Fluorescence based spectroscopy and imaging techniques provide qualitative and quantitative diagnostic information about biological systems. Some tissue cells have inherent fluorescence characteristics, and when excited with light at a certain frequency, they can emit light of a slightly longer wavelength; a phenomenon known as autofluorescence. Differences in the autofluorescence emission spectra between healthy and diseased tissue may be used as a non-invasive diagnostic tool for the detection of diseases. In this thesis, I describe the design, fabrication, and testing of a miniaturized fluorescence imaging device for non-invasive clinical diagnosis in the gastrointestinal tract. The device is designed such that it can be turned completely wireless. The system includes three sub-modules: optical imaging, electronics control and image acquisition, and information processing and transmission. These modules were individually developed and tested before being integrated into a complete, externally powered device. The final integrated system is small in size (diameter: ~ 2.5 cm; length: ~ 11 cm). The performance of each individual module and the overall integrated system has been evaluated using fluorescent phantoms. It has been demonstrated that the miniaturized device can acquire spectrally-resolved fluorescence images. It has also been separately demonstrated that the image stream can be transmitted wirelessly. An important outcome of this feasibility study is the identification of important technological issues and pathways for future prototype development. / Thesis / Master of Applied Science (MASc)

Content Based Image Retrieval (CBIR) is an important research area in the field of multimedia information retrieval. The application of CBIR in the medical domain has been attempted before, however the use of CBIR in medical diagnostics is a daunting task. The goal of diagnostic medical image retrieval is to provide diagnostic support by displaying relevant past cases, along with proven pathologies as ground truths. Moreover, medical image retrieval can be extremely useful as a training tool for medical students and residents, follow-up studies, and for research purposes. Despite the presence of an impressive amount of research in the area of CBIR, its acceptance for mainstream and practical applications is quite limited. The research in CBIR has mostly been conducted as an academic pursuit, rather than for providing the solution to a need. For example, many researchers proposed CBIR systems where the image database consists of images belonging to a heterogeneous mixture of man-made objects and natural scenes while ignoring the practical uses of such systems. Furthermore, the intended use of CBIR systems is important in addressing the problem of "Semantic Gap". Indeed, the requirements for the semantics in an image retrieval system for pathological applications are quite different from those intended for training and education. Moreover, many researchers have underestimated the level of accuracy required for a useful and practical image retrieval system. The human eye is extremely dexterous and efficient in visual information processing; consequently, CBIR systems should be highly precise in image retrieval so as to be useful to human users. Unsurprisingly, due to these and other reasons, most of the proposed systems have not found useful real world applications. In this dissertation, an attempt is made to address the challenging problem of developing a retrieval system for medical diagnostics applications. More specifically, a system for semantic retrieval of Magnetic Resonance (MR) images in 3D brain volumes is proposed. The proposed retrieval system has a potential to be useful for clinical experts where the human eye may fail. Previously proposed systems used imprecise segmentation and feature extraction techniques, which are not suitable for precise matching requirements of the image retrieval in this application domain. This dissertation uses multiscale representation for image retrieval, which is robust against noise and MR inhomogeneity. In order to achieve a higher degree of accuracy in the presence of misalignments, an image registration based retrieval framework is developed. Additionally, to speed-up the retrieval system, a fast discrete wavelet based feature space is proposed. Further improvement in speed is achieved by semantically classifying of the human brain into various "Semantic Regions", using an SVM based machine learning approach. A novel and fast identification system is proposed for identifying a 3D volume given a 2D image slice. To this end, we used SVM output probabilities for ranking and identification of patient volumes. The proposed retrieval systems are tested not only for noise conditions but also for healthy and abnormal cases, resulting in promising retrieval performance with respect to multi-modality, accuracy, speed and robustness. This dissertation furnishes medical practitioners with a valuable set of tools for semantic retrieval of 2D images, where the human eye may fail. Specifically, the proposed retrieval algorithms provide medical practitioners with the ability to retrieve 2D MR brain images accurately and monitor the disease progression in various lobes of the human brain, with the capability to monitor the disease progression in multiple patients simultaneously. Additionally, the proposed semantic classification scheme can be extremely useful for semantic based categorization, clustering and annotation of images in MR brain databases. This research framework may evolve in a natural progression towards developing more powerful and robust retrieval systems. It also provides a foundation to researchers in semantic based retrieval systems on how to expand existing toolsets for solving retrieval problems.

Content Based Image Retrieval (CBIR) is an important research area in the field of multimedia information retrieval. The application of CBIR in the medical domain has been attempted before, however the use of CBIR in medical diagnostics is a daunting task. The goal of diagnostic medical image retrieval is to provide diagnostic support by displaying relevant past cases, along with proven pathologies as ground truths. Moreover, medical image retrieval can be extremely useful as a training tool for medical students and residents, follow-up studies, and for research purposes. Despite the presence of an impressive amount of research in the area of CBIR, its acceptance for mainstream and practical applications is quite limited. The research in CBIR has mostly been conducted as an academic pursuit, rather than for providing the solution to a need. For example, many researchers proposed CBIR systems where the image database consists of images belonging to a heterogeneous mixture of man-made objects and natural scenes while ignoring the practical uses of such systems. Furthermore, the intended use of CBIR systems is important in addressing the problem of "Semantic Gap". Indeed, the requirements for the semantics in an image retrieval system for pathological applications are quite different from those intended for training and education. Moreover, many researchers have underestimated the level of accuracy required for a useful and practical image retrieval system. The human eye is extremely dexterous and efficient in visual information processing; consequently, CBIR systems should be highly precise in image retrieval so as to be useful to human users. Unsurprisingly, due to these and other reasons, most of the proposed systems have not found useful real world applications. In this dissertation, an attempt is made to address the challenging problem of developing a retrieval system for medical diagnostics applications. More specifically, a system for semantic retrieval of Magnetic Resonance (MR) images in 3D brain volumes is proposed. The proposed retrieval system has a potential to be useful for clinical experts where the human eye may fail. Previously proposed systems used imprecise segmentation and feature extraction techniques, which are not suitable for precise matching requirements of the image retrieval in this application domain. This dissertation uses multiscale representation for image retrieval, which is robust against noise and MR inhomogeneity. In order to achieve a higher degree of accuracy in the presence of misalignments, an image registration based retrieval framework is developed. Additionally, to speed-up the retrieval system, a fast discrete wavelet based feature space is proposed. Further improvement in speed is achieved by semantically classifying of the human brain into various "Semantic Regions", using an SVM based machine learning approach. A novel and fast identification system is proposed for identifying a 3D volume given a 2D image slice. To this end, we used SVM output probabilities for ranking and identification of patient volumes. The proposed retrieval systems are tested not only for noise conditions but also for healthy and abnormal cases, resulting in promising retrieval performance with respect to multi-modality, accuracy, speed and robustness. This dissertation furnishes medical practitioners with a valuable set of tools for semantic retrieval of 2D images, where the human eye may fail. Specifically, the proposed retrieval algorithms provide medical practitioners with the ability to retrieve 2D MR brain images accurately and monitor the disease progression in various lobes of the human brain, with the capability to monitor the disease progression in multiple patients simultaneously. Additionally, the proposed semantic classification scheme can be extremely useful for semantic based categorization, clustering and annotation of images in MR brain databases. This research framework may evolve in a natural progression towards developing more powerful and robust retrieval systems. It also provides a foundation to researchers in semantic based retrieval systems on how to expand existing toolsets for solving retrieval problems.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / One of the main forms of diagnosis used nowadays matches the exams performed by analysis of diagnostic images. Due to a growing request for this kind of diagnostic and the repetitive manual procedure of the used methods by radiologists new ways are emerging to aid procedures. A tool that can help the physician to report a diagnosis is searching similar cases for that which is being held with the main function of increased safety to the radiologist in his notes. For this, a modular architecture for content-based diagnostic image retrieval was developed as a tool to aid diagnosis. Through the DICOM SR standard used to store radiological findings and measurements - commonly from CAD - was implemented in a PACS environment a structure that will provide storage and query contents extracted from diagnostic images. The contents extraction from images can be done by different processing methods that generate different parameters for storage and retrieval. The project was developed in partnership with a provider of solutions for PACS and the Applied Computing Laboratory of the Federal University of Santa Maria. / Uma das principais formas de diagnóstico utilizadas atualmente corresponde aos exames realizados por meio da análise de imagens diagnósticas. Devido à demanda crescente por esse tipo de exame e ao processo manual e repetitivo dos métodos utilizados pelos médicos radiologistas, começam a surgir novos meios para auxiliar os procedimentos. Uma ferramenta que pode ajudar o médico na formulação de diagnósticos é a busca de casos semelhantes àquele que está sendo realizado, tendo como função principal conferir maior segurança ao radiologista em seus apontamentos. Para tanto, foi desenvolvida uma arquitetura modular para recuperação de imagens diagnósticas baseada em conteúdo como uma ferramenta de auxílio a diagnósticos. Através do padrão DICOM SR, utilizado para armazenar achados radiológicos e mensurações - comumente provenientes de CAD - implementou-se, em um ambiente PACS, uma estrutura capaz de permitir o armazenamento e consulta de características extraídas das imagens diagnósticas. A extração de características das imagens pode ocorrer através de diferentes métodos de processamento que, por sua vez, geram diferentes parâmetros para armazenamento e consulta. O projeto foi desenvolvido em conjunto com uma empresa fornecedora de soluções de PACS e com o Laboratório de Computação Aplicada da Universidade Federal de Santa Maria.