Foram avaliados 25 cães portadores de discopatia cervical aos exames radiográficos simples, mielografia e tomografia computadorizada. A dor foi o principal sinal clínico em 64% dos casos. Os animais com raça definida foram os mais acometidos (85%), tendo maior incidência da raça Teckel. A faixa etária mais acometida foi entre 7-9 anos (72%). O exame radiográfico simples indicou aspectos compatíveis com extrusão em 14 observações. A mielografia diagnosticou 15 extrusões, 18 protrusões e 4 hérnias de disco e forneceu informações quanto ao grau de compressão medular e extensão das lesões. A tomografia computadorizada (TC) indicou 16 extrusões, 22 protrusões e 3 hérnias de disco. O espaço de C2-3 foi o mais acometido. A TC permitiu o diagnóstico de extrusões calcificadas, mesmo na presença de pouca quantidade ou ausência de meio de contraste e indicou com precisão o grau de compressão medular, a extensão e principalmente, a localização das lesões. Concluiu-se com este estudo que os três exames se complementam e constituem importantes ferramentas para o planejamento clínico-cirúrgico. / Twenty-five dogs with disc disease in cervical spine were evaluated by radiological and computed tomographic exams. The most common clinical signs were neck pain present in 64% of the dogs. Of the animals 85% were pure breed, amongst them Teckel were most frequent (28%). The most cases occurred in animals between seven and nine years. C2-3 was the preferred site of cervical involvement. Radiographic plain indicated fourteen extrusion. Myelography demonstrated fifteen extrusions, eighteen protrusions and four disc hernias and indicated spinal cord grade compression and lesions extension. Computed tomographic (CT) demonstred sixteen extrusions, twenty-two protrusions and three disc hernias. The CT showed to be more sensitive for soft tissue calcification, and his superior contrast resolution allowed visualization small quantities of contrast material in the subarachnoid space and indicated with precision the site and extension of lesions as well as the degree of spinal cord compression. The three exams are complementary and give valuable information for clinical and chirurgical procedures.

El retratamiento de canales radiculares es una alternativa ante el fracaso endodóntico. Este procedimiento tiene como objetivo reducir los síntomas que pueden presentarse o agravarse posterior al tratamiento de endodoncia. El procedimiento del retratamiento de canales sigue la premisa que aparentemente la calidad del material de obturación en todo el sistema de canales es deficiente, por consiguiente, todo el material debe ser retirado. Actualmente, con mejores técnicas de análisis imagenológico es posible identificar el origen de la lesión apical, por lo tanto, es posible seleccionar los canales pulpares con tratamiento deficiente y poder ser tratados de forma individual. De esta manera, el retratamiento selectivo de canales podría evitar el desgaste innecesario de canales en buen estado. / Root canal Retreatment is an alternative in the face off endodontic failure. This procedure aims to reduce the symptoms that may occur or worsen after the endodontic treatment. The root canal retreatment procedure follows the premise that apparently the quality of the filling material in the entire canal system is deficient, therefore, all the material must be removed. Currently, with better techniques of image analysis it is possible to identify the origin of the apical lesion, therefore, it is possible to select the pulp canals with poor treatment and be able to treat them individually. In this way, the selective root canal retreatment could avoid the unnecessary wear of root canals in good condition. / Trabajo académico

This thesis contains basic theoretical information about SVM-based image segmentation and data classification. Basic information about 3D Slicer software are presented. Aspects of medical images segmentation are described. Workplan and implemetation of SVM method for MRI segmentation in 3D Slicer sofware as extension module is created. SVM method is compared with simple segmentation algorithms included in 3D Slicer. Quality of segmentation, based on SVM, tested on real subjects is experimentaly demonstrated.

<p>Multiphase fields find wide applications in the fields of combustion, sprays, turbomachinery, heating and cooling systems, blasts, energetic materials, and several more areas of engineering interest. As the efficiency and performance of these systems depend heavily on the underlying multiphase field, studying their intricate structural features becomes important. The current study follows the development of a three-dimensional Wide-Angle Relay Plenoptic (WARP) imaging system with two image quadruplers for the tomographic imaging of multiphase fields. 3D printed targets were used to simulate both semi-transparent as well as opaque particle fields to emulate multiphase systems. Tomographic reconstruction of the targets was performed using the iterative MART reconstruction algorithm in a commercial image processing software. Reconstructions were performed at different angular separations between the cameras as well as for varied separation distance between the object and the imaging system. Quantitative analysis of the reconstruction quality of the developed system was performed to study the effectiveness and accuracy of this system in imaging multiphase fields. The effect of varying different system parameters on reconstruction quality has been studied to evaluate the best system configuration for imaging multiphase fields.</p>

Optical Tomography is an imaging modality that enhances early diagnosis of disease through use of harmless Near-Infrared rays instead of conventional x-rays. The subsequent images are used to reconstruct the object. However Optical Tomography has not been effectively utilized due to the complicated photon scattering phenomenon and ill-posed nature of the corresponding image reconstruction scheme. The major method for reconstruction of the object is based on an iterative loop that constantly minimizes the difference between the predicted model of photon scattering with acquired images. Currently the most effective method of predicting the photon scattering pattern is the solution of the Radiative Transfer Equation (RTE) using the Finite Elements Method (FEM). However, the conventional FEM uses classical C0 interpolation functions, which have shortcomings in terms of continuity of the solution over the domain as well as proper representation of geometry. Hence higher discretization is necessary to maintain accuracy of gradient-based results which may significantly increase the computational cost in each iteration. This research implements the recently developed Isogeometric Approach (IGA) and particularly IGA-based FEM to address the aforementioned issues. The IGA-based FEM has the potential to enhance adaptivity and reduce the computational cost of discretization schemes. The research in this study applies the IGA method to solve the RTE with the diffusion approximation and studies its behavior in comparison to conventional FEM. The results show comparison of the IGA-based solution with analytical and conventional FEM solutions in terms of accuracy and efficiency. While both methods show high levels of accuracy in reference to the analytical solution, the IGA results clearly excel in accuracy. Furthermore, FE solutions tend to have shorter runtimes in low accuracy results. However, in higher accuracy solutions, where it matters the most, the IGA proves to be considerably faster. / Doctor of Philosophy / CT scans can save lives by allowing medical practitioners observe inside the patient's body without use of invasive surgery. However, they use high energy, potentially harmful x-rays to penetrate the organs. Due to limits of the mathematical algorithm used to reconstruct the 3D figure of the organs from the 2D x-ray images, many such images are required. Thus, a high level of x-ray exposure is necessary, which in periodic use can be harmful. Optical Tomography is a promising alternative which replaces x-rays with harmless Near-infrared (NIR) visible light. However, NIR photons have lower energy and tend to scatter before leaving the organs. Therefore, an additional algorithm is required to predict the distribution of light photons inside the body and their resulting 2D images. This is called the forward problem of Optical Tomography. Only then, like conventional CT scans, can another algorithm, called the inverse solution, reconstruct the 3D image by diminishing the difference between the predicted and registered images. Currently Optical Tomography cannot replace x-ray CT scans for most cases, due to shortcomings in the forward and inverse algorithms to handle real life usages. One obstacle stems from the fact that the forward problem must be solved numerous times for the inverse solution to reach the correct visualization. However, the current numerical method, Finite Element Method (FEM), has limitations in generating accurate solutions fast enough using economically viable computers. This limitation is mostly caused by the FEM's use of a simpler mathematical construct that requires more computations and is limited in accurately modelling the geometry and shape. This research implements the recently developed Isogeometric Analysis (IGA) and particularly IGA-based FEM to address this issue. The IGA-based FEM uses the same mathematical construct that is used to visualize the geometry for complicated applications such as some animations and computer games. They are also less complicated to apply due to much lower need for partitioning the domain. This study applies the IGA method to solve the forward problem of diffuse Optical Tomography and compare the accuracy and speed of IGA solution to the conventional FEM solution. The comparison reveals that while both methods can reach high accuracy, the IGA solutions are relatively more accurate. Also, while low accuracy FEM solutions have shorter runtimes, in solutions with required higher accuracy levels, the IGA proves to be considerably faster.

The use of computed tomography in patients with gastrointestinal disease is increasing. However, the triple-phase computed tomographic angiographic appearance of the canine small intestine and the effects that phase of contrast enhancement and plane of reconstruction have on the appearance of the small intestine have not been fully evaluated. The purposes of this study were to investigate these effects on the appearance of the small intestinal wall. The minimal and maximal small intestinal diameter, wall thickness, number of wall layers identified, and degree of mucosal enhancement were recorded. The plane of reconstruction did not have any significant effects on wall thickness, diameter, degree of mucosal enhancement, or number of wall layers identified. There was a positive association between body weight and intestinal diameter. The arterial phase demonstrated the greatest mucosal enhancement and number of wall layers identified. The transverse plane was subjectively the most useful for evaluation of the small intestines.

<p dir="ltr">Computed tomography (CT) imaging is widely used in industrial and medical appli- cations for non-destructive visualization of internal sample morphology. Traditional CT reconstruction methods use projection images from a single rotation axis with a predefined set of orientations. However, for objects containing dense materials like metal, the use of a single rotation axis may leave some regions of the object obscured by the metal, even though projections from other rotation axes (or poses) might contain complementary information that would better resolve these obscured regions. Additionally, for certain CT applications, it is also desirable to reduce data acquisition time with an adaptive orientation selection strategy. </p><p dir="ltr">In this thesis, we propose advanced algorithms to improve reconstruction quality and reduce data acquisition time by efficiently leveraging the complementary information from the different orientations and rotation axes of a single object.</p><p dir="ltr">In the first portion of this thesis, we propose Multi-pose Fusion, an algorithm for reducing CT reconstruction artifacts by integrating CT measurements from multiple poses of a single object. Our approach uses multi-agent consensus equilibrium (MACE), an extension of plug- and-play, as a framework for integrating projection data from different poses. We present experimental results using both synthetic and measured CT data, and demonstrate that the Multi-pose Fusion reconstruction method is effective in reducing artifacts and improving image quality.</p><p dir="ltr">In the second portion of the this thesis, we propose an adaptive orientation selection method for the application of neutron computed tomography (nCT), in which the information from previously acquired measurements is used to decide the next measurement orientation. Using simulated and experimental data, we demonstrate that our method produces high- quality reconstructions using significantly fewer total measurements than the conventional approach.</p>

Biomedical optical imaging is capable of providing functional information of the soft bi-ological tissues, whose applications include imaging large tissues, such breastand brain in-vivo. Biomedical optical imaging uses near infrared light (600nm-900nm) as the probing media, givin ganaddedadvantageofbeingnon-ionizingimagingmodality. The tomographic technologies for imaging large tissues encompasses diffuse optical tomogra-phyandphotoacoustictomography. Traditional image reconstruction methods indiffuse optical tomographyemploysa �2-norm based regularization, which is known to remove high frequency no is either econstructed images and make the mappearsmooth. Hence as parsity based image reconstruction has been deployed for diffuse optical tomography, these sparserecov-ery methods utilize the �p-norm based regularization in the estimation problem with 0≤ p<1. These sparse recovery methods, along with an approximation to utilizethe �0-norm, have been used forther econstruction of diffus eopticaltomographic images.The comparison of these methods was performed by increasing the sparsityinthesolu-tion. Further a model resolution matrix based framework was proposed and shown to in-duceblurinthe�2-norm based regularization framework for diffuse optical tomography. This model-resolution matrix framework was utilized in the optical imaged econvolution framework. A basis pursuitdeconvolution based on Split AugmentedLagrangianShrink-ageAlgorithm(SALSA)algorithm was used along with the Tikhonovregularization step making the image reconstruction into a two-step procedure. This new two-step approach was found to be robust with no iseandwasabletobetterdelineatethestructureswhichwasevaluatedusingnumericalandgelatinphantom experiments. Modern diffuse optical imaging systems are multi-modalin nature, where diffuse optical imaging is combined with traditional imaging modalitiessuc has Magnetic Res-onanceImaging(MRI),or Computed Tomography(CT). Image-guided diffuse optical tomography has the advantage of reducingthetota lnumber of optical parameters beingreconstructedtothenumber of distinct tissue types identified by the traditional imaging modality, converting the optical image-reconstruction problem fromunder-determined innaturetoover-determined. In such cases, the minimum required measurements might be farless compared to those of the traditional diffuse optical imaging. An approach to choose these measurements optimally based on a data-resolution matrix is proposed, and it is shown that it drastically reduces the minimum required measurements (typicalcaseof240to6) without compromising the image reconstruction performance. In the last part of the work , a model-based image reconstruction approaches in pho-toacoustic tomography (which combines light and ultra sound) arestudied as it is know that these methods have a distinct advantage compared to traditionalanalytical methods in limited datacase. These model-based methods deployTikhonovbasedregularizationschemetoreconstruct the initial pressure from the boundary acoustic data. Again a model-resolution for these cases tend to represent the blurinduced by the regularization scheme. A method that utilizes this blurringmodelandper forms the basis pursuit econ-volution to improve the quantitative accuracy of the reconstructed photoacoustic image is proposed and shown to be superior compared to other traditional methods. Moreover, this deconvolution including the building of model-resolution matrixis achievedvia the Lanczosbidiagonalization (least-squares QR) making this approach computationally ef-ficient and deployable inreal-time. Keywords Medical imaging, biomedical optical imaging, diffuse optical tomography, photoacous-tictomography, multi-modalimaging, inverse problems,sparse recovery,computational methods inbiomedical optical imaging.

Diffuse Optical Tomography is a diagnostic imaging modality where optical parameters such as absorption coefficient, scattering coefficient and refractive index distributions are recovered to form the internal tissue metabolic image. Near-infrared (NIR) light has the potential to be used as a noninvasive means of diagnostic imaging within the human breast. Due to the diffusive nature of light in tissue, computational model-based methods are required for functional imaging. The main goal is to recover the spatial variation of optical properties which shed light on the different metabolic states of tissue and tissue like media. This thesis addresses the issue of quantitative recovery of optical properties of tissue-mimicking phantom and pork tissue using diffuse optical tomography (DOT). The main contribution of the present work is the development of robust, efficient and fast optical property reconstruction algorithms for a direct 3-D DOT imaging system. There are both theoretical and experimental contributions towards the development of an imaging system and procedures to minimize accurate data collection time, overall system automation as well as development of computational algorithms. In nurturing the idea of imaging using NIR light into a fully developed direct 3-D imaging system, challenges from the theoretical and computational aspects have to be met. The recovery of the optical property distribution in the interior of the object from the often noisy boundary measurements on light, is an ill-posed ( and nonlinear) problem. This is particularly true, when one is interested in a direct 3-D image reconstruction instead of the often employed stacking of 2-D cross-sections obtained from solving a set of 2-D DOT problems. In order to render the DOT, a useful diagnostic imaging tool and a robust reconstruction procedure giving accurate and reliable parameter recovery in the scenario, where the number of unknowns far outnumbers the number of independent data sets that can be gathered (for example, the direct 3-D recovery mentioned earlier) is essential. Here, the inversion problem is often solved through iterative methods based on nonlinear optimization for the minimization of a data-model misfit function. An interesting development in this direction has been the development of Broyden’ s and adjoint Broyden’ s methods that avoids direct Jacobian computation in each iteration thereby making the full 3-D a reality. Conventional model based iterative image reconstruction (MoBIIR) algorithm uses Newton’ s and it’s variant methods, where it required repeated evaluation of whole Jacobian, which consumes bulk time in reconstruction process. The explicit secant and adjoint information based fast 2-D/3-D image reconstruction algorithms without repeated evaluation of the Jacobian is proposed in diffuse optical tomography, where the computational time has been decreased many folds by updating the Jacobian successively through low rank update. An alternative route to the iterative solution is attempted by introducing an artificial dynamics in the system and treating the steady-state response of the artificially evolving dynamical system as a solution. The objective is to consider a novel family of pseudo-dynamical 2-D and 3-D systems whose numerical integration in time provides an asymptotic solution to the inverse problem at hand. We convert Gauss-Newton’ s equation for updates into a pseudo-dynamical (PD) form by explicitly adding a time derivative term. As the pseudo-time integration schemes do not need such explicit matrix inversion and depending on the pseudo-time step size, provides for a layer of regularization that in turn helps in superior quality of 2-D and 3-D image reconstruction. A cost effective frequency domain Matlab based 2-D/3-D automated imaging system is designed and built. The complete instrumentation (including PC-based control software) has been developed using a single modulated laser source (wavelength 830nm) and a photo-multiplier tube (PMT). The source and detector fiber change their positions dynamically allowing us to gather data at multiple source and detector locations. The fiber positions are adjusted on the phantom surface automatically for scanning variable size phantoms. A heterodyning scheme was used for reading out the measurement using a lock-in-amplifier. The Matlab program carries out sequence of actions such as instrument control, data acquisition, data organization, data calibration and reconstruction of image. The Gauss-Newton’ s, Broyden’ s, adjoint Broyden’ s and pseudo-time integration algorithms are evaluated using the simulation data as well as data from the experimental DOT system. Validation of the system and the reconstruction algorithms were carried out on a real tissue, a pork tissue with an embedded fat inhomogeneity. The results were found to match the known parameters closely.

Soft x-ray microscopes routinely perform high-resolution 3D imaging of biological cells in their near-native environment with short exposure times at synchrotron radiation facilities. Some laboratory-sized microscopes are aiming to make this imaging technique more accessible to a wider scientific community. However, these systems have been hampered by source instabilities hindering routine imaging of biological samples with short exposure times. This Thesis presents work performed on the Stockholm laboratory x-ray microscope. A novel heat control system has been implemented, improving the stability of the laser-produced plasma source. In combination with recent upgrades to the imaging system and an improved cryofixation method, the microscope now has the capability to routinely produce images with 10-second exposure time of cryofixed biological samples. This has allowed for tomographic imaging of cell autophagy and cell-cell interactions. Furthermore, a numerical 3D image formation model is presented as well as a novel reconstruction approach dealing with the limited depth of focus in x-ray microscopes. / <p>QC 20170505</p>