Fluorescence microscopy is a pivotal imaging technique to visualize biological processes and has been extensively utilized in live-cell morphology analysis. Despite its utility, related object detection and tracking tasks still face challenges due to large data scales, inferior data quality, and insufficient annotations, leading to reliance on adaptive thresholding. Current adaptive thresholding approaches have two significant limitations: Firstly, they cannot handle the heteroscedasticity of image data well and result in biased outputs. Secondly, they deal with frames of time-series imaging data independently and result in inconsistent detections over time. We introduce two novel optimization techniques to address these limitations and enhance detection and tracking results in live-cell imaging. The first one, ConvexVST, is a convex optimization approach to transform heteroscedastic data into homoscedastic data, making them more tractable for subsequent analysis. The second one, Joint Thresholding, is a graph-based approach to get the optimal adaptive thresholds while maintaining temporal consistency. Our methods demonstrate superior performance across various object detection and tracking tasks. Specifically, when applied to microglia imaging data, our techniques enable the acquisition of more complete cell morphology and more accurate detection of microglia tips. Furthermore, by integrating these techniques with existing frameworks, we propose an advanced pipeline for embryonic cell detection and tracking in light-sheet microscopy images, which is streets ahead of state-of-the-art peer methods and sets a new benchmark in the field. / Doctor of Philosophy / Fluorescence microscopy is an important imaging tool for observing biological processes and is widely used to study live-cell structures and activities. However, detecting and tracking objects in these images can be difficult because of the large amount of data, poor image quality, and lack of accurate annotations. It leads to the reliance on basic image segmentation approaches, which try to distinguish foreground from background by setting intensity thresholds. These methods have two main problems: they don't handle varying noise in image data well, resulting in inaccurate outputs, and they analyze each frame in a sequence of images independently, causing inconsistencies over time. To solve these issues, we developed two new techniques to improve detection performance in live-cell imaging. The first one, ConvexVST, makes the noise levels in image data more uniform, simplifying the following analysis. The second one, Joint Thresholding, can find the best intensity thresholds while maintaining consistency across frames over time. Our methods have shown significant improvements in detecting and tracking objects. For example, when applied to images of microglia (a type of brain cell), they provide more complete cell shapes and more accurate detection of cell structures. Additionally, by combining these techniques with existing frameworks, we create an advanced pipeline for detecting and tracking embryonic cells that outperforms current leading methods.

No Brasil, carrapatos do gênero Rhipicephalus são representados pelas espécies Rhipicephalus sanguineuss.l. (Latreille) e Rhipicephalus (Boophilus) microplus (Canestrini), sendo que a primeira espécie possui especificidade com cães domésticos e a segunda com bovinos. Para o cão, R. sanguineus s.l. é o principal vetor de agentes causadores da babesiose canina e da erliquiose, enquanto que nos bovinos, R. microplus é responsável, principalmente, pela transmissão de agentes causadores da babesiose e anaplasmose. Alguns dos patógenos causadores dessas doenças são difíceis de serem cultivados in vitro, e não crescem em meios artificiais, especialmente Anaplasma spp. Assim, muitas linhagens celulares de carrapatos foram desenvolvidas nos últimos 40 anos e têm sido amplamente utilizadas para isolamento e propagação de microrganismos patogênicos. Cultivos celulares obtidos de células embrionárias de carrapatos oferecem um sistema de vetor in vitro, que é útil principalmente para estudos de agentes intracelulares. Dessa forma, a obtenção de culturas de células embrionárias de R. sanguineus (origens tropical e temperada) e de R. (B.) microplus, bem como, sua infecção com Ehrlichia canis e Anaplasma marginale, respectivamente, são objetivos do presente estudo. Os cultivos celulares dessas espécies de carrapatos foram preparados com massas de ovos de diferentes idades e mantidos à 30 °C em meio de cultura L15-B, suplementado com 10% de Triptose Fosfato e 20% de Soro Fetal Bovino. Subcultivos foram realizados após a formação da monocamada celular confluente. As identidades celulares foram confirmadas pela PCR e sequenciamento, utilizando um fragmento do gene mitocondrial 16S rDNA. As sequências das culturas de células de R. sanguineus (tropical e temperada) e de R. microplus foram depositadas no GenBank. Essas culturas de células foram infectadas com E. canis e A. marginale (cepas Jaboticabal), respectivamente, e mantidas em meio L-15B (Vitrocell) suplementado com Soro Fetal Bovino enriquecido com ferro (Hyclone) nas concentrações de 2% e 5%. As células infectadas foram mantidas em propagações sucessivas até a terceira passagem, para novas culturas de células não infectadas, sendo então criopreservadas. O DNA extraído das células infectadas e não infectadas de R. sanguineus (de ambas as origens) e de R. microplus, foi analisado pela PCR quantitativa em tempo real (qPCR), utilizando os genes E. canis-dsb e msp1β, respectivamente. Propagações de células de carrapatos infectadas para as novas culturas de R. sanguineus (origem tropical) e R. (B) microplus, foram bem sucedidas. Por outro lado, as células de R. sanguineus (origem temperada) não se tornaram infectadas no presente estudo. / In Brazil, ticks of the genus Rhipicephalus are represented by the species Rhipicephalus sanguineus s.l. (Latreille) and Rhipicephalus (Boophilus) microplus (Canestrini), being that the first one has specificity with domestic dogs and the second with cattle. For dogs, R. sanguineus s.l. is the main vector of causative agents of canine babesiosis and ehrlichiosis, whereas in cattle, R. microplus is responsible, mainly, for the transmission of agents that cause babesiosis and anaplasmosis. Some of the pathogens that cause these diseases are difficult to grow in vitro, and do not grow on artificial media, especially Anaplasma spp. Therefore, many tick cell lines were developed in the last 40 years and have been used for the isolation and propagation of pathogenic microorganisms. Cell cultures obtained from embryonic tick cells offer an in vitro vector system, which is mainly useful for studies of intracellular agents. The aim of the present study was to obtain cultures of R. sanguineus (tropical and temperate lineages) and R. microplus embryonic cells and their infection with Ehrlichia canis and Anaplasma marginale. Cell cultures from the tick species were prepared with egg masses of different ages and kept at 30 ° C in L15-B culture medium supplemented with 10% Tryptose Broth and 20% Fetal Bovine Serum. Subcultures were done after confluent cell monolayer formation. Cellular identities were confirmed by PCR and sequencing using a 16S rDNA mitochondrial gene fragment. Sequences of R. sanguineus (tropical and temperate) and R. microplus cell cultures were deposited on GenBank. These cell cultures were infected with E. canis and A. marginale (Jaboticabal strains), respectively, and maintained in L-15B medium and Fetal Bovine Serum with iron (Hyclone) supplemented at 2% and 5% concentrations. The infected cells were maintained in successive propagations until the third passage, to new cultures of uninfected cells, and then were cryopreserved. DNA extracted from infected and uninfected R. sanguineus (both origin) and R. microplus cells was analyzed by quantitative real-time PCR (qPCR) using the E. canis-dsb and msp1β genes, respectively. Propagations of infected tick cells to the new cultures of R. sanguineus (tropical origin) and R. microplus, were successful. On the other hand, the R. sanguineus cells (temperate origin) did become infected in the present study.