<p>The knowledge of the human genome sequence, as revealed in the HUGO project, has created exciting new possibilities for biomedical research. The Swedish Human Proteome Resource (HPR) program aims to make use of this information to gain further insight into the human proteome. Recombinant proteins are generated from coding sequences identified from the human genome sequence and used to produce specific antibodies to target proteins. Antibodies are subsequently utilized for functional analysis of the corresponding proteins using tissue micro arrays. The aim of my project was to investigate the possibility of distinguishing characteristic distribution patterns of intracellular proteins in the resolution capacity offered by light microscopy. A map of representative distribution patterns was created using immunohistological staining with commercially available antibodies toward well-characterised proteins in the cell. Such a map could then aid in interpreting the results of immunohistological staining of intracellular proteins using antibodies produced within the Human Proteome Resource program. Proteins manifested in nucleus, nuclear membrane and plasma membrane were clearly visible at the expected location. Proteins manifested in different organelles in the cytoplasm however, showed all a similar staining pattern, making determination of exact protein location uncertain. A possible explanation is the resolution of the light microscope not being sufficient to visualize certain proteins specific to organelles in the cytoplasm. Results may also have been influenced by the choice of secondary antibody, where the strenghtened signal generated by an enzyme labelled polymer may have a negative effect on depiction of details in the image generated.</p>

The knowledge of the human genome sequence, as revealed in the HUGO project, has created exciting new possibilities for biomedical research. The Swedish Human Proteome Resource (HPR) program aims to make use of this information to gain further insight into the human proteome. Recombinant proteins are generated from coding sequences identified from the human genome sequence and used to produce specific antibodies to target proteins. Antibodies are subsequently utilized for functional analysis of the corresponding proteins using tissue micro arrays. The aim of my project was to investigate the possibility of distinguishing characteristic distribution patterns of intracellular proteins in the resolution capacity offered by light microscopy. A map of representative distribution patterns was created using immunohistological staining with commercially available antibodies toward well-characterised proteins in the cell. Such a map could then aid in interpreting the results of immunohistological staining of intracellular proteins using antibodies produced within the Human Proteome Resource program. Proteins manifested in nucleus, nuclear membrane and plasma membrane were clearly visible at the expected location. Proteins manifested in different organelles in the cytoplasm however, showed all a similar staining pattern, making determination of exact protein location uncertain. A possible explanation is the resolution of the light microscope not being sufficient to visualize certain proteins specific to organelles in the cytoplasm. Results may also have been influenced by the choice of secondary antibody, where the strenghtened signal generated by an enzyme labelled polymer may have a negative effect on depiction of details in the image generated.

Bright field cellular microscopy offers an image capturing method that is both non-invasive and simple to implement. However, the resulting micrographs pose challenges for image segmentation which are compounded when the subject cells are tightly clustered or overlapping. Filamentous cyanobacteria are a type of organism that grow as linearly arranged cells forming chain-like filaments. Existing methods for bright field cell segmentation perform poorly on micrographs of these bacteria, and are incapable of identifying the filaments. Existing filament tracking methods are rudimentary, and cannot reliably account for overlapping or parallel touching filaments. We propose a new approach for identifying filaments in bright field micrographs by combining information about both filaments and cells. This information is used by an evolutionary strategy to iteratively construct a continuous spline representation that tracks the medial line of the filaments. We demonstrate that overlapping and parallel touching filaments are handled appropriately in many difficult cases.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Estudos em animais experimentais evidenciaram associações significativas entre esquistossomose mansoni e hipercolesterolemia. Estudos in vitro e in vivo já demonstraram que o colesterol é essencial para Schistosoma mansoni, embora este não tenha capacidade de sintetizá-lo. A captação é realizada a partir do ambiente (cultivo ou hospedeiro) através do tegumento. O colesterol está envolvido nos mecanismos de evasão do helminto contra a resposta imunológica, além de poder participar na modulação da sinalização celular e reprodução, estimulando os órgãos reprodutores dos helmintos adultos como observado na fase aguda da infecção experimental. Este trabalho tem como objetivo avaliar se o mesmo fenômeno ocorre na fase crônica. Os helmintos foram recuperados de dez camundongos submetidos à dieta hiperlipídica ou padrão (controle) foram corados pelo carmin cloridrico e montados, individualmente, em lâmina histológica com bálsamo do Canadá. A preparação foi analisada por microscopia de campo claro nos seguintes caracteres: tegumento e o sistema reprodutor nos vermes machos (lobos testiculares, vesícula seminal, lobos testiculares supranumerários e canal ginecóforo) e, nas fêmeas (ovário, oótipo, útero, ovo, glândulas vitelínicas e espermateca). Posteriormente, algumas lâminas foram separadas para visualização pela microscopia confocal dos órgãos do sistema reprodutores acima descritos. Apesar de ter sido observado uma maior quantidade de espermatozoides, uma maior quantidade de oócitos sendo liberados no grupo da dieta, não houve diferença estatística significativa (p>0,05) entre os grupos analisados. Houve um aumento na oogênese como observado na fase aguda. Dessa forma, o colesterol pode estar relacionado com a estimulação na atividade dos órgãos reprodutores dos helmintos adultos na fase crônica da infecção. / Studies in experimental animals showed significant associations between with schistosomiasis and hypercholesterolemia. In vitro and in vivo studies have demonstrated that cholesterol is essential for Schistosoma mansoni, although this is not able to synthesize it. The capture is carried out from the environment (cultivation or host) through the tegument. The capture is carried out from the middle (cultivation or host) through the tegument. Cholesterol is involved in the helminth evasion mechanisms against the immune response, and can participate in the modulation of cell signaling and reproduction of worms by stimulating the reproductive organs of adult worms as observed in the acute phase of experimental infection. This study aims to evaluate whether the same phenomenon occurs in the chronic phase. Helminthes recovered from ten mice subjected to high fat diet or standard (control) were stained with hydrochloric carmine and mounted individually on histological slide with Canada balsam. The preparation was analyzed by bright field microscopy the following characteristics: oral sucker and ventral sucker, tubercles on tegument and the reproductive system in male worms (lobes testicular, seminal vesicles, supernumerary testicular lobes and gynaecophoric canal), and in females (ovary, ootype, uterus, egg, vitelline glands and spermatheca). Subsequently, some slides were separated for confocal microscopy for visualization of the organs of the reproductive system described above. Despite having been observed a higher amount of sperm, a larger number of oocytes are released in the diet group, there was no statistically significant difference (p> 0.05) between the groups. There was an increase in oogenesis as observed in the acute phase. Thus, cholesterol may be related to the stimulation of the activity of the reproductive organs of adult helminths in the chronic phase of infection.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Estudos em animais experimentais evidenciaram associações significativas entre esquistossomose mansoni e hipercolesterolemia. Estudos in vitro e in vivo já demonstraram que o colesterol é essencial para Schistosoma mansoni, embora este não tenha capacidade de sintetizá-lo. A captação é realizada a partir do ambiente (cultivo ou hospedeiro) através do tegumento. O colesterol está envolvido nos mecanismos de evasão do helminto contra a resposta imunológica, além de poder participar na modulação da sinalização celular e reprodução, estimulando os órgãos reprodutores dos helmintos adultos como observado na fase aguda da infecção experimental. Este trabalho tem como objetivo avaliar se o mesmo fenômeno ocorre na fase crônica. Os helmintos foram recuperados de dez camundongos submetidos à dieta hiperlipídica ou padrão (controle) foram corados pelo carmin cloridrico e montados, individualmente, em lâmina histológica com bálsamo do Canadá. A preparação foi analisada por microscopia de campo claro nos seguintes caracteres: tegumento e o sistema reprodutor nos vermes machos (lobos testiculares, vesícula seminal, lobos testiculares supranumerários e canal ginecóforo) e, nas fêmeas (ovário, oótipo, útero, ovo, glândulas vitelínicas e espermateca). Posteriormente, algumas lâminas foram separadas para visualização pela microscopia confocal dos órgãos do sistema reprodutores acima descritos. Apesar de ter sido observado uma maior quantidade de espermatozoides, uma maior quantidade de oócitos sendo liberados no grupo da dieta, não houve diferença estatística significativa (p>0,05) entre os grupos analisados. Houve um aumento na oogênese como observado na fase aguda. Dessa forma, o colesterol pode estar relacionado com a estimulação na atividade dos órgãos reprodutores dos helmintos adultos na fase crônica da infecção. / Studies in experimental animals showed significant associations between with schistosomiasis and hypercholesterolemia. In vitro and in vivo studies have demonstrated that cholesterol is essential for Schistosoma mansoni, although this is not able to synthesize it. The capture is carried out from the environment (cultivation or host) through the tegument. The capture is carried out from the middle (cultivation or host) through the tegument. Cholesterol is involved in the helminth evasion mechanisms against the immune response, and can participate in the modulation of cell signaling and reproduction of worms by stimulating the reproductive organs of adult worms as observed in the acute phase of experimental infection. This study aims to evaluate whether the same phenomenon occurs in the chronic phase. Helminthes recovered from ten mice subjected to high fat diet or standard (control) were stained with hydrochloric carmine and mounted individually on histological slide with Canada balsam. The preparation was analyzed by bright field microscopy the following characteristics: oral sucker and ventral sucker, tubercles on tegument and the reproductive system in male worms (lobes testicular, seminal vesicles, supernumerary testicular lobes and gynaecophoric canal), and in females (ovary, ootype, uterus, egg, vitelline glands and spermatheca). Subsequently, some slides were separated for confocal microscopy for visualization of the organs of the reproductive system described above. Despite having been observed a higher amount of sperm, a larger number of oocytes are released in the diet group, there was no statistically significant difference (p> 0.05) between the groups. There was an increase in oogenesis as observed in the acute phase. Thus, cholesterol may be related to the stimulation of the activity of the reproductive organs of adult helminths in the chronic phase of infection.

Understanding biology paves the way for discovering drugs targeting deadly diseases like cancer, and microscopy imaging is one of the most informative ways to study biology. However, analysis of large numbers of samples is often required to draw statistically verifiable conclusions. Automated approaches for analysis of microscopy image data makes it possible to handle large data sets, and at the same time reduce the risk of bias. Quantitative microscopy refers to computational methods for extracting measurements from microscopy images, enabling detection and comparison of subtle changes in morphology or behavior induced by varying experimental conditions. This thesis covers computational methods for segmentation and classification of biological samples imaged by microscopy. Recent increase in computational power has enabled the development of deep neural networks (DNNs) that perform well in solving real world problems. This thesis compares classical image analysis algorithms for segmentation of bacteria cells and introduces a novel method that combines classical image analysis and DNNs for improved cell segmentation and detection of rare phenotypes. This thesis also demonstrates a novel DNN for segmentation of clusters of cells (spheroid), with varying sizes, shapes and textures imaged by phase contrast microscopy. DNNs typically require large amounts of training data. This problem is addressed by proposing an automated approach for creating ground truths by utilizing multiple imaging modalities and classical image analysis. The resulting DNNs are applied to segment unstained cells from bright field microscopy images. In DNNs, it is often difficult to understand what image features have the largest influence on the final classification results. This is addressed in an experiment where DNNs are applied to classify zebrafish embryos based on phenotypic changes induced by drug treatment. The response of the trained DNN is tested by ablation studies, which revealed that the networks do not necessarily learn the features most obvious at visual examination. Finally, DNNs are explored for classification of cervical and oral cell samples collected for cancer screening. Initial results show that the DNNs can respond to very subtle malignancy associated changes. All the presented methods are developed using open-source tools and validated on real microscopy images.

The demountable splicing of optical fibres uses different types of connectors which ensures accurate position of connected fibres. If the optical fibres are aligned in free space, a view from two perpendicular viewing directions is necessary for a maximum aligning accuracy. The method of direct monitoring of optical fibres provides this possibility however, it is necessary to use two imaging systems. This problem can be solved by a special microscope, which is designed in this thesis. The microscope can visualize the alignment of optical fibres from two mutually perpendicular directions by moving the objective lens and inclined mirror. The diploma thesis also describes the procedure of designing an optical simulation of the connection of optical fibres. Based on it, the microscope is designed, adjusted and tested with various optical fibres.