handy information acquisition, and growing data rate, a critical challenge emerges in efficient handling. Even with advanced technical hardware developments and multiple Graphics Processing Units (GPUs) availability, this demand is still highly promoted to utilise these technologies effectively. Health-care systems are one of the domains yielding explosive data growth. Especially when considering their modern scanners abilities, which annually produce higher-resolution and more densely sampled medical images, with increasing requirements for massive storage capacity. The bottleneck in data transmission and storage would essentially be handled with an effective compression method. Since medical information is critical and imposes an influential role in diagnosis accuracy, it is strongly encouraged to guarantee exact reconstruction with no loss in quality, which is the main objective of any lossless compression algorithm. Given the revolutionary impact of Deep Learning (DL) methods in solving many tasks while achieving the state of the art results, includ-ing data compression, this opens tremendous opportunities for contributions. While considerable efforts have been made to address lossy performance using learning-based approaches, less attention was paid to address lossless compression. This PhD thesis investigates and proposes novel learning-based approaches for compressing 3D medical images losslessly.Firstly, we formulate the lossless compression task as a supervised sequential prediction problem, whereby a model learns a projection function to predict a target voxel given sequence of samples from its spatially surrounding voxels. Using such 3D local sampling information efficiently exploits spatial similarities and redundancies in a volumetric medical context by utilising such a prediction paradigm. The proposed NN-based data predictor is trained to minimise the differences with the original data values while the residual errors are encoded using arithmetic coding to allow lossless reconstruction.Following this, we explore the effectiveness of Recurrent Neural Networks (RNNs) as a 3D predictor for learning the mapping function from the spatial medical domain (16 bit-depths). We analyse Long Short-Term Memory (LSTM) models’ generalisabil-ity and robustness in capturing the 3D spatial dependencies of a voxel’s neighbourhood while utilising samples taken from various scanning settings. We evaluate our proposed MedZip models in compressing unseen Computerized Tomography (CT) and Magnetic Resonance Imaging (MRI) modalities losslessly, compared to other state-of-the-art lossless compression standards.This work investigates input configurations and sampling schemes for a many-to-one sequence prediction model, specifically for compressing 3D medical images (16 bit-depths) losslessly. The main objective is to determine the optimal practice for enabling the proposed LSTM model to achieve a high compression ratio and fast encoding-decoding performance. A solution for a non-deterministic environments problem was also proposed, allowing models to run in parallel form without much compression performance drop. Compared to well-known lossless codecs, experimental evaluations were carried out on datasets acquired by different hospitals, representing different body segments, and have distinct scanning modalities (i.e. CT and MRI).To conclude, we present a novel data-driven sampling scheme utilising weighted gradient scores for training LSTM prediction-based models. The objective is to determine whether some training samples are significantly more informative than others, specifically in medical domains where samples are available on a scale of billions. The effectiveness of models trained on the presented importance sampling scheme was evaluated compared to alternative strategies such as uniform, Gaussian, and sliced-based sampling

OPTIMIZING LEMPEL-ZIV FACTORIZATION FOR THE GPU ARCHITECTURE

Lossless data compression is used to reduce storage requirements, allowing for the relief of I/O channels and better utilization of bandwidth. The Lempel-Ziv lossless compression algorithms form the basis for many of the most commonly used compression schemes. General purpose computing on graphic processing units (GPGPUs) allows us to take advantage of the massively parallel nature of GPUs for computations other that their original purpose of rendering graphics. Our work targets the use of GPUs for general lossless data compression. Specifically, we developed and ported an algorithm that constructs the Lempel-Ziv factorization directly on the GPU. Our implementation bypasses the sequential nature of the LZ factorization and attempts to compute the factorization in parallel. By breaking down the LZ factorization into what we call the PLZ, we are able to outperform the fastest serial CPU implementations by up to 24x and perform comparatively to a parallel multicore CPU implementation. To achieve these speeds, our implementation outputted LZ factorizations that were on average only 0.01 percent greater than the optimal solution that what could be computed sequentially. We are also able to reevaluate the fastest GPU suffix array construction algorithm, which is needed to compute the LZ factorization. We are able to find speedups of up to 5x over the fastest CPU implementations

Parallel implementation of fractal image compression

Thesis (M.Sc.Eng.)-University of Natal, Durban, 2000.Fractal image compression exploits the piecewise self-similarity present in real images as a form of information redundancy that can be eliminated to achieve compression. This theory based on Partitioned Iterated Function Systems is presented. As an alternative to the established JPEG, it provides a similar compression-ratio to fidelity trade-off. Fractal techniques promise faster decoding and potentially higher fidelity, but the computationally intensive compression process has prevented commercial acceptance. This thesis presents an algorithm mapping the problem onto a parallel processor architecture, with the goal of reducing the encoding time. The experimental work involved implementation of this approach on the Texas Instruments TMS320C80 parallel processor system. Results indicate that the fractal compression process is unusually well suited to parallelism with speed gains approximately linearly related to the number of processors used. Parallel processing issues such as coherency, management and interfacing are discussed. The code designed incorporates pipelining and parallelism on all conceptual and practical levels ensuring that all resources are fully utilised, achieving close to optimal efficiency. The computational intensity was reduced by several means, including conventional classification of image sub-blocks by content with comparisons across class boundaries prohibited. A faster approach adopted was to perform estimate comparisons between blocks based on pixel value variance, identifying candidates for more time-consuming, accurate RMS inter-block comparisons. These techniques, combined with the parallelism, allow compression of 512x512 pixel x 8 bit images in under 20 seconds, while maintaining a 30dB PSNR. This is up to an order of magnitude faster than reported for conventional sequential processor implementations. Fractal based compression of colour images and video sequences is also considered. The work confirms the potential of fractal compression techniques, and demonstrates that a parallel implementation is appropriate for addressing the compression time problem. The processor system used in these investigations is faster than currently available PC platforms, but the relevance lies in the anticipation that future generations of affordable processors will exceed its performance. The advantages of fractal image compression may then be accessible to the average computer user, leading to commercial acceptance

Embedded Vision Systems: A Review of the Literature

Over the past two decades, the use of low power Field Programmable Gate Arrays (FPGA) for the acceleration of various vision systems mainly on embedded devices have become widespread. The reconfigurable and parallel nature of the FPGA opens up new opportunities to speed-up computationally intensive vision and neural algorithms on embedded and portable devices. This paper presents a comprehensive review of embedded vision algorithms and applications over the past decade. The review will discuss vision based systems and approaches, and how they have been implemented on embedded devices. Topics covered include image acquisition, preprocessing, object detection and tracking, recognition as well as high-level classification. This is followed by an outline of the advantages and disadvantages of the various embedded implementations. Finally, an overview of the challenges in the field and future research trends are presented. This review is expected to serve as a tutorial and reference source for embedded computer vision systems

Parallel implementation of fractal image compression

Thesis (M.Sc.Eng.)-University of Natal, Durban, 2000.Fractal image compression exploits the piecewise self-similarity present in real images as a form of information redundancy that can be eliminated to achieve compression. This theory based on Partitioned Iterated Function Systems is presented. As an alternative to the established JPEG, it provides a similar compression-ratio to fidelity trade-off. Fractal techniques promise faster decoding and potentially higher fidelity, but the computationally intensive compression process has prevented commercial acceptance. This thesis presents an algorithm mapping the problem onto a parallel processor architecture, with the goal of reducing the encoding time. The experimental work involved implementation of this approach on the Texas Instruments TMS320C80 parallel processor system. Results indicate that the fractal compression process is unusually well suited to parallelism with speed gains approximately linearly related to the number of processors used. Parallel processing issues such as coherency, management and interfacing are discussed. The code designed incorporates pipelining and parallelism on all conceptual and practical levels ensuring that all resources are fully utilised, achieving close to optimal efficiency. The computational intensity was reduced by several means, including conventional classification of image sub-blocks by content with comparisons across class boundaries prohibited. A faster approach adopted was to perform estimate comparisons between blocks based on pixel value variance, identifying candidates for more time-consuming, accurate RMS inter-block comparisons. These techniques, combined with the parallelism, allow compression of 512x512 pixel x 8 bit images in under 20 seconds, while maintaining a 30dB PSNR. This is up to an order of magnitude faster than reported for conventional sequential processor implementations. Fractal based compression of colour images and video sequences is also considered. The work confirms the potential of fractal compression techniques, and demonstrates that a parallel implementation is appropriate for addressing the compression time problem. The processor system used in these investigations is faster than currently available PC platforms, but the relevance lies in the anticipation that future generations of affordable processors will exceed its performance. The advantages of fractal image compression may then be accessible to the average computer user, leading to commercial acceptance

Need for speed:Achieving fast image processing in acute stroke care

This thesis aims to investigate the use of high-performance computing (HPC) techniques in developing imaging biomarkers to support the clinical workflow of acute stroke patients. In the first part of this thesis, we evaluate different HPC technologies and how such technologies can be leveraged by different image analysis applications used in the context of acute stroke care. More specifically, we evaluated how computers with multiple computing devices can be used to accelerate medical imaging applications in Chapter 2. Chapter 3 proposes a novel data compression technique that efficiently processes CT perfusion (CTP) images in GPUs. Unfortunately, the size of CTP datasets makes data transfers to computing devices time-consuming and, therefore, unsuitable in acute situations. Chapter 4 further evaluates the algorithm's usefulness proposed in Chapter 3 with two different applications: a double threshold segmentation and a time-intensity profile similarity (TIPS) bilateral filter to reduce noise in CTP scans. Finally, Chapter 5 presents a cloud platform for deploying high-performance medical applications for acute stroke patients. In Part 2 of this thesis, Chapter 6 presents a convolutional neural network (CNN) for detecting and volumetric segmentation of subarachnoid hemorrhages (SAH) in non-contrast CT scans. Chapter 7 proposed another method based on CNNs to quantify the final infarct volumes in follow-up non-contrast CT scans from ischemic stroke patients

The Fifth NASA Symposium on VLSI Design

The fifth annual NASA Symposium on VLSI Design had 13 sessions including Radiation Effects, Architectures, Mixed Signal, Design Techniques, Fault Testing, Synthesis, Signal Processing, and other Featured Presentations. The symposium provides insights into developments in VLSI and digital systems which can be used to increase data systems performance. The presentations share insights into next generation advances that will serve as a basis for future VLSI design

Storage Solutions for Big Data Systems: A Qualitative Study and Comparison

Big data systems development is full of challenges in view of the variety of application areas and domains that this technology promises to serve. Typically, fundamental design decisions involved in big data systems design include choosing appropriate storage and computing infrastructures. In this age of heterogeneous systems that integrate different technologies for optimized solution to a specific real world problem, big data system are not an exception to any such rule. As far as the storage aspect of any big data system is concerned, the primary facet in this regard is a storage infrastructure and NoSQL seems to be the right technology that fulfills its requirements. However, every big data application has variable data characteristics and thus, the corresponding data fits into a different data model. This paper presents feature and use case analysis and comparison of the four main data models namely document oriented, key value, graph and wide column. Moreover, a feature analysis of 80 NoSQL solutions has been provided, elaborating on the criteria and points that a developer must consider while making a possible choice. Typically, big data storage needs to communicate with the execution engine and other processing and visualization technologies to create a comprehensive solution. This brings forth second facet of big data storage, big data file formats, into picture. The second half of the research paper compares the advantages, shortcomings and possible use cases of available big data file formats for Hadoop, which is the foundation for most big data computing technologies. Decentralized storage and blockchain are seen as the next generation of big data storage and its challenges and future prospects have also been discussed