Advances in image reconstruction using either single or multimodality imaging data provide increasingly accurate three-dimensional (3D) patient's arterial models for shear stress evaluation using... Show moreAdvances in image reconstruction using either single or multimodality imaging data provide increasingly accurate three-dimensional (3D) patient's arterial models for shear stress evaluation using computational fluid dynamics (CFD). We aim to evaluate the impacts on endothelial shear stress (ESS) derived from a simple image reconstruction using 3D-quantitative coronary angiography (3D-QCA) versus a multimodality reconstruction method using optical coherence tomography (OCT) in patients' vessels treated with bioresorbable scaffolds. Seven vessels at baseline and five-year follow-up of seven patients from a previous CFD investigation were retrospectively selected for a head-to-head comparison of angiography-derived versus OCT-derived ESS. 3D-QCA significantly underestimated the minimum stent area [MSA] (-2.38mm2) and the stent length (-1.46 mm) compared to OCT-fusion method reconstructions. After carefully co-registering the region of interest for all cases with a sophisticated statistical method, the difference in MSA measurements as well as the inability of angiography to visualise the strut footprint in the lumen surface have translated to higher angiography-derived ESS than OCT-derived ESS (1.76 Pa or 1.52 times for the overlapping segment). The difference in ESS widened with a more restricted region of interest (1.97 Pa or 1.63 times within the scaffold segment). Angiography and OCT offer two distinctive methods of ESS calculation. Angiography-derived ESS tends to overestimate the ESS compared to OCT-derived ESS. Further investigations into ESS analysis resolution play a vital role in adopting OCT-derived ESS. Show less
The amount of 3D modelling applications in archaeology has increased enourmously over the last decade. 3D recording techniques allow researchers to quickly and accurately document... Show moreThe amount of 3D modelling applications in archaeology has increased enourmously over the last decade. 3D recording techniques allow researchers to quickly and accurately document archaeological evidence, and 3D reconstructions have created new possibilities to communicate the results to a larger public. In this latter case, however, numerous scholars have expressed their concern regarding the ethics of such digital representations, since they give prominence to a crystallized image of the past. The study presented here aims to make a practical contribution to a new understanding and use of 3D reconstructions, namely as “laboratories” to test hypotheses and visualize and evaluate alternative interpretations. In order to do so, an analysis of visual reconstructions of the early and late modern period is presented first, followed by a discussion of current applications of 3D digital reconstructions, with a special focus on cityscapes. Lastly, the implementation of a research-driven, intellectually transparent and GIS-based 3D reconstruction is proposed for the urban site of Koroneia, in Boeotia, Central Greece. With a strong focus on the automation and iteration of the reconstruction process, our 3D visualization provides an intuitive insight into hidden relationships and associations among data, and allows the creation and evaluation of alternative reconstruction hypotheses. Show less
We have studied shape with a particular focus on the zebrafish model system. The shape is an essential appearance of the phenotype of a biological specimen and it can be used to read out a... Show moreWe have studied shape with a particular focus on the zebrafish model system. The shape is an essential appearance of the phenotype of a biological specimen and it can be used to read out a current state or response or to study gene expression. So accurate shape analysis requires a precise shape description. Moreover, a sufficiently large sampling size of the specimens is necessary to ensure a justified and unbiased shape analysis. The latter is very important for high-throughput in compound screening. Therefore, top performance in zebrafish analysis requires high-throughput imaging (HTI). To deal with HTI, we aim to design an elaborate and well-performing HTI architecture. For the essential operations we need computational approaches to obtain the 2D/3D shape representations that are precise and yet can be acquired fast. The quality of the obtained shape descriptions will be validated in a straightforward manner with scalar primitives, i.e., the volume and surface area of a 3D shape. These primitives serve as 3D measurements for a robust primary shape assessment in the phenotype characterisation. Using only shape description is not sufficient, e.g., for high-resolution imaging on tissue and cellular level, so texture should be considered to complement and enhance the shape analysis. Show less
In this thesis, we discuss solutions of phenotype description based on the microscopy image analysis to deal with biological problems both in 2D and 3D space. Our description of patterns goes... Show moreIn this thesis, we discuss solutions of phenotype description based on the microscopy image analysis to deal with biological problems both in 2D and 3D space. Our description of patterns goes beyond conventional features and helps to visualize the unseen in feature dataset. These solutions share several common processes which are based on similar principles. Furthermore, we notice that advanced features and classier strategies can help us improve the performance of the solutions. The biological problems that we have studied include the endocytosis routing using high-throughput screening in 2D and time and 3D geometrical representation from biological structures. Show less
In developmental biology, the expression of genes is studied to understand development, phenotypes and to construct models to understand disease. In this thesis, we explore and validate biological... Show moreIn developmental biology, the expression of genes is studied to understand development, phenotypes and to construct models to understand disease. In this thesis, we explore and validate biological as well as computerized tools, to address research questions in developmental biology. Based on these techniques, we developed a workflow to generate a large number of 3D spatio-temporal patterns of gene expression. Though several techniques for gene expression analysis are available, most spatial gene expression data are only in 2D. In order to study gene expression and differentiation of structures during development at the same time, both spatial 3D information, and temporal data are essential. These spatio-temporal patterns of gene expression have to be generated. To that end, we have developed a workflow based on fluorescent in situ hybridization (FISH) (ZebraFISH;), confocal laser scanning microscopy (CLSM) and subsequent three-dimensional modeling with, in our case, TDR-3Dbase software- resulting in a large amount of 3D spatio-temporal patterns of gene expression, obtained in a straightforward and non-destructive manner. In the work described in this thesis, we applied the workflow to 30 genes in 5 developmental processes. 3D modeling and data mining software are used to analyse gene expression patterns in zebrafish embryos and across species Show less
