Lossy-to-Lossless Compression of Biomedical Images Based on Image Decomposition

The use of medical imaging has increased in the last years, especially with magnetic resonance imaging (MRI) and computed tomography (CT). Microarray imaging and images that can be extracted from RNA interference (RNAi) experiments also play an important role for large-scale gene sequence and gene expression analysis, allowing the study of gene function, regulation, and interaction across a large number of genes and even across an entire genome. These types of medical image modalities produce huge amounts of data that, for several reasons, need to be stored or transmitted at the highest possible fidelity between various hospitals, medical organizations, or research units

High Dynamic Range Visual Content Compression

This thesis addresses the research questions of High Dynamic Range (HDR) visual contents compression. The HDR representations are intended to represent the actual physical value of the light rather than exposed value. The current HDR compression schemes are the extension of legacy Low Dynamic Range (LDR) compressions, by using Tone-Mapping Operators (TMO) to reduce the dynamic range of the HDR contents. However, introducing TMO increases the overall computational complexity, and it causes the temporal artifacts. Furthermore, these compression schemes fail to compress non-salient region differently than the salient region, when Human Visual System (HVS) perceives them differently. The main contribution of this thesis is to propose a novel Mapping-free visual saliency-guided HDR content compression scheme. Firstly, the relationship of Discrete Wavelet Transform (DWT) lifting steps and TMO are explored. A novel approach to compress HDR image by Joint Photographic Experts Group (JPEG) 2000 codec while backward compatible to LDR is proposed. This approach exploits the reversibility of tone mapping and scalability of DWT. Secondly, the importance of the TMO in the HDR compression is evaluated in this thesis. A mapping-free post HDR image compression based on JPEG and JPEG2000 standard codecs for current HDR image formats is proposed. This approach exploits the structure of HDR formats. It has an equivalent compression performance and the lowest computational complexity compared to the existing HDR lossy compressions (50% lower than the state-of-the-art). Finally, the shortcomings of the current HDR visual saliency models, and HDR visual saliency-guided compression are explored in this thesis. A spatial saliency model for HDR visual content outperform others by 10% for spatial visual prediction task with 70% lower computational complexity is proposed. Furthermore, the experiment suggested more than 90% temporal saliency is predicted by the proposed spatial model. Moreover, the proposed saliency model can be used to guide the HDR compression by applying different quantization factor according to the intensity of predicted saliency map

Algoritmos de compressão sem perdas para imagens de microarrays e alinhamento de genomas completos

Doutoramento em InformáticaNowadays, in the 21st century, the never-ending expansion of information is a major global concern. The pace at which storage and communication resources are evolving is not fast enough to compensate this tendency. In order to overcome this issue, sophisticated and efficient compression tools are required. The goal of compression is to represent information with as few bits as possible. There are two kinds of compression, lossy and lossless. In lossless compression, information loss is not tolerated so the decoded information is exactly the same as the encoded one. On the other hand, in lossy compression some loss is acceptable. In this work we focused on lossless methods. The goal of this thesis was to create lossless compression tools that can be used in two types of data. The first type is known in the literature as microarray images. These images have 16 bits per pixel and a high spatial resolution. The other data type is commonly called Whole Genome Alignments (WGA), in particularly applied to MAF files. Regarding the microarray images, we improved existing microarray-specific methods by using some pre-processing techniques (segmentation and bitplane reduction). Moreover, we also developed a compression method based on pixel values estimates and a mixture of finite-context models. Furthermore, an approach based on binary-tree decomposition was also considered. Two compression tools were developed to compress MAF files. The first one based on a mixture of finite-context models and arithmetic coding, where only the DNA bases and alignment gaps were considered. The second tool, designated as MAFCO, is a complete compression tool that can handle all the information that can be found in MAF files. MAFCO relies on several finite-context models and allows parallel compression/decompression of MAF files.Hoje em dia, no século XXI, a expansão interminável de informação é uma grande preocupação mundial. O ritmo ao qual os recursos de armazenamento e comunicação estão a evoluir não é suficientemente rápido para compensar esta tendência. De forma a ultrapassar esta situação, são necessárias ferramentas de compressão sofisticadas e eficientes. A compressão consiste em representar informação utilizando a menor quantidade de bits possível. Existem dois tipos de compressão, com e sem perdas. Na compressão sem perdas, a perda de informação não é tolerada, por isso a informação descodificada é exatamente a mesma que a informação que foi codificada. Por outro lado, na compressão com perdas alguma perda é aceitável. Neste trabalho, focámo-nos apenas em métodos de compressão sem perdas. O objetivo desta tese consistiu na criação de ferramentas de compressão sem perdas para dois tipos de dados. O primeiro tipo de dados é conhecido na literatura como imagens de microarrays. Estas imagens têm 16 bits por píxel e uma resolução espacial elevada. O outro tipo de dados é geralmente denominado como alinhamento de genomas completos, particularmente aplicado a ficheiros MAF. Relativamente às imagens de microarrays, melhorámos alguns métodos de compressão específicos utilizando algumas técnicas de pré-processamento (segmentação e redução de planos binários). Além disso, desenvolvemos também um método de compressão baseado em estimação dos valores dos pixéis e em misturas de modelos de contexto-finito. Foi também considerada, uma abordagem baseada em decomposição em árvore binária. Foram desenvolvidas duas ferramentas de compressão para ficheiros MAF. A primeira ferramenta, é baseada numa mistura de modelos de contexto-finito e codificação aritmética, onde apenas as bases de ADN e os símbolos de alinhamento foram considerados. A segunda, designada como MAFCO, é uma ferramenta de compressão completa que consegue lidar com todo o tipo de informação que pode ser encontrada nos ficheiros MAF. MAFCO baseia-se em vários modelos de contexto-finito e permite compressão/descompressão paralela de ficheiros MAF