Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images

We study the problem of segmenting, reconstructing, and analyzing the structure growth of thrombi (clots) in blood vessels in vivo based on 2-photon microscopic image data. First, we develop an algorithm for segmenting clots in 3D microscopic images based on density-based clustering and methods for dealing with imaging artifacts. Next, we apply the union-of-balls (or alpha-shape) algorithm to reconstruct the boundary of clots in 3D. Finally, we perform experimental studies and analysis on the reconstructed clots and obtain quantitative data of thrombus growth and structures. We conduct experiments on laser-induced injuries in vessels of two types of mice (the wild type and the type with low levels of coagulation factor VII) and analyze and compare the developing clot structures based on their reconstructed clots from image data. The results we obtain are of biomedical significance. Our quantitative analysis of the clot composition leads to better understanding of the thrombus development, and is valuable to the modeling and verification of computational simulation of thrombogenesis

Molecular Imaging

The present book gives an exceptional overview of molecular imaging. Practical approach represents the red thread through the whole book, covering at the same time detailed background information that goes very deep into molecular as well as cellular level. Ideas how molecular imaging will develop in the near future present a special delicacy. This should be of special interest as the contributors are members of leading research groups from all over the world

Overcoming conventional modeling limitations using image- driven lattice-boltzmann method simulations for biophysical applications

The challenges involved in modeling biological systems are significant and push the boundaries of conventional modeling. This is because biological systems are distinctly complex, and their emergent properties are results of the interplay of numerous components/processes. Unfortunately, conventional modeling approaches are often limited by their inability to capture all these complexities. By using in vivo data derived from biomedical imaging, image-based modeling is able to overcome this limitation. In this work, a combination of imaging data with the Lattice-Boltzmann Method for computational fluid dynamics (CFD) is applied to tissue engineering and thrombogenesis. Using this approach, some of the unanswered questions in both application areas are resolved. In the first application, numerical differences between two types of boundary conditions: “wall boundary condition” (WBC) and “periodic boundary condition” (PBC), which are commonly utilized for approximating shear stresses in tissue engineering scaffold simulations is investigated. Surface stresses in 3D scaffold reconstructions, obtained from high resolution microcomputed tomography images are calculated for both boundary condition types and compared with the actual whole scaffold values via image-based CFD simulations. It is found that, both boundary conditions follow the same spatial surface stress patterns as the whole scaffold simulations. However, they under-predict the absolute stress values approximately by a factor of two. Moreover, it is found that the error grows with higher scaffold porosity. Additionally, it is found that the PBC always resulted in a lower error than the WBC. In a second tissue engineering study, the dependence of culture time on the distribution and magnitude of fluid shear in tissue scaffolds cultured under flow perfusion is investigated. In the study, constructs are destructively evaluated with assays for cellularity and calcium deposition, imaged using µCT and reconstructed for CFD simulations. It is found that both the shear stress distributions within scaffolds consistently increase with culture time and correlate with increasing levels of mineralized tissues within the scaffold constructs as seen in calcium deposition data and µCT reconstructions. In the thrombogenesis application, detailed analysis of time lapse microscopy images showing yielding of thrombi in live mouse microvasculature is performed. Using these images, image-based CFD modeling is performed to calculate the fluid-induced shear stresses imposed on the thrombi’s surfaces by the surrounding blood flow. From the results, estimates of the yield stress (A critical parameter for quantifying the extent to which thrombi material can resist deformation and breakage) are obtained for different blood vessels. Further, it is shown that the yielding observed in thrombi occurs mostly in the outer shell region while the inner core remains intact. This suggests that the core material is different from the shell. To that end, we propose an alternative mechanism of thrombogenesis which could help explain this difference. Overall, the findings from this work reveal that image-based modeling is a versatile approach which can be applied to different biomedical application areas while overcoming the difficulties associated with conventional modeling

Micro Soft Tissues Visualization Based on X-Ray Phase-Contrast Imaging

The current imaging methods have a limited ability to visualize microstructures of biological soft tissues. Small lesions cannot be detected at the early stage of the disease. Phase contrast imaging (PCI) is a novel non-invasive imaging technique that can provide high contrast images of soft tissues by the use of X-ray phase shift. It is a new choice in terms of non-invasively revealing soft tissue details. In this study, the lung and hepatic fibrosis models of mice and rats were used to investigate the ability of PCI in microstructures observation of soft tissues. Our results demonstrated that different liver fibrosis stages could be distinguished non-invasively by PCI. The three-dimensional morphology of a segment of blood vessel was constructed. Noteworthy, the blood clot inside the vessel was visualized in three dimensions which provided a precise description of vessel stenosis. Furthermore, the whole lung airways including the alveoli were obtained. We had specifically highlighted its use in the visualization and assessment of the alveoli. To our knowledge, this was the first time for non-invasive alveoli imaging using PCI. This finding may offer a new perspective on the diagnosis of respiratory disease. All the results confirmed that PCI will be a valuable tool in biological soft tissues imaging

Carotid plaque vulnerability assessment by microscopic morphology analysis, ultrasound and 3D model reconstruction

This thesis was submitted for the degree of Docter of Philosophy and awarded by Brunel University.Research suggests that plaque morphology plays a crucial role in determining plaque vulnerability. However the relationship between plaque morphology and rupture is still not clearly understood due to the limited information of plaque morphology. The aim of this study is to improve our understanding of the relationship between plaque morphology and rupture, and to use this to predict the risk of plaque rupture from the morphology at the molecular level. This can enable the identification of culprit lesions in clinical situations for assessing plaque rupture risk. Histological assessments were carried out on 18 carotid plaque specimens. The 3-D collagen, lipid and macrophage distributions along the entire length of the plaque were analysed in both ruptured and non-ruptured symptomatic plaques. In addition, plaque morphology on the rupture sites were examined and compared with the surrounding regions. It was found that ruptured plaques had thinner fibrous caps and larger lipid cores compared to non-ruptured plaques. Also, ruptured plaques had lower collagen content compared to non-ruptured plaques, and higher collagen contents upstream compared to downstream region from the plaque throat. At the rupture site there was lower collagen content, and a larger lipid core thickness behind a thin fibrous cap compared with the mean for the longitudinally adjacent and circumferential regions. Macrophage cells were located nearer to the boundary of the luminal wall in ruptured plaques. For both groups, the area occupied by macrophages is greater at the upstream shoulder of the plaque. There is a positive correlation between macrophage area and lipid core area, a negative correlation between macrophage area and collagen content, and between lipid core size and collagen content for both plaque groups. 3D reconstruction of ex-vivo specimens of carotid plaques were carried out by a combined analysis of US imaging and histology. To reconstruct accurate 3D plaque morphology, the non-linear tissue distortion in histological images caused by specimen preparation was corrected by a finite element (FE) based deformable registration procedure. This study shows that it is possible to generate a 3D patient specific plaque model using this method. In addition, the study also quantitatively assesses the tissue distortion caused by histological procedures. It shows that at least 30% tissue shrinkage is expected for plaque tissues. The histology analysis result was also used to evaluate ultrasound (US) tissue characterization accuracy. An ex-vivo 2D ultrasound scan set-up was used to obtain serial transverse images through an atherosclerotic plaque. The different plaque component region obtained from ultrasound images was compared with the associated histology result and photograph of the sections. Plaque tissue characterisation using ex-vivo US can be performed qualitatively, whereas lipid core assessment from ultrasound scan can be semi-quantitative. This finding combined with the negative correlation between lipid core size and collagen content, suggests the ability of US to indirectly quantify plaque collagen content. This study may serve as a platform for future studies on improving ultrasound tissue characterization, and may also potentially be used in risk assessment of plaque rupture