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 role of pathology in patient management has evolved over time from the retrospective review of cells, tissue, and disease ('what happened') to a prospective outlook ('what will happen').... Show moreThe role of pathology in patient management has evolved over time from the retrospective review of cells, tissue, and disease ('what happened') to a prospective outlook ('what will happen'). Examination of a static, two-dimensional hematoxylin and eosin (H&E)-stained tissue slide has traditionally been the pathologist's primary task, but novel ancillary techniques enabled by technological breakthroughs have supported pathologists in their increasing ability to predict disease status and behaviour. Nevertheless, the informational limits of 2D, fixed tissue are now being reached and technological innovation is urgently needed to ensure that our understanding of disease entities continues to support improved individualized treatment options. Here we review pioneering work currently underway in the field of cancer pathology that has the potential to capture information beyond the current basic snapshot. A selection of exciting new technologies is discussed that promise to facilitate integration of the functional and multidimensional (space and time) information needed to optimize the prognostic and predictive value of cancer pathology. Learning how to analyse, interpret, and apply the wealth of data acquired by these new approaches will challenge the knowledge and skills of the pathology community. (c) 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. Show less
Understanding the mechanisms that regulate atherosclerotic plaque formation and evolution is a crucial step for developing treatment strategies that will prevent plaque progression and reduce... Show moreUnderstanding the mechanisms that regulate atherosclerotic plaque formation and evolution is a crucial step for developing treatment strategies that will prevent plaque progression and reduce cardiovascular events. Advances in signal processing and the miniaturization of medical devices have enabled the design of multimodality intravascular imaging catheters that allow complete and detailed assessment of plaque morphology and biology. However, a significant limitation of these novel imaging catheters is that they provide two-dimensional (2D) visualization of the lumen and vessel wall and thus they cannot portray vessel geometry and 3D lesion architecture. To address this limitation computer-based methodologies and user-friendly software have been developed. These are able to off-line process and fuse intravascular imaging data with X-ray or computed tomography coronary angiography (CTCA) to reconstruct coronary artery anatomy. The aim of this review article is to summarize the evolution in the field of coronary artery modeling; we thus present the first methodologies that were developed to model vessel geometry, highlight the modifications introduced in revised methods to overcome the limitations of the first approaches and discuss the challenges that need to be addressed, so these techniques can have broad application in clinical practice and research. Show less
In conclusion, this thesis proposes a new approach for reconstruction of coronary artery and the implanted BRS by fusion of OCT and X-ray angiography to analyze intracoronary ESS in vivo. The... Show moreIn conclusion, this thesis proposes a new approach for reconstruction of coronary artery and the implanted BRS by fusion of OCT and X-ray angiography to analyze intracoronary ESS in vivo. The studies conducted in this thesis demonstrate the feasibility of the proposed approach to analyze the detailed local coronary hemodynamics in patients, including the SS patterns after BRS implantation in coronary bifurcations. We observed that in vivo assessment of ESS was closely related to: (1) reconstruction of the side branches; (2) reconstruction of the BRS; (3) patient-specific flow; (4) post-processing portion size in which ESS was calculated. Based on these findings, we propose the following standard analysis procedures for assessment of intracoronary ESS in vivo: (1) reconstruct both the main vessel and its side branches to create a more accurate geometric model. (2) reconstruct BRS in naturally-bent shape and include it in the CFD analysis for assessment of ESS after BRS implantation; (3) use patient-specific coronary flow in the CFD analysis to have more accurate boundary condition; (4) set the proportion size according to the interrogated region of interest for quantification of the ESS in portions. 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
Lier, M.G.J.T.B. van; Lopriore, E.; Vandenbussche, F.P.H.A.; Streekstra, G.J.; Siebes, M.; Nikkels, P.G.J.; ... ; Wijngaard, J.P.H.M. van den 2016
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
