Missing Data Estimation Using Polynomial Kernels

Abstract. In this paper, we deal with the problem of partially observed objects. These objects are defined by a set of points and their shape variations are represented by a statistical model. We present two models in this paper: a linear model based on PCA and a non-linear model based on KPCA. The present work attempts to localize of non visible parts of an object, from the visible part and from the model, using the variability represented by the models. Both are applied to synthesis data and to cephalometric data with good results

Three dimensional study to quantify the relationship between facial hard and soft tissue movement as a result of orthognathic surgery

Introduction Prediction of soft tissue changes following orthognathic surgery has been frequently attempted in the past decades. It has gradually progressed from the classic “cut and paste” of photographs to the computer assisted 2D surgical prediction planning; and finally, comprehensive 3D surgical planning was introduced to help surgeons and patients to decide on the magnitude and direction of surgical movements as well as the type of surgery to be considered for the correction of facial dysmorphology. A wealth of experience was gained and numerous published literature is available which has augmented the knowledge of facial soft tissue behaviour and helped to improve the ability to closely simulate facial changes following orthognathic surgery. This was particularly noticed following the introduction of the three dimensional imaging into the medical research and clinical applications. Several approaches have been considered to mathematically predict soft tissue changes in three dimensions, following orthognathic surgery. The most common are the Finite element model and Mass tensor Model. These were developed into software packages which are currently used in clinical practice. In general, these methods produce an acceptable level of prediction accuracy of soft tissue changes following orthognathic surgery. Studies, however, have shown a limited prediction accuracy at specific regions of the face, in particular the areas around the lips. Aims The aim of this project is to conduct a comprehensive assessment of hard and soft tissue changes following orthognathic surgery and introduce a new method for prediction of facial soft tissue changes.   Methodology The study was carried out on the pre- and post-operative CBCT images of 100 patients who received their orthognathic surgery treatment at Glasgow dental hospital and school, Glasgow, UK. Three groups of patients were included in the analysis; patients who underwent Le Fort I maxillary advancement surgery; bilateral sagittal split mandibular advancement surgery or bimaxillary advancement surgery. A generic facial mesh was used to standardise the information obtained from individual patient’s facial image and Principal component analysis (PCA) was applied to interpolate the correlations between the skeletal surgical displacement and the resultant soft tissue changes. The identified relationship between hard tissue and soft tissue was then applied on a new set of preoperative 3D facial images and the predicted results were compared to the actual surgical changes measured from their post-operative 3D facial images. A set of validation studies was conducted. To include: • Comparison between voxel based registration and surface registration to analyse changes following orthognathic surgery. The results showed there was no statistically significant difference between the two methods. Voxel based registration, however, showed more reliability as it preserved the link between the soft tissue and skeletal structures of the face during the image registration process. Accordingly, voxel based registration was the method of choice for superimposition of the pre- and post-operative images. The result of this study was published in a refereed journal. • Direct DICOM slice landmarking; a novel technique to quantify the direction and magnitude of skeletal surgical movements. This method represents a new approach to quantify maxillary and mandibular surgical displacement in three dimensions. The technique includes measuring the distance of corresponding landmarks digitized directly on DICOM image slices in relation to three dimensional reference planes. The accuracy of the measurements was assessed against a set of “gold standard” measurements extracted from simulated model surgery. The results confirmed the accuracy of the method within 0.34mm. Therefore, the method was applied in this study. The results of this validation were published in a peer refereed journal. • The use of a generic mesh to assess soft tissue changes using stereophotogrammetry. The generic facial mesh played a major role in the soft tissue dense correspondence analysis. The conformed generic mesh represented the geometrical information of the individual’s facial mesh on which it was conformed (elastically deformed). Therefore, the accuracy of generic mesh conformation is essential to guarantee an accurate replica of the individual facial characteristics. The results showed an acceptable overall mean error of the conformation of generic mesh 1 mm. The results of this study were accepted for publication in peer refereed scientific journal. Skeletal tissue analysis was performed using the validated “Direct DICOM slices landmarking method” while soft tissue analysis was performed using Dense correspondence analysis. The analysis of soft tissue was novel and produced a comprehensive description of facial changes in response to orthognathic surgery. The results were accepted for publication in a refereed scientific Journal. The main soft tissue changes associated with Le Fort I were advancement at the midface region combined with widening of the paranasal, upper lip and nostrils. Minor changes were noticed at the tip of the nose and oral commissures. The main soft tissue changes associated with mandibular advancement surgery were advancement and downward displacement of the chin and lower lip regions, limited widening of the lower lip and slight reversion of the lower lip vermilion combined with minimal backward displacement of the upper lip were recorded. Minimal changes were observed on the oral commissures. The main soft tissue changes associated with bimaxillary advancement surgery were generalized advancement of the middle and lower thirds of the face combined with widening of the paranasal, upper lip and nostrils regions. In Le Fort I cases, the correlation between the changes of the facial soft tissue and the skeletal surgical movements was assessed using PCA. A statistical method known as ’Leave one out cross validation’ was applied on the 30 cases which had Le Fort I osteotomy surgical procedure to effectively utilize the data for the prediction algorithm. The prediction accuracy of soft tissue changes showed a mean error ranging between (0.0006mm±0.582) at the nose region to (-0.0316mm±2.1996) at the various facial regions

Development of procedures for the design, optimization and manufacturing of customized orthopaedic and trauma implants: Geometrical/anatomical modelling from 3D medical imaging

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)The introduction of imaging techniques in 1970 is one of the most relevant historical milestones in modern medicine. Medical imaging techniques have dramatically changed our understanding of the Human anatomy and physiology. The ability to non-invasively extract visual information allowed, not only the three-dimensional representation of the internal organs and musculo-skeletal system, but also the simulation of surgical procedures, the execution of computer aided surgeries, the development of more accurate biomechanical models, the development of custom-made implants, among others. The combination of the most advanced medical imaging systems with the most advanced CAD and CAM techniques, may allow the development of custom-made implants that meet patient-speci c traits. The geometrical and functional optimization of these devices may increase implant life-expectancy, especially in patients with marked deviations from the anatomical standards. In the implant customization protocol from medical image data, there are several steps that need to be followed in a sequential way, namely: Medical Image Processing and Recovering; Accurate Image Segmentation and 3D Surface Model Generation; Geometrical Customization based on CAD and CAE techniques; FEA Optimization of the Implant Geometry; and Manufacturing using CAD-CAM Technologies. This work aims to develop the necessary procedures for custom implant development from medical image data. This includes the extraction of highly accurate three-dimensional representation of the musculo-skeletal system from the Computed Tomography imaging, and the development of customized implants, given the speci c requirements of the target anatomy, and the applicable best practices found in the literature. A two-step segmentation protocol is proposed. In the rst step the region of interest is pre-segmented in order to obtain a good approximation to the desired geometry. Next, a fully automatic segmentation re nement is applied to obtain a more accurate representation of the target domain. The re nement step is composed by several sub-steps, more precisely, the recovery of the original image, considering the limiting resolution of the imaging system; image cropping; image interpolation; and segmentation re nement over the up-sampled domain. Highly accurate segmentations of the target domain were obtained with the proposed pipeline. The limiting factor to the accurate description of the domain accuracy is the image acquisition process, rather the following image processing, segmentation and surface meshing steps. The new segmentation pipeline was used in the development of three tailor-made implants, namely, a tibial nailing system, a mandibular implant, and a Total Hip Replacement system. Implants optimization is carried with Finite Element Analysis, considering the critical loading conditions that may be applied to each implant in working conditions. The new tibial nailing system is able of sustaining critical loads without implant failure; the new mandibular endoprosthesis that allows the recovery of the natural stress and strain elds observed in intact mandibles; and the Total Hip Replacement system that showed comparable strain shielding levels as commercially available stems. In summary, in the present thesis the necessary procedures for custom implant design are investigated, and new algorithms proposed. The guidelines for the characterization of the image acquisition, image processing, image segmentation and 3D reconstruction are presented and discussed. This new image processing pipeline is applied and validated in the development of the three abovementioned customized implants, for di erent medical applications and that satisfy speci c anatomical needs.Um dos principais marcos da história moderna da medicina e a introdução da imagem médica, em meados da década de 1970. As tecnologias de imagem permitiram aumentar e potenciar o nosso conhecimento acerca da anatomia e fisiologia do corpo Humano. A capacidade de obter informação imagiológica de forma não invasiva permitiu, não são a representação tridimensional de órgãos e do sistema músculo-esquelético, mas também a simulação de procedimentos cirúrgicos, a realização de cirurgias assistidas por computador, a criação de modelos biomecânicos mais realistas, a criação de implantes personalizados, entre outros. A conjugação dos sistemas mais avançados de imagem medica com as técnicas mais avançadas de modelação e maquinagem, pode permitir o desenvolvimento de implantes personalizados mais otimizados, que vão de encontro as especificidades de cada paciente. Por sua vez, a otimização geométrica e biomecânica destes dispositivos pode permitir, quer o aumento da sua longevidade, quer o tratamento de pessoas com estruturas anatómicas que se afastam dos padrões normais. O processo de modelação de implantes a partir da imagem medica passa por um conjunto de procedimentos a adotar, sequencialmente, ate ao produto final, a saber: Processamento e Recuperação de Imagem; Segmentação de Imagem e Reconstrução tridimensional da Região de Interesse; Modelação Geométrica do Implante; Simulação Numérica para a Otimização da Geometria; a Maquinagem do Implante. Este trabalho visa o desenvolvimento dos procedimentos necessários para a criação de implantes personalizados a partir da imagem medica, englobando a extração de modelos ósseos geométricos rigorosos a partir de imagens de Tomografia Computorizada e, a partir desses modelos, desenvolver implantes personalizados baseados nas melhores praticas existentes na literatura e que satisfaçam as especificidades da anatomia do paciente. Assim, apresenta-se e discute-se um novo procedimento de segmentação em dois passos. No primeiro e feita uma pre-segmentação que visa obter uma aproximação iniciala região de interesse. De seguida, um procedimento de refinamento da segmentação totalmente automático e aplicada a segmentação inicial para obter uma descrição mais precisa do domínio de interesse. O processo de refinamento da segmentação e constituído por vários procedimentos, designadamente: recuperação da imagem original, tendo em consideração a resolução limitante do sistema de imagem; o recorte da imagem na vizinhança da região pre-segmentada; a interpolação da região de interesse; e o refinamento da segmentação aplicando a técnica de segmentação Level-Sets sobre o domínio interpolado. O procedimento de segmentação permitiu extrair modelos extremamente precisos a partir da informação imagiológica. Os resultados revelam que o fator limitante a descrição do domínio e o processo de aquisição de imagem, em detrimento dos diversos passos de processamento subsequentes. O novo protocolo de segmentação foi utilizado no desenvolvimento de três implantes personalizados, a saber: um sistema de fixação interna para a tíbia; um implante mandibular; e um sistema para a Reconstrução Total da articulação da Anca. A otimização do comportamento mecânico dos implantes foi feita utilizado o Método dos Elementos Finitos, tendo em conta os carregamentos críticos a que estes podem estar sujeitos durante a sua vida útil. O sistema de fixação interna para a tíbia e capaz de suportar os carregamentos críticos, sem que a sua integridade mecânica seja comprometida; o implante mandibular permite recuperar os campos de tensão e deformação observados em mandíbulas intactas; e a Prótese Total da Anca apresenta níveis de strain shielding ao longo do fémur proximal comparáveis com os níveis observados em dispositivos comercialmente disponíveis. Em suma, nesta tese de Doutoramento são investigados e propostos novos procedimentos para o projeto de implantes feitos por medida. São apresentadas e discutidas as linhas orientadoras para a caracterização precisa do sistema de aquisição de imagem, para o processamento de imagem, para a segmentação, e para a reconstrução 3D das estruturas anatómicas a partir da imagem medica. Este conjunto de linhas orientadoras é aplicado e validado no desenvolvimento de três implantes personalizados, citados anteriormente, para aplicações médicas distintas e que satisfazem as necessidades anatómicas específicas de cada paciente.Fundação para a Ciência e Tecnologia (FCT

Advanced Applications of Rapid Prototyping Technology in Modern Engineering

Rapid prototyping (RP) technology has been widely known and appreciated due to its flexible and customized manufacturing capabilities. The widely studied RP techniques include stereolithography apparatus (SLA), selective laser sintering (SLS), three-dimensional printing (3DP), fused deposition modeling (FDM), 3D plotting, solid ground curing (SGC), multiphase jet solidification (MJS), laminated object manufacturing (LOM). Different techniques are associated with different materials and/or processing principles and thus are devoted to specific applications. RP technology has no longer been only for prototype building rather has been extended for real industrial manufacturing solutions. Today, the RP technology has contributed to almost all engineering areas that include mechanical, materials, industrial, aerospace, electrical and most recently biomedical engineering. This book aims to present the advanced development of RP technologies in various engineering areas as the solutions to the real world engineering problems

Characterization of normal facial features and their association with genes

ABSTRACT Background: Craniofacial morphology has been reported to be highly heritable, but little is known about which genetic variants influence normal facial variation in the general population. Aim: To identify facial variation and explore phenotype-genotype associations in a 15-year-old population (2514 females and 2233 males). Subjects and Methods: The subjects involved in this study were recruited from the Avon Longitudinal Study of Parents and Children (ALSPAC). Three-dimensional (3D) facial images were obtained for each subject using two high-resolution Konica Minolta laser scanners. Twenty-one reproducible facial soft tissue landmarks and one constructed mid-endocanthion point (men) were identified and their coordinates were recorded. The 3D facial images were registered using Procrustes analysis (with and without scaling). Principal Component Analysis (PCA) was then employed to identify independent groups ‘principal components, PCs’ of correlated landmark coordinates that represent key facial features contributing to normal facial variation. A novel surface-based method of facial averaging was employed to visualize facial variation. Facial parameters (distances, angles, and ratios) were also generated using facial landmarks. Sex prediction based on facial parameters was explored using discriminant function analysis. A discovery-phase genome-wide association analysis (GWAS) was carried out for 2,185 ALSPAC subjects and replication was undertaken in a further 1,622 ALSPAC individuals. Results: 14 (unscaled) and 17 (scaled) PCs were identified explaining 82% of the total variance in facial form and shape. 250 facial parameters were derived (90 distances, 118 angles, 42 ratios). 24 facial parameters were found to provide sex prediction efficiency of over 70%, 23 of these parameters are distances that describe variation in face height, nose width, and prominence of various facial structures. 54 distances associated with previous reported high heritability and the 14 (unscaled) PCs were included in the discovery-phase GWAS. Four genetic associations with the distances were identified in the discovery analysis, and one of these, the association between the common ‘intronic’ SNP (rs7559271) in PAX3 gene on chromosome (2) and the nasion to mid-endocanthion 3D distance (n-men) was replicated strongly (p = 4 x 10-7). PAX3 gene encodes a transcription factor that plays crucial role in fetal development including craniofacial bones. PAX3 contains two DNA-binding domains, a paired-box domain and a homeodomain. The protein made from PAX3 gene directs the activity of other genes that signal neural crest cells to form specialized tissues such as craniofacial bones. PAX3 different mutations may lead to non-functional PAX3 polypeptides and destroy the ability of the PAX3 proteins to bind to DNA and regulate the activity of other genes to form bones and other specific tissues. Conclusions: The variation in facial form and shape can be accurately quantified and visualized as a multidimensional statistical continuum with respect to the principal components. The derived PCs may be useful to identify and classify faces according to a scale of normality. A strong genetic association was identified between the common SNP (rs7559271) in PAX3 gene on chromosome (2) and the nasion to mid-endocanthion 3D distance (n-men). Variation in this distance leads to nasal bridge prominence

A three dimensional analysis of soft tissue and bone changes following orthognathic surgery

Introduction: This report investigates the ability of surgeons to achieve predicted surgical movements in five different groups of patients, and analyses both the predictions and the changes in two dimensions using scale space analyses (Campos 1991). The report then progresses to the three dimensional analysis of the bone, the soft tissues and the ratio of soft tissue to bone following surgery, using a colour coded techniques (Fright and Linney, 1991) to illustrate the changes. The average soft tissue scans from each group of patients were averaged and compared to a control group at the preoperative, three months and 1 year postoperative stages (Fright, 1991) Data Acquisition: Bone measurements were recorded from lateral skull radiographs preoperatively and 48 hrs postoperatively, and CT scans preoperatively and 1 year postoperatively. Soft tissue measurements from an optical scanner, preoperatively, three months and 1 year postoperatively. Patients 1) Control group: 30 females and 30 males 2) Skeletal class 2 patients: 15 Females and 2 Males 3) Skeletal class 3 patients: 9 Females and 7 Males 4) Cleft Palate Patients a) Unilateral cleft lip and palate: I 6 Females: 2 left and 4 right sided clefts 7 Males: 3 left and 4 right sided clefts b) Bilateral cleft lip and palate: 5 Males and 1 Female c) Clefts of the Hard and Soft palate: 5 Females. Results: Prediction: There was a surprisingly poor match between the predicted and achieved movements in both the horizontal and vertical direction in all patient groups. The scale space analysis provided an efficient method of illustrating profile changes. Soft tissue movements There were definite patterns of change and relapse in the patient groups. The relapse being most marked in the cleft palate patients. Bone movements and soft tissue to bone ratios Definite patterns of movement for the maxilla and the mandible became apparent for both the bone and soft tissue to bone ratio of movement in each group. For maxillary impactions in the skeletal 2 group there was a 1:1 ratio of movement of the soft tissue to bone in the midline increasing to 1.25:1 in the canine region and 1.5:1 in the paranasal region. Conclusions: There is a need to develop a technique to aid the the surgeons in carrying out planned surgical movements. The colour coded method was shown to be a simple, efficient and easily understandable way of analysing surgical change. Diagnosis of surgical requirements was aided by the ability to objectively compare the individual to a control group. The prediction of surgical change should be greatly aided by adapting the current database to include the distinct patterns of movement in the bone and ratio of movements of the soft tissues to the bone

Three Dimensional Nonlinear Statistical Modeling Framework for Morphological Analysis

This dissertation describes a novel three-dimensional (3D) morphometric analysis framework for building statistical shape models and identifying shape differences between populations. This research generalizes the use of anatomical atlases on more complex anatomy as in case of irregular, flat bones, and bones with deformity and irregular bone growth. The foundations for this framework are: 1) Anatomical atlases which allow the creation of homologues anatomical models across populations; 2) Statistical representation for output models in a compact form to capture both local and global shape variation across populations; 3) Shape Analysis using automated 3D landmarking and surface matching. The proposed framework has various applications in clinical, forensic and physical anthropology fields. Extensive research has been published in peer-reviewed image processing, forensic anthropology, physical anthropology, biomedical engineering, and clinical orthopedics conferences and journals. The forthcoming discussion of existing methods for morphometric analysis, including manual and semi-automatic methods, addresses the need for automation of morphometric analysis and statistical atlases. Explanations of these existing methods for the construction of statistical shape models, including benefits and limitations of each method, provide evidence of the necessity for such a novel algorithm. A novel approach was taken to achieve accurate point correspondence in case of irregular and deformed anatomy. This was achieved using a scale space approach to detect prominent scale invariant features. These features were then matched and registered using a novel multi-scale method, utilizing both coordinate data as well as shape descriptors, followed by an overall surface deformation using a new constrained free-form deformation. Applications of output statistical atlases are discussed, including forensic applications for the skull sexing, as well as physical anthropology applications, such as asymmetry in clavicles. Clinical applications in pelvis reconstruction and studying of lumbar kinematics and studying thickness of bone and soft tissue are also discussed