Browsing by Subject "Fluorescence microscopy."

Now showing 1 - 3 of 3

Open Access
Perceptual watersheds for cell segmentation in fluorescence microscopy images
(2012) Arslan, Salim
High content screening aims to analyze complex biological systems and collect quantitative data via automated microscopy imaging to improve the quality of molecular cellular biology research in means of speed and accuracy. More rapid and accurate high-throughput screening becomes possible with advances in automated microscopy image analysis, for which cell segmentation commonly constitutes the core step. Since the performance of cell segmentation directly a ects the output of the system, it is of great importance to develop e ective segmentation algorithms. Although there exist several promising methods for segmenting monolayer isolated and less con uent cells, it still remains an open problem to segment more con uent cells that grow in aggregates on layers. In order to address this problem, we propose a new marker-controlled watershed algorithm that incorporates human perception into segmentation. This incorporation is in the form of how a human locates a cell by identifying its correct boundaries and piecing these boundaries together to form the cell. For this purpose, our proposed watershed algorithm de nes four di erent types of primitives to represent di erent types of boundaries (left, right, top, and bottom) and constructs an attributed relational graph on these primitives to represent their spatial relations. Then, it reduces the marker identi cation problem to the problem of nding prede ned structural patterns in the constructed graph. Moreover, it makes use of the boundary primitives to guide the ooding process in the watershed algorithm. Working with uorescence microscopy images, our experiments demonstrate that the proposed algorithm results in locating better markers and obtaining better cell boundaries for both less and more con uent cells, compared to previous cell segmentation algorithms.
Open Access
Sensing and sensitizer activation by biological thiols and 1,2-dioxetanes based chemiluminescence probes
(2014) Turan, İlke Şimşek
Biologically important biothiols like Cystein (Cys), Homocystein (Hcy) and Glutathione (GSH) are vital for the maintenance of cellular redox status and alterations in their levels is linked to a number of severe diseases such as AIDS, cancer and Alzheimer‟s therefore the design and synthesis of nitroolefin functionalized bodipy dyes responding to biological thiols by both absorbance and emission changes have been accomplished. Through the incorporation of hydrophilic groups, bright signaling of biothiols in the longer wavelength region of the visible spectrum is deemed to operate in biological environment. With this knowledge, bioconjugation of the nitroolefin functionalized dyes with thiol groups like those belonging to cysteine residues on proteins has been proved via large spectral changes and targeted to visualize dynamics of proteins, cell-cell interactions, mechanisms of life cycles of proteins. Hence, the result suggests that nitroolefin functionalization of BODIPY dyes is a promising way to sense biological thiols and hence labeling proteins having thiol groups. Since GSH plays vital roles in the oxidative stress exists within the cells and thus, high concentration of it is the indication of cancer development, design and synthesis of cancer related parameter based activation of bodipy based photosensitizers have been achieved to enhance spatiotemporal selectivity in photonic sensitization of dissolved molecular oxygen and thus, improves the potential and practice of photodynamic therapy and their effectiveness are validated by cell culture studies. Chemiluminescence in principle can provide a rapid, qualitative and/or quantitative test for analytes of interest; because of that synthesis of novel probes for the sensing of biologically important (fluoride) anion have been devised to combine the power of chemiluminescence and self immolative amplifiers which offers a chemical avenue for enhancing the signal produced in response to a given analyte. Through the development of chemiluminogenic perspective for sensing of palladium ions, rapid and selective response of probe to palladium ions with regardless of their charge in aqueous environment have been accomplished. Considering the convenience of the methods and substantial results, we are confident that other probes combining the power of chemiluminescence will emerge.
Open Access
Smart markers for watershed-based cell segmentation
(2012) Koyuncu, Can Fahrettin
Automated cell imaging systems facilitate fast and reliable analysis of biological events at the cellular level. In these systems, the first step is usually cell segmentation that greatly affects the success of the subsequent system steps. On the other hand, similar to other image segmentation problems, cell segmentation is an ill-posed problem that typically necessitates the use of domain specific knowledge to obtain successful segmentations even by human subjects. The approaches that can incorporate this knowledge into their segmentation algorithms have a potential to greatly improve the segmentation results. In this study, we propose a new approach for the effective segmentation of live cells from phase-contrast microscopy. This approach introduces a new set of “smart markers” for a marker-controlled watershed algorithm, for which the identification of its markers is critical. The proposed approach relies on using domain specific knowledge, in the form of visual characteristics of the cells, to define the markers. We evaluate our approach on a total of 1954 cells. The experimental results demonstrate that the proposed approach is quite effective in identifying better markers compared to its counterparts. This will in turn be effective in improving the segmentation performance of a marker-controlled watershed algorithm.