Prog Biophys Mol Biol

Patient-specific modeling of ventricular electrophysiology requires an interpolated reconstruction of the 3-dimensional (3D) geometry of the patient ventricles from the low-resolution (Lo-res) clinical images. The goal of this study was to implement a processing pipeline for obtaining the interpolated reconstruction, and thoroughly evaluate the efficacy of this pipeline in comparison with alternative methods. The pipeline implemented here involves contouring the epi- and endocardial boundaries in Lo-res images, interpolating the contours using the variational implicit functions method, and merging the interpolation results to obtain the ventricular reconstruction. Five alternative interpolation methods, namely linear, cubic spline, spherical harmonics, cylindrical harmonics, and shape-based interpolation were implemented for comparison. In the thorough evaluation of the processing pipeline, Hi-res magnetic resonance (MR), computed tomography (CT), and diffusion tensor (DT) MR images from numerous hearts were used. Reconstructions obtained from the Hi-res images were compared with the reconstructions computed by each of the interpolation methods from a sparse sample of the Hi-res contours, which mimicked Lo-res clinical images. Qualitative and quantitative comparison of these ventricular geometry reconstructions showed that the variational implicit functions approach performed better than others. Additionally, the outcomes of electrophysiological simulations (sinus rhythm activation maps and pseudo-ECGs) conducted using models based on the various reconstructions were compared. These electrophysiological simulations demonstrated that our implementation of the variational implicit functions-based method had the best accuracy.DP1 HL123271/HL/NHLBI NIH HHS/United StatesDP1HL123271/DP/NCCDPHP CDC HHS/United StatesR01 HL103428/HL/NHLBI NIH HHS/United StatesR01-HL103428/HL/NHLBI NIH HHS/United States2015-08-19T00:00:00Z25148771PMC425386

Volumetric rendering for holographic display of medical data

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Architecture, 1988.Includes bibliographical references.Work funded by a joint IBM/MIT agreement.by Wendy J. Plesniak.M.S

3D Image Processing in System FOTOM NG

Import 06/11/2014V mé diplomové práci s názvem 3D zpracování fotografie v rámci systému FOTOM NG, se zabývám implementací nového modulu na platformě NetBeans, který bude připojen do systému FOTOM NG. Tento modul slouží k vytvoření 3D modelu pozorovaného objektu a disponuje velkou škálou funkcí pro manipulaci a analýzu. Vstupní data modulu jsou tvořena sérií snímků, například ultrazvuku krční tepny. Dále se v mé práci zmiňuji o měřící technice fotogrammetrii, teoretickým podkladem provázející 3D modelování a problematikou spojenou s procesem vývoje nového modulu. Samotná implementace je realizována v jazyce Java s využitím knihovny Java3D. Cílem je také navrhnout uživatelskou příručku a programátorskou dokumentaci.In my master thesis, titled 3D Image Processing in System FOTOM NG, I deal with the implementation of a new module on the NetBeans platform, which will be attached into the FOTOM NG system. This module serves to create a 3D model of the observed object and has a large range of functions for manipulation and analyzing. Input data of the module are consists of series of images, such as ultrasound of carotid artery. Next, in this thesis I writting about photogrammetric measurment technique, theoretical basis for 3D modeling and issues associated with the developing process of a new module. The implementation itself is realized in Java with using of the Java3D library. I will design user guide and programming documentation.460 - Katedra informatikyvelmi dobř

Computational estimation of haemodynamics and tissue stresses in abdominal aortic aneurysms

'o e Abdominal aortic aneurysm is a vascular disease involving a focal dilation of the aorta. The exact cause is unknown but possibilities include infection and weakening of the connective tissue. Risk factors include a history of atherosclerosis, current smoking and a close relative with the disease. Although abdominal aortic aneurysm can affect anyone, it is most often seen in older men, and may be present in up to 5.9 % of the population aged 80 years. Biomechanical factors such as tissue stresses and shear stresses have been shown to play a part in aneurysm progression, although the specific mechanisms are still to be determined. The growth rate of the abdominal aortic aneurysm has been found to correlate with the peak stress in the aneurysm wall and the blood flow is thought to influence disease development. In order to resolve the connections between biology and biomechanics, accurate estimations of the forces involved are required. The first part of this thesis assesses the use of computational fluid dynamics for modelling haemodynamics in abdominal aortic aneurysms. Boundary conditions from the literature o

Mapping Myocardial Elasticity with Intracardiac Acoustic Radiation Force Impulse Methods

<p>Implemented on an intracardiac echocardiography transducer, acoustic radiation force methods may provide a useful means of characterizing the heart's elastic properties. Elasticity imaging may be of benefit for diagnosis and characterization of infarction and heart failure, as well as for guidance of ablation therapy for the treatment of arrhythmias. This thesis tests the hypothesis that with appropriately designed imaging sequences, intracardiac acoustic radiation force impulse (ARFI) imaging and shear wave elasticity imaging (SWEI) are viable tools for quantification of myocardial elasticity, both temporally and spatially. Multiple track location SWEI (MTL-SWEI) is used to show that, in healthy in vivo porcine ventricles, shear wave speeds follow the elasticity changes with contraction and relaxation of the myocardium, varying between 0.9 and 2.2 m/s in diastole and 2.6 and 5.1 m/s in systole. Infarcted tissue is less contractile following infarction, though not unilaterally stiffer. Single-track-location SWEI (STL-SWEI) is proven to provide suppression of speckle noise and enable improved resolution of structures smaller than 2 mm in diameter compared to ARFI and MTL-SWEI. Contrast to noise ratio and lateral edge resolution are shown to vary with selection of time step for ARFI and arrival time regression filter size for STL-SWEI and MTL-SWEI. </p><p>In 1.5 mm targets, STL-SWEI achieves alternately the tightest resolution (0.3 mm at CNR = 3.5 for a 0.17 mm filter) and highest CNR (8.5 with edge width = 0.7 mm for a 0.66 mm filter) of the modalities, followed by ARFI and then MTL-SWEI.</p><p>In larger, 6 mm targets, the CNR-resolution tradeoff curves for ARFI and STL-SWEI overlap for ARFI time steps up to 0.5 ms and kernels $\leq$1 mm for STL-SWEI. STL-SWEI can operate either with a 25 dB improvement over MTL-SWEI in CNR at the same resolution, or with edge widths 5$\times$ as narrow at equivalent CNR values, depending on the selection of regression filter size. Ex vivo ablations are used to demonstrate that ARFI, STL-SWEI and MTL-SWEI each resolve ablation lesions between 0.5 and 1 cm in diameter and gaps between lesions smaller than 5 mm in 3-D scans. Differences in contrast, noise, and resolution between the modalities are discussed. All three modalities are also shown to resolve ``x''-shaped ablations up to 22 mm in depth with good visual fidelity and correspondence to surface photographs, with STL-SWEI providing the highest quality images. Series of each type of image, registered using 3-D data from an electroanatomical mapping system, are used to build volumes that show ablations in in vivo canine atria. In vivo images are shown to be subject to increased noise due to tissue and transducer motion, and the challenges facing the proposed system are discussed. Ultimately, intracardiac acoustic radiation force methods are demonstrated to be promising tools for characterizing dynamic myocardial elasticity and imaging radiofrequency ablation lesions.</p>Dissertatio

Méthode de mise en correspondance tridimensionnelle entre des coupes IRM de la prostate et les coupes histologiques des pièces de prostatectomie

Prostate cancer is the most frequently diagnosed cancer of men in Europe, yet no current imaging technique is capable of detecting with precision tumours in the prostate. The histology slices are the gold standard for the diagnosis. Therefore, in order to evaluate each imaging technique, the histology slices must be precisely registered to the imaged data. As it cannot be assumed that the histology slices are cut along the same plane as the imaged data is acquired, the registration must be considered as a 3D problem. An apparatus has been developed that enables internal fiducial markers to be created in the histology slices in a rapid and standardised manner. An algorithm has been developed that automatically detects and identifies these markers, enabling the alignment of the histology slices. The method has been tested on 10 prostate specimens, with 19.2 slices on average per specimen. The accuracy of the alignment at the fiducial markers was on average 0.18±0.13 mm. A second algorithm was developed to 3D register the aligned histology slices with the MR images. The registration is designed to be guided by the ejaculatory ducts, an anatomical landmark present in every prostate and visible in both histology and MR images acquired at standard clinical resolution. The algorithm was first tested by using the fiducial needles to guide the registration. The average registration accuracy was 0.45 ± 0.25 mm at the fiducial needles and 1.04±0.21 mm at the ejaculatory ducts. The algorithm was then tested by using the ejaculatory ducts to guide the registration. The average registration accuracy was 0.16±0.05 mm at the ejaculatory ducts and 2.82 ± 0.41 mm at the fiducial needles. The results suggest that the histology shrinkage factor is of the order 1.07±0.03 and the tilt of the histology slicing plane is 13.6◦ ±9.61◦, with both parameters showing significant varianceLe cancer de la prostate est le cancer le plus fréquent chez l'homme en Europe, néanmoins il n'existe actuellement pas de technique d'imagerie permettant de détecter avec précision les tumeurs dans la glande. Sachant que les coupes histologiques contiennent la réalité de terrain concernant le diagnostic, il est nécessaire de recaler les images de chaque technique d'imagerie aux coupes histologiques afin de pouvoir les évaluer. De plus, comme il n'existe pas de méthode permettant de contrôler précisément le plan de coupe histologique, le recalage doit être considéré comme un problème 3D. Un dispositif permettant de réaliser, de manière rapide et standardisée, des marqueurs internes dans les coupes histologiques a été développé, de même qu'un algorithme permettant de détecter automatiquement ces marqueurs, de les identifier et d'aligner les coupes histologiques. La méthode a été testée sur 10 prostates, avec en moyenne 19.2 coupes par prostate, et a permis d'obtenir une précision de recalage moyenne de 0.18 ± 0.13 mm au niveau des marqueurs. Un deuxième algorithme a été développé pour recaler les coupes histologiques, une fois alignées, avec les images IRM. Ce recalage a été conçu pour être guidé par les canaux éjaculateurs, un repère anatomique présent dans chaque prostate et visible à la fois en histologie et dans les images IRM cliniques, acquises avec une résolution standard. L'algorithme a d'abord été testé en s'appuyant sur les marqueurs artificiels. La précision obtenue pour le recalage était en moyenne de 0.45±0.25 mm au niveau des marqueurs et de 1.04 ± 0.21 mm au niveau des canaux éjaculateurs. L'algorithme a enfin été testé en guidant le recalage à l'aide de la position des canaux éjaculateurs. La précision moyenne obtenue était alors de 0.16±0.05 mm au niveau des canaux éjaculateurs et de 2.82±0.41 mm au niveau des marqueurs. Ces résultats suggèrent une valeur du facteur de rétrécissement de l'ordre de 1.07±0.03 et une inclinaison vis à vis du plan de coupe histologique de l'ordre de 13.6◦ ± 9.61◦, avec une variance importante pour ces deux paramètre

Multiscale Modeling of the Ventricles: From Cellular Electrophysiology to Body Surface Electrocardiograms

This work is focused on different aspects within the loop of multiscale modeling: On the cellular level, effects of adrenergic regulation and the Long-QT syndrome have been investigated. On the organ level, a model for the excitation conduction system was developed and the role of electrophysiological heterogeneities was analyzed. On the torso level a dynamic model of a deforming heart was created and the effects of tissue conductivities on the solution of the forward problem were evaluated

Flow Assessment Using Optical Coherence Microscopy Based Particle Image Velocimetry

Congenital heart diseases (CHDs) are the most common forms of congenital malformation in newborns. Among all types of CHDs, a large portion is contributed by malformation of endocardial cushion malformation during early heart development. Although the etiology of endocardial cushion malformation is unclear, it is a result of interactions between genetic and environmental factors has been confirmed. There is hypothesis indicating that malformation of endocardial cushion is caused by altered shear stress conditions where in cushion forming area the shear stress is supposed to be high compare with other area in congenital heart. However it is difficult to justify due to lack of in vivo imaging modality that is able to monitor structure and hemodynamic conditions simultaneously and over long time period. To address this problem, we present an optical coherence microscopy based particle image velocimetry system. This system is capable of invasively imaging biological sample structures at micrometer resolution and providing velocity information at the same time. With this imaging set up we successfully assessed velocity profile in a microfluidic system with simultaneous structure details demonstration of the microfluidic channel. Both flow measurement and structural information were verified using conventional microscopy. As a result, OCM-based PIV imaging modality not only makes it feasible to study in detail the process of congenital heart remodeling in response to environmental alterations, but also provides new options for measuring fluid flow in live tissue

Neuro-imagerie multimodale et multirésolution de cerveaux de souris combinant l’histologie sérielle par tomographie en cohérence optique et l’IRM de diffusion

L’histologie sérielle est une technique d’imagerie permettant d’observer des échantillons entiers à haute résolution. Cette technique consiste à trancher de fines couches de tissu, puis à déplacer l’échantillon sous un objectif de microscope afin d’acquérir autant d’images que nécessaire pour couvrir toute la surface révélée par la coupe. Ce processus est automatisé et est répété jusqu’à ce que tout l’échantillon soit imagé, c’est-à-dire un cerveau de souris dans cette thèse. Couplée à un microscope par tomographie en cohérence optique (OCT), cette modalité est capable de cartographier la distribution spatiale de la matière blanche dans des cerveaux entiers de souris. L’objectif principal de cette thèse était de développer les méthodes de reconstruction nécessaires à l’assemblage en un seul volume des milliers d’images acquises par un système d’histologie massive. De plus, dans cette première phase du projet, des méthodes permettant d’aligner les données sur des images IRM acquises pour les mêmes animaux ont été développées. Cela a permis de mieux comprendre l’origine du contraste optique dans le cerveau et cela offre maintenant la possibilité d’intégrer l’histologie massive dans les études de neuro-imagerie employant des groupes d’animaux. Dans une seconde phase du projet, un microscope à cohérence optique haute résolution a été ajouté au système d’histologie par OCT existant. Cette nouvelle plateforme d’imagerie utilise les images à basse résolution comme repère pour localiser au sein du cerveau les images à haute résolution du second microscope. L’utilité d’une telle plateforme réside dans le fait qu’il est maintenant possible de cibler des régions spécifiques à observer en détail sans avoir à imager un cerveau entier à cette grande résolution, ce qui représenterait plusieurs semaines de mesurage et des quantités immenses de données à assembler. Les données mesurées avec la nouvelle plateforme ont été intégrées à la procédure de reconstruction et d’alignement développé pour la première phase du projet. Ainsi, il a été possible de comparer les images à grande résolution avec les données d’IRM de diffusion acquises pour les mêmes cerveaux de souris. Ceci a permis de confirmer des hypothèses posées lors de l’analyse des données IRM de diffusion à partir de la microscopie. Les méthodes de reconstruction, d’alignement et d’analyse développées, ainsi que la nouvelle plateforme d’histologie sérielle bi-résolution par OCT, offrent enfin la possibilité d’utiliser cette modalité optique pour réaliser des études de groupes animales ou bien pour valider des mesures faites dans le cerveau avec d’autres modalités d’imagerie telle que l’IRM de diffusion.----------ABSTRACT Serial histology is an imaging technique able to observe whole samples at high resolution. This technique involves cutting thin tissue layers, followed by the positioning of the sample under a microscope objective and the acquisition of as many images as necessary to cover the entire area revealed by the cut. This process is automated and is repeated until the entire brain has been imaged. Coupled with an optical coherence tomography (OCT) microscope, this modality is able to map the spatial distribution of white matter in whole mouse brains. The main objective of this thesis was to develop the reconstruction methods necessary for the assembly into a single volume of the thousands of images acquired with a massive histology system. In addition, in this first project phase, methods for aligning data on MRI images acquired for the same animals have been developed. This has led to a better understanding of the optical contrast origin in the brain and it now offers the possibility of integrating massive histology into neuroimaging studies using animal groups. In a second phase of the project, a high resolution optical coherence microscope was added to the existing OCT histology system. This new imaging platform uses low-resolution images as a reference to locate the high-resolution images of the second microscope within the brain. The usefulness of such a platform lies in the fact that it is now possible to target specific regions to observe in detail without having to image an entire brain at this high resolution, which would represent several weeks for measurements and immense quantities of data to assemble. The data measured with the new platform have been incorporated into the reconstruction and alignment procedure developed for the first phase of the project. Thus, it was possible to compare the high resolution images with the diffusion MRI data acquired for the same mouse brains. This made it possible to confirm hypotheses posed during the analysis of diffusion MRI data. The methods of reconstruction, alignment and analysis developed during this thesis, as well as the new dual resolution serial OCT histology platform, finally offer the possibility of using this optical modality to carry out studies of animal groups or to validate measurements made in a brain with other imaging modalities such as diffusion MRI