Prospective Estimation of Organ Dose Prior to Examination: Matching Patient to Digital Phantoms

Prospective estimation of patient CT organ dose prior to examination can help technologist adjust CT scan settings to reduce radiation dose to patient while maintaining certain image quality. One possible way to achieve this is matching patient to digital models precisely. In previous work, patient matching was performed manually by matching the trunk height which was defined as the distance from top of clavicle to bottom of pelvis. However, this matching method is time consuming and impractical in scout images where entire trunk is not included. Purpose of this work was to develop an automatic patient matching strategy and verify its accuracy.

Coding Strategies for X-ray Tomography

This work focuses on the construction and application of coded apertures to compressive X-ray tomography. Coded apertures can be made in a number of ways, each method having an impact on system background and signal contrast. Methods of constructing coded apertures for structuring X-ray illumination and scatter are compared and analyzed. Apertures can create structured X-ray bundles that investigate specific sets of object voxels. The tailored bundles of rays form a code (or pattern) and are later estimated through computational inversion. Structured illumination can be used to subsample object voxels and make inversion feasible for low dose computed tomography (CT) systems, or it can be used to reduce background in limited angle CT systems.

On the detection side, coded apertures modulate X-ray scatter signals to determine the position and radiance of scatter points. By forming object dependent projections in measurement space, coded apertures multiplex modulated scatter signals onto a detector. The multiplexed signals can be inverted with knowledge of the code pattern and system geometry. This work shows two systems capable of determining object position and type in a 2D plane, by illuminating objects with an X-ray `fan beam,' using coded apertures and compressive measurements. Scatter tomography can help identify materials in security and medicine that may be ambiguous with transmission tomography alone.

The application of next generation sequencing to profile microbe related cheese quality defects

High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencing-based approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbe-associated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.

Paire stéréoscopique Panomorphe pour la reconstruction 3D d’objets d’intérêt dans une scène

Il existe désormais une grande variété de lentilles panoramiques disponibles sur le marché dont certaines présentant des caractéristiques étonnantes. Faisant partie de cette dernière catégorie, les lentilles Panomorphes sont des lentilles panoramiques anamorphiques dont le profil de distorsion est fortement non-uniforme, ce qui cause la présence de zones de grandissement augmenté dans le champ de vue. Dans un contexte de robotique mobile, ces particularités peuvent être exploitées dans des systèmes stéréoscopiques pour la reconstruction 3D d’objets d’intérêt qui permettent à la fois une bonne connaissance de l’environnement, mais également l’accès à des détails plus fins en raison des zones de grandissement augmenté. Cependant, à cause de leur complexité, ces lentilles sont difficiles à calibrer et, à notre connaissance, aucune étude n’a réellement été menée à ce propos. L’objectif principal de cette thèse est la conception, l’élaboration et l’évaluation des performances de systèmes stéréoscopiques Panomorphes. Le calibrage a été effectué à l’aide d’une technique établie utilisant des cibles planes et d’une boîte à outils de calibrage dont l’usage est répandu. De plus, des techniques mathématiques nouvelles visant à rétablir la symétrie de révolution dans l’image (cercle) et à uniformiser la longueur focale (cercle uniforme) ont été développées pour voir s’il était possible d’ainsi faciliter le calibrage. Dans un premier temps, le champ de vue a été divisé en zones à l’intérieur desquelles la longueur focale instantanée varie peu et le calibrage a été effectué pour chacune d’entre elles. Puis, le calibrage général des systèmes a aussi été réalisé pour tout le champ de vue simultanément. Les résultats ont montré que la technique de calibrage par zone ne produit pas de gain significatif quant à la qualité des reconstructions 3D d’objet d’intérêt par rapport au calibrage général. Cependant, l’étude de cette nouvelle approche a permis de réaliser une évaluation des performances des systèmes stéréoscopiques Panomorphes sur tout le champ de vue et de montrer qu’il est possible d’effectuer des reconstructions 3D de qualité dans toutes les zones. De plus, la technique mathématique du cercle a produit des résultats de reconstructions 3D en général équivalents à l’utilisation des coordonnées originales. Puisqu’il existe des outils de calibrage qui, contrairement à celui utilisé dans ce travail, ne disposent que d’un seul degré de liberté sur la longueur focale, cette technique pourrait rendre possible le calibrage de lentilles Panomorphes à l’aide de ceux-ci. Finalement, certaines conclusions ont pu être dégagées quant aux facteurs déterminants influençant la qualité de la reconstruction 3D à l’aide de systèmes stéréoscopiques Panomorphes et aux caractéristiques à privilégier dans le choix des lentilles. La difficulté à calibrer les optiques Panomorphes en laboratoire a mené à l’élaboration d’une technique de calibrage virtuel utilisant un logiciel de conception optique et une boîte à outils de calibrage. Cette approche a permis d’effectuer des simulations en lien avec l’impact des conditions d’opération sur les paramètres de calibrage et avec l’effet des conditions de calibrage sur la qualité de la reconstruction. Des expérimentations de ce type sont pratiquement impossibles à réaliser en laboratoire mais représentent un intérêt certain pour les utilisateurs. Le calibrage virtuel d’une lentille traditionnelle a aussi montré que l’erreur de reprojection moyenne, couramment utilisée comme façon d’évaluer la qualité d’un calibrage, n’est pas nécessairement un indicateur fiable de la qualité de la reconstruction 3D. Il est alors nécessaire de disposer de données supplémentaires pour juger adéquatement de la qualité d’un calibrage.

Equipment quality control

Mammography equipment must be evaluated to ensure that images will be of acceptable diagnostic quality with lowest radiation dose. Quality Assurance (QA) aims to provide systematic and constant improvement through a feedback mechanism to address the technical, clinical and training aspects. Quality Control (QC), in relation to mammography equipment, comprises a series of tests to determine equipment performance characteristics. The introduction of digital technologies promoted changes in QC tests and protocols and there are some tests that are specific for each manufacturer. Within each country specifi c QC tests should be compliant with regulatory requirements and guidance. Ideally, one mammography practitioner should take overarching responsibility for QC within a service, with all practitioners having responsibility for actual QC testing. All QC results must be documented to facilitate troubleshooting, internal audit and external assessment. Generally speaking, the practitioner’s role includes performing, interpreting and recording the QC tests as well as reporting any out of action limits to their service lead. They must undertake additional continuous professional development to maintain their QC competencies. They are usually supported by technicians and medical physicists; in some countries the latter are mandatory. Technicians and/or medical physicists often perform many of the tests indicated within this chapter. It is important to recognise that this chapter is an attempt to encompass the main tests performed within European countries. Specific tests related to the service that you work within must be familiarised with and adhered too.

Registration-by-regression of coronary CTA and X-ray angiography

We evaluate the integration of 3D preoperative computed tomography angiography of the coronary arteries with intraoperative 2D X-ray angiographies by a recently proposed novel registration-by-regression method. The method relates image features of 2D projection images to the transformation parameters of the 3D image. We compared different sets of features and studied the influence of preprocessing the training set. For the registration evaluation, a gold standard was developed from eight X-ray angiography sequences from six different patients. The alignment quality was measured using the 3D mean target registration error (mTRE). The registration-by-regression method achieved moderate accuracy (median mTRE of 15 mm) on real images. It does therefore not provide yet a complete solution to the 3D–2D registration problem but it could be used as an initialisation method to eliminate the need for manual initialisation.

Three-dimensional, in-silico breast phantom for multimodality image simulations

We report on the construction of anatomically realistic three-dimensional in-silico breast phantoms with adjustable sizes, shapes and morphologic features. The concept of multiscale spatial resolution is implemented for generating breast tissue images from multiple modalities. Breast epidermal boundary and subcutaneous fat layer is generated by fitting an ellipsoid and 2nd degree polynomials to reconstructive surgical data and ultrasound imaging data. Intraglandular fat is simulated by randomly distributing and orienting adipose ellipsoids within a fibrous region immediately within the dermal layer. Cooper’s ligaments are simulated as fibrous ellipsoidal shells distributed within the subcutaneous fat layer. Individual ductal lobes are simulated following a random binary tree model which is generated based upon probabilistic branching conditions described by ramification matrices, as originally proposed by Bakic et al [3, 4]. The complete ductal structure of the breast is simulated from multiple lobes that extend from the base of the nipple and branch towards the chest wall. As lobe branching progresses, branches are reduced in height and radius and terminal branches are capped with spherical lobular clusters. Biophysical parameters are mapped onto the complete anatomical model and synthetic multimodal images (Mammography, Ultrasound, CT) are generated for phantoms of different adipose percentages (40%, 50%, 60%, and 70%) and are analytically compared with clinical examples. Results demonstrate that the in-silico breast phantom has applications in imaging performance evaluation and, specifically, great utility for solving image registration issues in multimodality imaging.

Optical micro-tomography “OPenT” allows the study of large toadfish Halobatrachus didactylus embryos and larvae

Batrachoidids, which include midshipman and toadfish are less known among embryologists, but are common in other fields. They are characteristic for their acoustic communication, and develop hearing and sound production while young juveniles. They lay large benthic eggs (>5mm) with a thick chorion and adhesive disk and slow development, which are particularly challenging for studying embryology. Here we took advantage of a classical tissue clearing technique and the OPenT open-source platform for optical tomography imaging, to image a series of embryos and larvae from 3 to 30mm in length, which allowed detailed 3D anatomical reconstructions non-destructively. We documented some of the developmental stages (early and late in development) and the anatomy of the delicate stato-acoustic organs, swimming bladder and associated sonic muscles. Compared to other techniques accessible to developmental biology labs, OPenT provided advantages in terms of image quality, cost of operation and data throughput, allowing identification and quantitative morphometrics of organs in larvae, earlier and with higher accuracy than is possible with other imaging techniques.

Waiting Time Screening in Diagnostic Medical Imaging - A Case-Based View

Due to the high standards expected from diagnostic medical imaging, the analysis of information regarding waiting lists via different information systems is of utmost importance. Such analysis, on the one hand, may improve the diagnostic quality and, on the other hand, may lead to the reduction of waiting times, with the concomitant increase of the quality of services and the reduction of the inherent financial costs. Hence, the purpose of this study is to assess the waiting time in the delivery of diagnostic medical imaging services, like computed tomography and magnetic resonance imaging. Thereby, this work is focused on the development of a decision support system to assess waiting times in diagnostic medical imaging with recourse to operational data of selected attributes extracted from distinct information systems. The computational framework is built on top of a Logic Programming Case-base Reasoning approach to Knowledge Representation and Reasoning that caters for the handling of in-complete, unknown, or even self-contradictory information.

Data driven regularization models of non-linear ill-posed inverse problems in imaging

Imaging technologies are widely used in application fields such as natural sciences, engineering, medicine, and life sciences. A broad class of imaging problems reduces to solve ill-posed inverse problems (IPs). Traditional strategies to solve these ill-posed IPs rely on variational regularization methods, which are based on minimization of suitable energies, and make use of knowledge about the image formation model (forward operator) and prior knowledge on the solution, but lack in incorporating knowledge directly from data. On the other hand, the more recent learned approaches can easily learn the intricate statistics of images depending on a large set of data, but do not have a systematic method for incorporating prior knowledge about the image formation model. The main purpose of this thesis is to discuss data-driven image reconstruction methods which combine the benefits of these two different reconstruction strategies for the solution of highly nonlinear ill-posed inverse problems. Mathematical formulation and numerical approaches for image IPs, including linear as well as strongly nonlinear problems are described. More specifically we address the Electrical impedance Tomography (EIT) reconstruction problem by unrolling the regularized Gauss-Newton method and integrating the regularization learned by a data-adaptive neural network. Furthermore we investigate the solution of non-linear ill-posed IPs introducing a deep-PnP framework that integrates the graph convolutional denoiser into the proximal Gauss-Newton method with a practical application to the EIT, a recently introduced promising imaging technique. Efficient algorithms are then applied to the solution of the limited electrods problem in EIT, combining compressive sensing techniques and deep learning strategies. Finally, a transformer-based neural network architecture is adapted to restore the noisy solution of the Computed Tomography problem recovered using the filtered back-projection method.

Inside standard and hyperspectral low-dose CT variational imaging: parameter identification and material decomposition

The main contribution of this thesis is the proposal of novel strategies for the selection of parameters arising in variational models employed for the solution of inverse problems with data corrupted by Poisson noise. In light of the importance of using a significantly small dose of X-rays in Computed Tomography (CT), and its need of using advanced techniques to reconstruct the objects due to the high level of noise in the data, we will focus on parameter selection principles especially for low photon-counts, i.e. low dose Computed Tomography. For completeness, since such strategies can be adopted for various scenarios where the noise in the data typically follows a Poisson distribution, we will show their performance for other applications such as photography, astronomical and microscopy imaging. More specifically, in the first part of the thesis we will focus on low dose CT data corrupted only by Poisson noise by extending automatic selection strategies designed for Gaussian noise and improving the few existing ones for Poisson. The new approaches will show to outperform the state-of-the-art competitors especially in the low-counting regime. Moreover, we will propose to extend the best performing strategy to the hard task of multi-parameter selection showing promising results. Finally, in the last part of the thesis, we will introduce the problem of material decomposition for hyperspectral CT, which data encodes information of how different materials in the target attenuate X-rays in different ways according to the specific energy. We will conduct a preliminary comparative study to obtain accurate material decomposition starting from few noisy projection data.

Correlation Between The Friedman Staging System And The Upper Airway Volume In Patients With Obstructive Sleep Apnea.

This study was designed to evaluate the correlation between computed tomography findings and data from the physical examination and the Friedman Staging System (FSS) in patients with obstructive sleep apnea (OSA). We performed a retrospective evaluation by reviewing the medical records of 33 patients (19 male and 14 female patients) with a mean body mass index of 30.38 kg/m(2) and mean age of 49.35 years. Among these patients, 14 presented with severe OSA, 7 had moderate OSA, 7 had mild OSA, and 5 were healthy. The patients were divided into 2 groups according to the FSS: Group A comprised patients with FSS stage I or II, and group B comprised patients with FSS stage III. By use of the Fisher exact test, a positive relationship between the FSS stage and apnea-hypopnea index (P = .011) and between the FSS stage and body mass index (P = .012) was found. There was no correlation between age (P = .55) and gender (P = .53) with the FSS stage. The analysis of variance test comparing the upper airway volume between the 2 groups showed P = .018. In this sample the FSS and upper airway volume showed an inverse correlation and were useful in analyzing the mechanisms of airway collapse in patients with OSA.

Discite em crianças: estudo de oito casos

The authors report the study of eight children with diskitis diagnosed through clinical, neurogical and orthopedic evaluation. The evidence of self limiting inflammation or infection of the intervertebral disk space and of soft tissue were avaliable by image studies. Findings with routine roentgenograms, computed tomography and magnetic resonance imaging are discussed.

Padronização de um método para mensuração das tábuas ósseas vestibular e lingual dos maxilares na Tomografia Computadorizada de Feixe Cônico (Cone Beam)

INTRODUÇÃO: a espessura das tábuas ósseas que recobrem os dentes por vestibular e lingual constitui um dos fatores limitantes da movimentação dentária. O avanço tecnológico em Imaginologia permitiu avaliar detalhadamente essas regiões anatômicas por meio da utilização da tomografia computadorizada de feixe cônico (TCFC). OBJETIVO: descrever e padronizar, pormenorizadamente, um método para mensuração das tábuas ósseas vestibular e lingual dos maxilares nas imagens de tomografia computadorizada de feixe cônico. METODOLOGIA: a padronização digital da posição da imagem da face deve constituir o primeiro passo antes da seleção dos cortes de TCFC. Dois cortes axiais de cada maxilar foram empregados para a mensuração da espessura do osso alveolar vestibular e lingual. Utilizou-se como referência a junção cemento-esmalte dos primeiros molares permanentes, tanto na arcada superior quanto na inferior. RESULTADOS: cortes axiais paralelos ao plano palatino foram indicados para avaliação quantitativa do osso alveolar na maxila. Na arcada inferior, os cortes axiais devem ser paralelos ao plano oclusal funcional. CONCLUSÃO: o método descrito apresenta reprodutibilidade para utilização em pesquisas, assim como para a avaliação clínica das repercussões periodontais da movimentação dentária, ao permitir a comparação de imagens pré e pós-tratamento.

Active sound quality control of engine induced cavity noise

Active control solutions appear to be a feasible approach to cope with the steadily increasing requirements for noise reduction in the transportation industry. Active controllers tend to be designed with a target on the sound pressure level reduction. However, the perceived control efficiency for the occupants can be more accurately assessed if psychoacoustic metrics can be taken into account. Therefore, this paper aims to evaluate, numerically and experimentally, the effect of a feedback controller on the sound quality of a vehicle mockup excited with engine noise. The proposed simulation scheme is described and experimentally validated. The engine excitation is provided by a sound quality equivalent engine simulator, running on a real-time platform that delivers harmonic excitation in function of the driving condition. The controller performance is evaluated in terms of specific loudness and roughness. It is shown that the use of a quite simple control strategy, such as a velocity feedback, can result in satisfactory loudness reduction with slightly spread roughness, improving the overall perception of the engine sound. (C) 2008 Elsevier Ltd. All rights reserved.