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

Visually Lossless Perceptual Image Coding Based on Natural- Scene Masking Models

Perceptual coding is a subdiscipline of image and video coding that uses models of human visual perception to achieve improved compression efficiency. Nearly, all image and video coders have included some perceptual coding strategies, most notably visual masking. Today, modern coders capitalize on various basic forms of masking such as the fact that distortion is harder to see in very dark and very bright regions, in regions with higher frequency content, and in temporal regions with abrupt changes. However, beyond these obvious forms of masking, there are many other masking phenomena that occur (and co-occur) when viewing natural imagery. In this chapter, we present our latest research in perceptual image coding using natural-scene masking models. We specifically discuss: (1) how to predict local distortion visibility using improved natural-scene masking models and (2) how to apply the models to high efficiency video coding (HEVC). As we will demonstrate, these techniques can offer 10–20% fewer bits than baseline HEVC in the ultra-high-quality regime

Real-time video compression using DVQ and suffix trees

Video processing is a wide and varied subject area. Video compression is an important but difficult problem in video processing. Several methods and standards exist which address this problem with varying degrees of success depending on the performance measures adopted. The present research work focuses on the real-time aspect of video processing.;In particular we propose a real-time video compression algorithm based on the concept of differential vector quantization and the suffix tree. Differential vector quantization is a relatively new area that focuses on efficient compression of data. The present work integrates the compression provided by Differential vector Quantization and the speed achieved by using the suffix tree data structure to develop a new real-time video compression scheme.;Traditionally Suffix trees are used for string searching. In the present work, we exploit the unique structure of the suffix tree to represent image data on a tree as a DVQ dictionary. To support the special characteristics of natural images and video, the traditional suffix tree is extended to handle k-errors in the matching. The result is an orders of magnitude speedup in the matching process, making it possible to compress the video in real-time, without any special hardware.;Experimental results show the performance of the proposed methodology

Implementation issues in source coding

An edge preserving image coding scheme which can be operated in both a lossy and a lossless manner was developed. The technique is an extension of the lossless encoding algorithm developed for the Mars observer spectral data. It can also be viewed as a modification of the DPCM algorithm. A packet video simulator was also developed from an existing modified packet network simulator. The coding scheme for this system is a modification of the mixture block coding (MBC) scheme described in the last report. Coding algorithms for packet video were also investigated

Memory-efficient lossless video compression using temporal extended JPEG-LS and on-line compression

Use of temporal predictors in lossless video coders play a significant role in terms of compression gain, but comes with a cost of significant memory requirement since this approach requires to save at least one frame in buffer for residue calculation. An improvement to standard JPEG-LS based lossless video coding algorithm is proposed in this work which requires very small amount of memory comparing to the regular approach keeping the computational complexity low. To obtain a higher compression, a combination of spatial and temporal predictor model has been used where appropriate mode is selected adaptively on a pixel based analysis. Using only one reference frame, the context based temporal coder performs its calculation regarding mode selection and prediction error calculation with already reconstructed pixels. This method eliminates the overhead of transmitting the coding mode in the decoder side. The need for storage space to save the only reference frame is further reduced by introducing on-line lossy compression on that frame. Relevant pixels from the stored reference frame are obtained by partial on-the-fly decompression. The combination of temporally extended context based prediction and on-line compression achieves a significant gain in compression ratio comparing to standard frame-by-frame JPEG-LS video coding keeping the memory requirement low, making it usable as a lightweight lossless video coder for embedded systems

On the Effectiveness of Video Recolouring as an Uplink-model Video Coding Technique

For decades, conventional video compression formats have advanced via incremental improvements with each subsequent standard achieving better rate-distortion (RD) efficiency at the cost of increased encoder complexity compared to its predecessors. Design efforts have been driven by common multi-media use cases such as video-on-demand, teleconferencing, and video streaming, where the most important requirements are low bandwidth and low video playback latency. Meeting these requirements involves the use of computa- tionally expensive block-matching algorithms which produce excellent compression rates and quick decoding times. However, emerging use cases such as Wireless Video Sensor Networks, remote surveillance, and mobile video present new technical challenges in video compression. In these scenarios, the video capture and encoding devices are often power-constrained and have limited computational resources available, while the decoder devices have abundant resources and access to a dedicated power source. To address these use cases, codecs must be power-aware and offer a reasonable trade-off between video quality, bitrate, and encoder complexity. Balancing these constraints requires a complete rethinking of video compression technology. The uplink video-coding model represents a new paradigm to address these low-power use cases, providing the ability to redistribute computational complexity by offloading the motion estimation and compensation steps from encoder to decoder. Distributed Video Coding (DVC) follows this uplink model of video codec design, and maintains high quality video reconstruction through innovative channel coding techniques. The field of DVC is still early in its development, with many open problems waiting to be solved, and no defined video compression or distribution standards. Due to the experimental nature of the field, most DVC codec to date have focused on encoding and decoding the Luma plane only, which produce grayscale reconstructed videos. In this thesis, a technique called “video recolouring” is examined as an alternative to DVC. Video recolour- ing exploits the temporal redundancies between colour planes, reducing video bitrate by removing Chroma information from specific frames and then recolouring them at the decoder. A novel video recolouring algorithm called Motion-Compensated Recolouring (MCR) is proposed, which uses block motion estimation and bi-directional weighted motion-compensation to reconstruct Chroma planes at the decoder. MCR is used to enhance a conventional base-layer codec, and shown to reduce bitrate by up to 16% with only a slight decrease in objective quality. MCR also outperforms other video recolouring algorithms in terms of objective video quality, demonstrating up to 2 dB PSNR improvement in some cases

A practical comparison between two powerful PCC codec’s

Recent advances in the consumption of 3D content creates the necessity of efficient ways to visualize and transmit 3D content. As a result, methods to obtain that same content have been evolving, leading to the development of new methods of representations, namely point clouds and light fields. A point cloud represents a set of points with associated Cartesian coordinates associated with each point(x, y, z), as well as being able to contain even more information inside that point (color, material, texture, etc). This kind of representation changes the way on how 3D content in consumed, having a wide range of applications, from videogaming to medical ones. However, since this type of data carries so much information within itself, they are data-heavy, making the storage and transmission of content a daunting task. To resolve this issue, MPEG created a point cloud coding normalization project, giving birth to V-PCC (Video-based Point Cloud Coding) and G-PCC (Geometry-based Point Cloud Coding) for static content. Firstly, a general analysis of point clouds is made, spanning from their possible solutions, to their acquisition. Secondly, point cloud codecs are studied, namely VPCC and G-PCC from MPEG. Then, a state of art study of quality evaluation is performed, namely subjective and objective evaluation. Finally, a report on the JPEG Pleno Point Cloud, in which an active colaboration took place, is made, with the comparative results of the two codecs and used metrics.Os avanços recentes no consumo de conteúdo 3D vêm criar a necessidade de maneiras eficientes de visualizar e transmitir conteúdo 3D. Consequentemente, os métodos de obtenção desse mesmo conteúdo têm vindo a evoluir, levando ao desenvolvimento de novas maneiras de representação, nomeadamente point clouds e lightfields. Um point cloud (núvem de pontos) representa um conjunto de pontos com coordenadas cartesianas associadas a cada ponto (x, y, z), além de poder conter mais informação dentro do mesmo (cor, material, textura, etc). Este tipo de representação abre uma nova janela na maneira como se consome conteúdo 3D, tendo um elevado leque de aplicações, desde videojogos e realidade virtual a aplicações médicas. No entanto, este tipo de dados, ao carregarem com eles tanta informação, tornam-se incrivelmente pesados, tornando o seu armazenamento e transmissão uma tarefa hercúleana. Tendo isto em mente, a MPEG criou um projecto de normalização de codificação de point clouds, dando origem ao V-PCC (Video-based Point Cloud Coding) e G-PCC (Geometry-based Point Cloud Coding) para conteúdo estático. Esta dissertação tem como objectivo uma análise geral sobre os point clouds, indo desde as suas possívei utilizações à sua aquisição. Seguidamente, é efectuado um estudo dos codificadores de point clouds, nomeadamente o V-PCC e o G-PCC da MPEG, o estado da arte da avaliação de qualidade, objectiva e subjectiva, e finalmente, são reportadas as actividades da JPEG Pleno Point Cloud, na qual se teve uma colaboração activa