3D statistical shape analysis of the face in Apert syndrome

Timely diagnosis of craniofacial syndromes as well as adequate timing and choice of surgical technique are essential for proper care management. Statistical shape models and machine learning approaches are playing an increasing role in Medicine and have proven its usefulness. Frameworks that automate processes have become more popular. The use of 2D photographs for automated syndromic identification has shown its potential with the Face2Gene application. Yet, using 3D shape information without texture has not been studied in such depth. Moreover, the use of these models to understand shape change during growth and its applicability for surgical outcome measurements have not been analysed at length. This thesis presents a framework using state-of-the-art machine learning and computer vision algorithms to explore possibilities for automated syndrome identification based on shape information only. The purpose of this was to enhance understanding of the natural development of the Apert syndromic face and its abnormality as compared to a normative group. An additional method was used to objectify changes as result of facial bipartition distraction, a common surgical correction technique, providing information on the successfulness and on inadequacies in terms of facial normalisation. Growth curves were constructed to further quantify facial abnormalities in Apert syndrome over time along with 3D shape models for intuitive visualisation of the shape variations. Post-operative models were built and compared with age-matched normative data to understand where normalisation is coming short. The findings in this thesis provide markers for future translational research and may accelerate the adoption of the next generation diagnostics and surgical planning tools to further supplement the clinical decision-making process and ultimately to improve patients’ quality of life

Assessment of facial landmarks for bone asymmetry in geometric morphometric studies: A review

BackgroundAnthropometrical points or landmarks are key for facial shape analysis using geometric morphometrics. In the early 1990s Fred Bookstein created a classification system with landmarks type 1., type 2., type 3. based on anatomical landmark homology. However, thirty years later, a uniform referece index of landmarks that can be used for assessing facial asymmetry still does not exist. The criteria for selecting landmark points are not fully defined, which makes classification of homology and and landmarks prone to arbitrary interpretations. A systematic review of literature indicates that authors of studies do not provide explanation for choosing exact points. Most of them also do not provide a clear definition of landmarks and landmarks classification according to homology.ObjectiveThe objective of this systematic review was to assess, in an evidence based manner, which landmarks inside the Bookstein groups of on facial hard tissues can be reccomended for facial asymmetry assessment using geometric mophometrics.Search methodsAn electronic search of 9 databases up to March 2020 by two reviewers was conducted to identify relevant articles.Selection criteriaProspective randomized, non-randomized controlled trials and cross sectional studies reporting on facial asymmetry using three-dimensional images and geometric morphometric methods. The reasons for assessing facial asymmetry were not considered.Data collection and analysisThe 23 selected studies were categorized according to the number and specification of the research subjects, types of three-dimensional images, number of landmarks, and the craniofacial region of interest. All landmarks were extracted with the following data: name, abbreviation, and the author’s definition of the location.ResultsThe craniofacial region is divided into neurobasic cranial part, ethmomaxillar part and the mandible. Assessment of neurobasic cranial asymmetry was conducted in 6 studies and 45 different landmarks were recorded, of which 11 were medial and 34 bilateral. Bregma and Lambda occur most frequently and according to homology both belong to type 1 landmarks.Assessment of ethmomaxillary asymmetry was conducted in 21 studies and 68 different landmarks were recorded, of which 16 were medial and 52 bilateral. Nasion and Jugale occur most frequently and according to homology Nasion belongs to type 1 landmarks and Jugale to type 2 landmarks. Conclusion The selection and definition of craniofacial hard tissue landmarks is one of the most important tasks in the design of morphometric studies, and thus for the purpose of assessing facial asymmetry. The review provides an extensive cross-section of possible landmarks with the definition of the location as well as the possible location variation. The list of these landmarks should be observed through the classification of landmarks according to their homology, as well as possible variations of the classification

Stenosis of the Nasal Entrance of Brachycephalic Dogs – Objective Measurement Using 3D Morphometry

Introduction: Stenotic nares are one of the most important characteristics of brachycephalic obstructive airway syndrome (BOAS), which was first described in 1949. However, although they have been mentioned in most texts about brachycephalic malformations, few studies have attempted to characterize the nasal entrance of dogs morphologically or functionally, and none of them have described it objectively with landmarks. Recently, as the popularity of brachycephalic dogs has exploded worldwide, innumumberable dogs are suffering from BOAS due to structural malformations. In the point of view of animal welfare, stenotic nares should be objectively evaluated to provide evidence of torture breeding. Objectives: The aim of this study was to objectively measure and thus characterize the nasal entrance stenosis of brachycephalic dogs in comparison to non-brachycephalic dogs. To this end, the following objectives were defined: 1. Our aim is to use three-dimensional (3D) soft-tissue morphometry to objectively measure the externally visible part of the nasal entrance of healthy and brachycephalic dogs. 2. Our aim is to define specific soft-tissue landmarks and parameters to objectively characterize the nasal entrance of dogs. 3. Compare 3D high-resolution scanning with computed tomography (CT) using the newly defined parameters. 4. Reexamine the nasal entrance with 3D scan six months after surgical correction of nasal entrance stenosis (Ala-vestibuloplasty). Animals, Material and Methods: Forty-five brachycephalic and 45 non-brachycephalic dogs were included in this study between 2018 and 2020. All the animals were referred to the Ear, Nose, and Throat Unit of the Small Animal Department at the University of Leipzig, either for surgical correction of BOAS or for endoscopic examination. Animals were excluded if their nasal entrance was potentially affected due to disease or previous surgery. All dogs were scanned with a 3D scanner under general anesthesia using a standardized anesthetic protocol before endoscopic intervention. The 3D scans and CT images were later imported into two advanced software (Amira, Thermo Fisher and Facial Analysis Tool) for objective measurement of the nasal entrance. Intra-observer error and ala-vestibuloplasty (AVP) efficacy of the CT images and 3D scans were tested and compared. All the data were normalized using Shapiro–Wilk normality test. All statistical analyses were later performed using Pearson or Spearman test for correlation, paired t-test, or t-test. Paired t-test was used to test whether the mean difference between pairs of measurements was zero. If it was not the same group of animals, t-test was used instead. Results: We defined new specific soft-tissue landmarks to calculate the nasal opening area (NOA) and stenotic angle (SA) to objectively describe the canine nasal entrance. The NOA and SA were significantly smaller in brachycephalic dogs than in non-brachycephalic dogs, and the NOA was significantly correlated with body weight, whereas SA was not. After nasal entrance correction via AVP, the nasal entrances were 295%left and 233%right larger than before surgery in brachycephalic dogs. Intra-observer reliability was tested with excellent significance through NOA measurements. Comparison between the 3D scanner and CT was measured with the NOA, and it did not show a significant difference between the methods. Conclusion: Obtaining the NOA and SA using 3D surface scans seems to be a reliable and reproducible tool for precise objective evaluation of the visible canine nasal entrance. With the measurement of derived NOA and SA, all the brachycephalic dogs in the study were found to have stenotic nares, and all they required AVP to relieve breathing difficulty. The brachycephalic nasal entrances were increased significantly after AVP, the modified nare correction surgery. We consider the results of our study strong evidence that the breeding of brachycephalic dogs is torture breeding. The restriction of nasal breathing due to the extreme reduction of the nasal entrance to a fraction of the size of that of non-brachycephalic dogs is obvious evidence of this.:1 INTRODUCTION - 1 - 1.1 General Introduction - 1 - 1.2 Objectives - 2 - 2 OVERVIEW OF THE LITERATURE - 3 - 2.1 Brachycephalic Obstructive Airway Syndrome (BOAS) - 3 - 2.1.1 General Introduction of BOAS - 3 - 2.1.2 How to Define Brachycephalic Dogs - 3 - 2.1.3 Commonly Affected Breeds - 4 - 2.2 The Canine Nasal Entrance - 4 - 2.2.1 Anatomy of the Canine Nasal Entrance and Stenosis - 4 - 2.2.2 Pathophysiology of Stenotic Nares in Brachycephalic Dogs - 5 - 2.3 Diagnosis of Stenotic Nares - 9 - 2.3.1 Visual Assessment - 9 - 2.3.2 Nostril Ratio - 11 - 2.3.3 Air Volume of the Nasal Entrance - 11 - 2.4 Development of Morphometry in Brachycephalic Dogs - 11 - 2.5 3D Scanners for 3D Model Reconstruction - 12 - 2.6 Landmarks - 14 - 2.6.1 Introduction of Landmarks - 14 - 2.6.2 Development of Landmarks in Human Medicine - 15 - 2.6.3 Development of Landmarks in Veterinary Medicine - 16 - 2.6.4 Cephalometric Analysis Software - 17 - 3 ANIMALS AND METHODS - 19 - 3.1 Animals - 19 - 3.2 Methods - 19 - 3.2.1 3D Scanning Process and Set-ups of Canine Nasal Entrance - 19 - 3.2.2 Cephalomorphometric Software - 20 - 3.2.3 Cephalometric Landmarks - 20 - 3.2.4 Advanced Morphometric Parameters for Nares - 22 - 3.2.5 Efficacy of Ala-Vestibuloplasty (AVP) - 24 - 3.2.6 Comparison between CT and the 3D Scanning Tool - 24 - 3.2.7 Intra-observer Reliability - 25 - 3.2.8 Statistics - 25 - 4 RESULTS - 26 - 4.1 Brachycephalic Dogs and Non-brachycephalic Dogs - 26 - 4.2 The Nasal Opening Area (NOA) - 28 - 4.3 Efficacy of Ala-Vestibulopasty - 30 - 4.4 Stenotic Angle (SA) - 31 - 4.5 Comparison between CT and the 3D Scanning Tool - 32 - 4.6 Intra-observer Reliability - 34 - 5 DISCUSSION - 36 - 5.1 The Nasal Entrance - 36 - 5.2 Method: the 3D Scanner - 37 - 5.3 Method: Comparison between CT and the 3D Scanner - 38 - 5.4 Method: Landmarks and Reproducibility, Intra-observer Reliability - 39 - 5.5 Nasal Opening Area (NOA) and Efficacy of Ala-Vestibuloplasty (AVP) - 42 - 5.6 Stenotic Angle (SA) - 44 - 5.7 Animal Welfare - 45 - 6 SUMMARY - 47 - 7 ZUSAMMENFASSUNG - 49 - 8 REFERENCES - 51 -Einleitung: Die Naseneingangstenose ist eine der wichtigsten Merkmale des brachyzephalen Syndroms (BOAS), das erstmals 1949 beschrieben wurde. Obwohl diese komplexe Stenose in den meisten Texten über brachyzephale Fehlbildungen erwähnt wird, haben nur wenige Studien versucht, den Naseneingang von Hunden morphologisch oder funktionell zu charakterisieren. Eine objektive Beschreibung mit Landmarken ist bisher nicht bekannt. In den letzten Jahren ist die Popularität brachyzephaler Hunde weltweit explodiert. Unzählige Hunde leiden aufgrund struktureller Fehlbildungen an BOAS. Unter dem Gesichtspunkt des Tierschutzes sollte die einzige, mit bloßem Auge sichtbare Stenose der oberen Atemwege brachyzephaler Hunde, die Stenose des Naseneingangs objektiv bewertet werden können, um Hinweise auf eine Qualzucht zu belegen. Zielsetzung: Ziel dieser Studie war es, den Naseneingang von brachyzephalen Hunden im Vergleich zu nicht-brachyzephalen Hunden objektiv zu messen und damit die Stenose des Naseneingangs zu charakterisieren und eine chirurgische Therapie, die Ala-Vestibuloplastie (AVP), zu evaluieren. Zu diesem Zweck wurden die folgenden Ziele definiert: 1. Anwendung der dreidimensionalen (3D) Weichteilmorphometrie zur objektiven Messung des äußerlich sichtbaren Teils des Naseneingangs von gesunden und brachyzephalen Hunden. 2. Definition spezifischer Weichteil-Landmarken und Parameter zur objektiven Charakterisierung des Naseneingangs von Hunden. 3. Methoden-Vergleich zwischen den hochauflösenden 3D-Scans und der Computertomographie (CT) unter Verwendung der neu definierten Parameter. 4. Kontrolluntersuchung mit 3D-Scan sechs Monate nach der chirurgischen Korrektur der Naseneingangsstenose (Ala-Vestibuloplastik). Tiere und Methoden: 45 brachyzephale und 45 nicht-brachyzephale Hunde wurden zwischen 2018 und 2020 in diese Studie aufgenommen und wurden an die Hals-Nasen-Ohren-Abteilung der Kleintierklinik der Universität Leipzig überwiesen, zur endoskopischen Untersuchung der oberen Atemwege und gegebenenfalls zur chirurgischen Korrektur der BOAS-assozierten Stenosen. Ausgeschlossen wurden Tiere, deren Naseneingang aufgrund von Krankheiten oder einer früheren Operation verändert war. Alle Hunde wurden nach einem standardisierten Anästhesieprotokoll anästhesiert, ein Computertomogramm des Kopfes erstellt und vor dem endoskopischen Eingriff wurde der Kopf mit einem 3D-Scanner gescannt. Die 3D-Scans und CT-Bilder wurden in zwei Softwareprogramme (Amira, Thermo Fisher und Facial Analysis Tool) zur objektiven Messung des Naseneingangs importiert. Zur genauen Charakterisierung wurden neue Landmarken am Naseneingang definiert und zur Berechnung von zwei neuen, abgeleiteten Parametern, der Nasenöffnungsfläche (NOA) und dem stenotischen Winkel (SA) verwendet. Der Intraobserver-Fehler und die Wirksamkeit der Ala-Vestibuloplastie wurden anhand der CT-Bilder und 3D-Scans mit demselben Verfahren geprüft und verglichen. Alle statistischen Analysen wurden später mit dem Pearson-Test oder dem Spearman-Test für die Korrelation, dem gepaarten t-Test oder dem t-Test durchgeführt. Der gepaarte t-Test wurde verwendet, um zu prüfen, ob der Mittelwertunterschied zwischen Paaren von Messungen gleich Null war. Handelte es sich nicht um dieselbe Gruppe von Tieren, wurde stattdessen der t-Test verwendet. Ergebnisse: Mit den neu definierten spezifischen Weichteil-Landmarken und den abgeleiteten Parametern NOA und SA konnte der Naseneingang aller brachyzephalen und nicht-brachyzephalen Hunde objektiv beschrieben werden. NOA und SA waren bei brachyzephalen Hunden signifikant kleiner als bei nicht-brachyzephalen Hunden. NOA korrelierte in beiden Gruppen signifikant mit dem Körpergewicht. Dagegen zeigte SA keine Korrelation mit dem Körpergewicht. Nach der chirurgischen AVP waren die Naseneingänge bei allen brachyzephalen Hunden größer als vor der Operation, mit einer Zunahme der NOA links um 295 % und rechts um 233 %. Die Intraobserver-Zuverlässigkeit wurde durch NOA-Messungen getestet und war hoch signifikant. Zum Methoden-Vergleich zwischen 3D-Scanner und CT wurde die Nasenöffnungsfläche jeweils am gemessen und zeigte keinen signifikanten Unterschied zwischen den Methoden. Schlussfolgerungen: Morphometrische Messungen mit 3D-Oberflächenscans scheinen ein zuverlässiges und reproduzierbares Instrument zur präzisen, objektiven Bewertung des Naseneingangs des Hundes zu sein. Bei der Messung der abgeleiteten Flächen (NOA) und Winkel (SA) wurde bei allen brachyzephalen Hunden dieser Studie eine Naseneingangsstenose festgestellt. Nach der chirurgischen Korrektur der brachyzephalen Naseneingangsstenose, der AVP, waren die Nasenöffnungen deutlich vergrößert. Die Einschränkung der Nasenatmung durch die extreme Verkleinerung des Naseneingangs auf einen Bruchteil der Größe von nicht-brachyzephalen Hunden, betrachten wir als eindeutigen Beweis dafür, dass die Zucht von brachyzephalen Hunden eine Qualzucht ist.:1 INTRODUCTION - 1 - 1.1 General Introduction - 1 - 1.2 Objectives - 2 - 2 OVERVIEW OF THE LITERATURE - 3 - 2.1 Brachycephalic Obstructive Airway Syndrome (BOAS) - 3 - 2.1.1 General Introduction of BOAS - 3 - 2.1.2 How to Define Brachycephalic Dogs - 3 - 2.1.3 Commonly Affected Breeds - 4 - 2.2 The Canine Nasal Entrance - 4 - 2.2.1 Anatomy of the Canine Nasal Entrance and Stenosis - 4 - 2.2.2 Pathophysiology of Stenotic Nares in Brachycephalic Dogs - 5 - 2.3 Diagnosis of Stenotic Nares - 9 - 2.3.1 Visual Assessment - 9 - 2.3.2 Nostril Ratio - 11 - 2.3.3 Air Volume of the Nasal Entrance - 11 - 2.4 Development of Morphometry in Brachycephalic Dogs - 11 - 2.5 3D Scanners for 3D Model Reconstruction - 12 - 2.6 Landmarks - 14 - 2.6.1 Introduction of Landmarks - 14 - 2.6.2 Development of Landmarks in Human Medicine - 15 - 2.6.3 Development of Landmarks in Veterinary Medicine - 16 - 2.6.4 Cephalometric Analysis Software - 17 - 3 ANIMALS AND METHODS - 19 - 3.1 Animals - 19 - 3.2 Methods - 19 - 3.2.1 3D Scanning Process and Set-ups of Canine Nasal Entrance - 19 - 3.2.2 Cephalomorphometric Software - 20 - 3.2.3 Cephalometric Landmarks - 20 - 3.2.4 Advanced Morphometric Parameters for Nares - 22 - 3.2.5 Efficacy of Ala-Vestibuloplasty (AVP) - 24 - 3.2.6 Comparison between CT and the 3D Scanning Tool - 24 - 3.2.7 Intra-observer Reliability - 25 - 3.2.8 Statistics - 25 - 4 RESULTS - 26 - 4.1 Brachycephalic Dogs and Non-brachycephalic Dogs - 26 - 4.2 The Nasal Opening Area (NOA) - 28 - 4.3 Efficacy of Ala-Vestibulopasty - 30 - 4.4 Stenotic Angle (SA) - 31 - 4.5 Comparison between CT and the 3D Scanning Tool - 32 - 4.6 Intra-observer Reliability - 34 - 5 DISCUSSION - 36 - 5.1 The Nasal Entrance - 36 - 5.2 Method: the 3D Scanner - 37 - 5.3 Method: Comparison between CT and the 3D Scanner - 38 - 5.4 Method: Landmarks and Reproducibility, Intra-observer Reliability - 39 - 5.5 Nasal Opening Area (NOA) and Efficacy of Ala-Vestibuloplasty (AVP) - 42 - 5.6 Stenotic Angle (SA) - 44 - 5.7 Animal Welfare - 45 - 6 SUMMARY - 47 - 7 ZUSAMMENFASSUNG - 49 - 8 REFERENCES - 51

A finite element study of the human cranium : the impact of morphological variation on biting performance

This thesis investigated the relationship between craniofacial morphology and masticatory mechanics using finite element analysis (FEA). Chapter 1 is a literature review of the relevant background: bone mechanics, jaw-elevator muscle anatomy, imaging techniques, FEA and geometric morphometrics.The second, third and fourth chapters comprise experimental work aiming to provide a framework for FE model construction and loading. The second chapter aimed to validate the method for FE model building and assess the sensitivity of models to simplifications. Models with simplified bone anatomy and resolution predicted strains close to those measured experimentally. The third chapter assessed the predictability of muscle cross-sectional area (CSA) from bony features. It was found that muscle CSA, an estimator of muscle force, has low predictability. The fourth chapter assessed FE model sensitivity to variations in applied muscle forces. Results showed that a cranial FE model behaved reasonably robustly under variations in the muscle loading regimen.Chapter 5 uses the conclusions from the previous studies to build FE models of six human crania, including two individuals with artificial deformations of the neurocranium. Despite differences in form and the presence of deformation, all performed similarly during biting, varying mainly in the magnitudes of performance parameters. The main differences related to the form of the maxilla, irrespective of neurocranial deformation. The most orthognatic individuals with the narrowest maxilla showed the most distinctive deformation during incisor and molar bites, and achieved the greatest bite force efficiency. However, bite forces were similar among individuals irrespective of the presence of artificial deformation. This appears to relate to the preservation of normal dental occlusion, which in turn maintains similar loading and so morphogenesis of the mid face. Altogether, the results of this thesis show that FEA is reliable in comparing masticatory system functioning and point to how variations in morphology impact skeletal performance

Understanding the influence of surgical parameters on craniofacial surgery outcomes: a computational study

Sagittal craniosynostosis (SC) is a congenital condition whereby the newborn skull develops abnormally owing to the premature ossification of the sagittal suture. Spring-assisted cranioplasty (SAC) is a minimally invasive surgical technique to treat SC, where metallic distractors are used to reshape the newborn’s head. Although safe and effective, SAC outcomes remain uncertain owing to the limited understanding of skull−distractor interaction and the limited information provided by the analysis of single surgical cases. In this work, an SC population-averaged skull model was created and used to simulate spring insertion by means of the finite-element analysis using a previously developed modelling framework. Surgical parameters were varied to assess the effect of osteotomy and spring positioning, as well as distractor combinations, on the final skull dimensions. Simulation trends were compared with retrospective measurements from clinical imaging (X-ray and three-dimensional photogrammetry scans). It was found that the on-table post-implantation head shape change is more sensitive to spring stiffness than to the other surgical parameters. However, the overall end-of-treatment head shape is more sensitive to spring positioning and osteotomy size parameters. The results of this work suggest that SAC surgical planning should be performed in view of long-term results, rather than immediate on-table reshaping outcomes

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

The 3D skull 0–4 years: A validated, generative, statistical shape model

BACKGROUND: This study aims to capture the 3D shape of the human skull in a healthy paediatric population (0–4 years old) and construct a generative statistical shape model. METHODS: The skull bones of 178 healthy children (55% male, 20.8 ± 12.9 months) were reconstructed from computed tomography (CT) images. 29 anatomical landmarks were placed on the 3D skull reconstructions. Rotation, translation and size were removed, and all skull meshes were placed in dense correspondence using a dimensionless skull mesh template and a non-rigid iterative closest point algorithm. A 3D morphable model (3DMM) was created using principal component analysis, and intrinsically and geometrically validated with anthropometric measurements. Synthetic skull instances were generated exploiting the 3DMM and validated by comparison of the anthropometric measurements with the selected input population. RESULTS: The 3DMM of the paediatric skull 0–4 years was successfully constructed. The model was reasonably compact - 90% of the model shape variance was captured within the first 10 principal components. The generalisation error, quantifying the ability of the 3DMM to represent shape instances not encountered during training, was 0.47 mm when all model components were used. The specificity value was <0.7 mm demonstrating that novel skull instances generated by the model are realistic. The 3DMM mean shape was representative of the selected population (differences <2%). Overall, good agreement was observed in the anthropometric measures extracted from the selected population, and compared to normative literature data (max difference in the intertemporal distance) and to the synthetic generated cases. CONCLUSION: This study presents a reliable statistical shape model of the paediatric skull 0–4 years that adheres to known skull morphometric measures, can accurately represent unseen skull samples not used during model construction and can generate novel realistic skull instances, thus presenting a solution to limited availability of normative data in this field

An automated computer-assisted approximation of the nose in South Africans from CBCT (Cone Beam Computed Tomography) scans

Thesis (PhD (Anatomy))--University of Pretoria, 2018.Each year in the Gauteng province of South Africa, approximately 1300 bodies are incinerated without a known identity (Bloom, 2015; Krüger et al., 2018). Because of various socio-economic reasons, identification is not always possible with conventional methods such as DNA comparisons and fingerprints. Therefore, more creative methods, including facial reconstruction, have been implemented to assist in the identification of unknown persons from their skeletal remains in South Africa. The aim of this thesis was to provide an automated computer-assisted method, independent of any forensic artistic interpretations, to create accurate statistical models for predicting nasal soft-tissue shape from information about the underlying skull substrate. The acquisition and extraction of the relevant anatomical structures (hard- and soft-tissue) were performed using an automatic dense landmarking procedure and analysed by geometric morphometrics. In this research, a validation of the precision of the automatic placement of landmarks, demonstrated its utilisation as a convenient prerequisite for geometric morphometric based shape analysis of the nasal complex. The automatic landmark positioning on hard- and soft-tissue 3D surfaces offered increased objectivity and the possibility of standardisation. In addition to reducing measurement errors in landmark placements, automatic landmarking, achieved a better precision for facial approximation, enabling the possibility to include more samples and populations with ease. A detailed study of the influence of factors (ancestry, sex, ageing and allometry) on the variability of the mid-facial skeleton among two South African ancestral groups were performed, revealing their statistically significant influences on the overall shape variation of the nose. Ancestry was found to be a very important factor in shape variation within the sample emphasising ancestral-specific differences. In addition, the expression of sexual dimorphism and effect of aging appeared to be different on distinct elements of the shape of the mid-facial region. From the findings, the two South African groups differed significantly regarding hard- and soft-tissue nasal complex morphology and their correlations, emphasising the importance of considering ancestry, sex and age as factors in the process of approximating the nose and highlighting the need for population specific accurate and reliable 3D statistical nose prediction methods. This study provided accurate statistical models using Partial Least Squared Regression (PLSR) algorithms which were optimised by including additional information such as ancestry, sex and age. Age and sex appeared to be important factors to be considered as additional information in order to improve the quality of the prediction. The predictions were based on a sample of 200 specimens resulting in an error when using the landmark-to-landmark distances on non-trained data, ranging between 2.139 mm and 2.833 mm for black South Africans at the tip of the nose and the alae, while they ranged from 2.575 mm to 2.859 mm for white South Africans. This research is the first attempt at a computer-assisted facial approximation of the nose with an automatic landmarking approach for the development of valid and reliable South African population specific standards using Cone Beam Computer-Tomography scans.AESOP + Erasmus Mundus ProgramAnatomyPhD (Anatomy)Unrestricte

ULTRA CLOSE-RANGE DIGITAL PHOTOGRAMMETRY AS A TOOL TO PRESERVE, STUDY, AND SHARE SKELETAL REMAINS

Skeletal collections around the world hold valuable and intriguing knowledge about humanity. Their potential value could be fully exploited by overcoming current limitations in documenting and sharing them. Virtual anthropology provides effective ways to study and value skeletal collections using three-dimensional (3D) data, e.g. allowing powerful comparative and evolutionary studies, along with specimen preservation and dissemination. CT- and laser scanning are the most used techniques for three-dimensional reconstruction. However, they are resource-intensive and, therefore, difficult to be applied to large samples or skeletal collections. Ultra close-range digital photogrammetry (UCR-DP) enables photorealistic 3D reconstructions from simple photographs of the specimen. However, it is the least used method in skeletal anthropology and the lack of appropriate protocols often limit the quality of its outcomes. This Ph.D. thesis explored UCR-DP application in skeletal anthropology. The state-of-the-art of this technique was studied, and a new approach based on cloud computing was proposed and validated against current gold standards. This approach relies on the processing capabilities of remote servers and a free-for-academic use software environment; it proved to produce measurements equivalent to those of osteometry and, in many cases, they were more precise than those of CT-scanning. Cloud-based UCR-DP allowed the processing of multiple 3D models at once, leading to a low-cost, quick, and effective 3D production. The technique was successfully used to digitally preserve an initial sample of 534 crania from the skeletal collections of the Museo Sardo di Antropologia ed Etnografia (MuSAE, Università degli Studi di Cagliari). Best practices in using the technique for skeletal collection dissemination were studied and several applications were developed including MuSAE online virtual tours, virtual physical anthropology labs and distance learning, durable online dissemination, and values-led participatorily designed interactive and immersive exhibitions at the MuSAE. The sample will be used in a future population study of Sardinian skeletal characteristics from the Neolithic to modern times. In conclusion, cloud-based UCR-DP offers many significant advantages over other 3D scanning techniques: greater versatility in terms of application range and technical implementation, scalability, photorealistic restitution, reduced requirements relating to hardware, labour, time, and cost, and is, therefore, the best choice to document and value effectively large skeletal samples and collections