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

Platforms for handling and development of audiovisual data

Estágio realizado na MOG Solutions e orientado por Vítor TeixeiraTese de mestrado integrado. Engenharia Informátca e Computação. Faculdade de Engenharia. Universidade do Porto. 200

Progressive Lossless Image Compression Using Image Decomposition and Context Quantization

Lossless image compression has many applications, for example, in medical imaging, space photograph and film industry. In this thesis, we propose an efficient lossless image compression scheme for both binary images and gray-scale images. The scheme first decomposes images into a set of progressively refined binary sequences and then uses the context-based, adaptive arithmetic coding algorithm to encode these sequences. In order to deal with the context dilution problem in arithmetic coding, we propose a Lloyd-like iterative algorithm to quantize contexts. Fixing the set of input contexts and the number of quantized contexts, our context quantization algorithm iteratively finds the optimum context mapping in the sense of minimizing the compression rate. Experimental results show that by combining image decomposition and context quantization, our scheme can achieve competitive lossless compression performance compared to the JBIG algorithm for binary images, and the CALIC algorithm for gray-scale images. In contrast to CALIC, our scheme provides the additional feature of allowing progressive transmission of gray-scale images, which is very appealing in applications such as web browsing

Data compression techniques applied to high resolution high frame rate video technology

An investigation is presented of video data compression applied to microgravity space experiments using High Resolution High Frame Rate Video Technology (HHVT). An extensive survey of methods of video data compression, described in the open literature, was conducted. The survey examines compression methods employing digital computing. The results of the survey are presented. They include a description of each method and assessment of image degradation and video data parameters. An assessment is made of present and near term future technology for implementation of video data compression in high speed imaging system. Results of the assessment are discussed and summarized. The results of a study of a baseline HHVT video system, and approaches for implementation of video data compression, are presented. Case studies of three microgravity experiments are presented and specific compression techniques and implementations are recommended

Investigation of the effects of image compression on the geometric quality of digital protogrammetric imagery

We are living in a decade, where the use of digital images is becoming increasingly important. Photographs are now converted into digital form, and direct acquisition of digital images is becoming increasing important as sensors and associated electronics. Unlike images in analogue form, digital representation of images allows visual information to· be easily manipulated in useful ways. One practical problem of the digital image representation is that, it requires a very large number of bits and hence one encounters a fairly large volume of data in a digital production environment if they are stored uncompressed on the disk. With the rapid advances in sensor technology and digital electronics, the number of bits grow larger in softcopy photogrammetry, remote sensing and multimedia GIS. As a result, it is desirable to find efficient representation for digital images in order to reduce the memory required for storage, improve the data access rate from storage devices, and reduce the time required for transfer across communication channels. The component of digital image processing that deals with this problem is called image compression. Image compression is a necessity for the utilisation of large digital images in softcopy photogrammetry, remote sensing, and multimedia GIS. Numerous image Compression standards exist today with the common goal of reducing the number of bits needed to store images, and to facilitate the interchange of compressed image data between various devices and applications. JPEG image compression standard is one alternative for carrying out the image compression task. This standard was formed under the auspices ISO and CCITT for the purpose of developing an international standard for the compression and decompression of continuous-tone, still-frame, monochrome and colour images. The JPEG standard algorithm &Us into three general categories: the baseline sequential process that provides a simple and efficient algorithm for most image coding applications, the extended DCT-based process that allows the baseline system to satisfy a broader range of applications, and an independent lossless process for application demanding that type of compression. This thesis experimentally investigates the geometric degradations resulting from lossy JPEG compression on photogrammetric imagery at various levels of quality factors. The effects and the suitability of JPEG lossy image compression on industrial photogrammetric imagery are investigated. Examples are drawn from the extraction of targets in close-range photogrammetric imagery. In the experiments, the JPEG was used to compress and decompress a set of test images. The algorithm has been tested on digital images containing various levels of entropy (a measure of information content of an image) with different image capture capabilities. Residual data was obtained by taking the pixel-by-pixel difference between the original data and the reconstructed data. The image quality measure, root mean square (rms) error of the residual was used as a quality measure to judge the quality of images produced by JPEG(DCT-based) image compression technique. Two techniques, TIFF (IZW) compression and JPEG(DCT-based) compression are compared with respect to compression ratios achieved. JPEG(DCT-based) yields better compression ratios, and it seems to be a good choice for image compression. Further in the investigation, it is found out that, for grey-scale images, the best compression ratios were obtained when the quality factors between 60 and 90 were used (i.e., at a compression ratio of 1:10 to 1:20). At these quality factors the reconstructed data has virtually no degradation in the visual and geometric quality for the application at hand. Recently, many fast and efficient image file formats have also been developed to store, organise and display images in an efficient way. Almost every image file format incorporates some kind of compression method to manage data within common place networks and storage devices. The current major file formats used in softcopy photogrammetry, remote sensing and · multimedia GIS. were also investigated. It was also found out that the choice of a particular image file format for a given application generally involves several interdependent considerations including quality; flexibility; computation; storage, or transmission. The suitability of a file format for a given purpose is · best determined by knowing its original purpose. Some of these are widely used (e.g., TIFF, JPEG) and serve as exchange formats. Others are adapted to the needs of particular applications or particular operating systems

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