Middle-Ear Imaging and Estimation of The Linear Elastic Properties of The Human Tympanic Membrane

Finite-element (FE) modeling of the human middle ear could improve diagnostic techniques, such as tympanometry. Accurate representation of the mechanical properties and geometry of the middle ear, especially of the soft tissues, are crucial for FE modeling of the middle ear. The objective of this work is to quantitatively evaluate the efficacy of iodine potassium iodide (IKI) solution as a contrast agent for imaging the middle-ear soft tissues and to estimate the linear elastic properties of the human tympanic membrane (TM). In the imaging study, six human temporal bones were used, which were obtained in right-left pairs, from three cadaveric heads. All bones were fixed using formaldehyde. Only one bone from each pair was stained using IKI solution. Samples were scanned using a micro-computed tomography system. Contrast-to-noise ratios of eight middle-ear soft tissues were calculated for each temporal bone. Results from Welch\u27s t-test indicate significant difference between the two soft tissues group, i.e., stained and unstained, at a 95% confidence interval. Results from a paired t-tests for each of the individual soft tissues also indicated significant improvement of contrast in all tissues after staining. The increase in contrast with IKI solution confirms its potential application in sample-specific FE modeling. In the linear elasticity study, experiments were performed on three specimens with a custom-built pressurization unit at a quasi-static pressure of 500 Pa. The shape of each TM before and after pressurization was recorded using a Fourier transform profilometer. The samples were also imaged using micro-CT to create sample-specific FE models. For each sample, the Young’s modulus was then estimated by numerically optimizing its value in the FE model so simulated pressurized shapes matched experimental data. Also, the effects of incorporating two forms of spatial non-uniformity in the distribution of Young’s modulus were studied, including partitioning the TM into 4 quadrants and 4 concentric rings. The estimated Young’s modulus values were 2.2 MPa, 2.4 MPa and 2.0 MPa, which are similar to recent literature values using an alternative method. An improved fit between simulated and experimental data were obtained when spatial non-uniformity was incorporated

Computational processing and analysis of ear images

Tese de mestrado. Engenharia Biomédica. Faculdade de Engenharia. Universidade do Porto. 201

Virtual Reality Simulator for Training in Myringotomy with Tube Placement

Myringotomy refers to a surgical incision in the eardrum, and it is often followed by ventilation tube placement to treat middle-ear infections. The procedure is difficult to learn; hence, the objectives of this work were to develop a virtual-reality training simulator, assess its face and content validity, and implement quantitative performance metrics and assess construct validity. A commercial digital gaming engine (Unity3D) was used to implement the simulator with support for 3D visualization of digital ear models and support for major surgical tasks. A haptic arm co-located with the stereo scene was used to manipulate virtual surgical tools and to provide force feedback. A questionnaire was developed with 14 face validity questions focusing on realism and 6 content validity questions focusing on training potential. Twelve participants from the Department of Otolaryngology were recruited for the study. Responses to 12 of the 14 face validity questions were positive. One concern was with contact modeling related to tube insertion into the eardrum, and the second was with movement of the blade and forceps. The former could be resolved by using a higher resolution digital model for the eardrum to improve contact localization. The latter could be resolved by using a higher fidelity haptic device. With regard to content validity, 64% of the responses were positive, 21% were neutral, and 15% were negative. In the final phase of this work, automated performance metrics were programmed and a construct validity study was conducted with 11 participants: 4 senior Otolaryngology consultants and 7 junior Otolaryngology residents. Each participant performed 10 procedures on the simulator and metrics were automatically collected. Senior Otolaryngologists took significantly less time to completion compared to junior residents. Junior residents had 2.8 times more errors as compared to experienced surgeons. The senior surgeons also had significantly longer incision lengths, more accurate incision angles, and lower magnification keeping both the umbo and annulus in view. All metrics were able to discriminate senior Otolaryngologists from junior residents with a significance of p \u3c 0.002. The simulator has sufficient realism, training potential and performance discrimination ability to warrant a more resource intensive skills transference study

Developing advanced mathematical models for detecting abnormalities in 2D/3D medical structures.

Detecting abnormalities in two-dimensional (2D) and three-dimensional (3D) medical structures is among the most interesting and challenging research areas in the medical imaging field. Obtaining the desired accurate automated quantification of abnormalities in medical structures is still very challenging. This is due to a large and constantly growing number of different objects of interest and associated abnormalities, large variations of their appearances and shapes in images, different medical imaging modalities, and associated changes of signal homogeneity and noise for each object. The main objective of this dissertation is to address these problems and to provide proper mathematical models and techniques that are capable of analyzing low and high resolution medical data and providing an accurate, automated analysis of the abnormalities in medical structures in terms of their area/volume, shape, and associated abnormal functionality. This dissertation presents different preliminary mathematical models and techniques that are applied in three case studies: (i) detecting abnormal tissue in the left ventricle (LV) wall of the heart from delayed contrast-enhanced cardiac magnetic resonance images (MRI), (ii) detecting local cardiac diseases based on estimating the functional strain metric from cardiac cine MRI, and (iii) identifying the abnormalities in the corpus callosum (CC) brain structure—the largest fiber bundle that connects the two hemispheres in the brain—for subjects that suffer from developmental brain disorders. For detecting the abnormal tissue in the heart, a graph-cut mathematical optimization model with a cost function that accounts for the object’s visual appearance and shape is used to segment the the inner cavity. The model is further integrated with a geometric model (i.e., a fast marching level set model) to segment the outer border of the myocardial wall (the LV). Then the abnormal tissue in the myocardium wall (also called dead tissue, pathological tissue, or infarct area) is identified based on a joint Markov-Gibbs random field (MGRF) model of the image and its region (segmentation) map that accounts for the pixel intensities and the spatial interactions between the pixels. Experiments with real in-vivo data and comparative results with ground truth (identified by a radiologist) and other approaches showed that the proposed framework can accurately detect the pathological tissue and can provide useful metrics for radiologists and clinicians. To estimate the strain from cardiac cine MRI, a novel method based on tracking the LV wall geometry is proposed. To achieve this goal, a partial differential equation (PDE) method is applied to track the LV wall points by solving the Laplace equation between the LV contours of each two successive image frames over the cardiac cycle. The main advantage of the proposed tracking method over traditional texture-based methods is its ability to track the movement and rotation of the LV wall based on tracking the geometric features of the inner, mid-, and outer walls of the LV. This overcomes noise sources that come from scanner and heart motion. To identify the abnormalities in the CC from brain MRI, the CCs are aligned using a rigid registration model and are segmented using a shape-appearance model. Then, they are mapped to a simple unified space for analysis. This work introduces a novel cylindrical mapping model, which is conformal (i.e., one to one transformation and bijective), that enables accurate 3D shape analysis of the CC in the cylindrical domain. The framework can detect abnormalities in all divisions of the CC (i.e., splenium, rostrum, genu and body). In addition, it offers a whole 3D analysis of the CC abnormalities instead of only area-based analysis as done by previous groups. The initial classification results based on the centerline length and CC thickness suggest that the proposed CC shape analysis is a promising supplement to the current techniques for diagnosing dyslexia. The proposed techniques in this dissertation have been successfully tested on complex synthetic and MR images and can be used to advantage in many of today’s clinical applications of computer-assisted medical diagnostics and intervention

Multi-Atlas Segmentation of the Facial Nerve

Medical image segmentation is an important step to identify the shape and position of patient anatomy prior to surgical simulation, surgical rehearsal, and surgical planning. It is crucial that the facial nerve (FN) is segmented accurately as damage to this nerve can severely impact facial expression, speech, and taste. Manual segmentation provides accurate results but is time-consuming and labor-intensive; semi-automatic methods of segmentation are more feasible in a clinical setting and can provide accurate results with minimal user involvement. The objective of this work was to create a novel, open-source, multi-atlas based segmentation algorithm of the entire FN requiring minimal user intervention. Twenty-eight temporal bones were segmented producing an average Dice metric of 0.76 and an average Hausdorff distance of 0.17 mm which is similar to previously published algorithms. These results indicate that this segmentation approach can accurately segment the FN and greatly reduce time spent with manual segmentation

Analysis of morphometric characteristics of different populations of Tabanus bromius linne 1758 (Diptera: Tabanidae)

Horse flies (Diptera: Tabanidae) are known world-wide as important mechanical vectors of viruses, bacteria, protozoans, and helminths that cause diseases in wild and domestic animals. Tabanus bromius L. is common species worldwide, which shows considerable variation in the size of the body due to its adaptation to different habitats. In this paper, thirteen populations of this species, which are collected from different habitats and ecological regions (forests, sea sides and alpines) at altitudes between 5-2200 meters in Anatolia and Aegean were compared using geometric morphometries. When the wing shape differences of populations were analyzed by UPGM, the cluster analyses recognized two main groups of populations, one group comprising Afyon (890 m), Amasya (800 m), Artvin (960 m), Bolu (1200 m), Eskisehir (1170 m), Kastamonu (600 m) and Zonguldak (1050 m) while the second group comprised Bursa (700 m), Giresun (150 m), Sinop (160 m), Samsun (340 m), Karabiik (230 m) and Trabzon (200 m).Anadolu Üniversitesi BAP-1502F07

Morphological Differences of the Articulating Surfaces of Mandibular Condyles in C3H/HeJ and A/J Mice

Characterize the normal variation of the articulating surfaces of mandibular condyle morphologies during periods of growth within and between two strains of mice (A/J and C3H/HeJ) using 3D micro-CT analysis and determine which parts of the microanatomy of the articulating surfaces of the condyle are less susceptible to morphologic variation during skeletal growth. Methods: Cross sectional study utilized micro-CT scans of the condyles of two strains of mice (A/J and C3H/HeJ) at 3-5 wks, 6-8 wks and 9-11 wks of age. Virtual 3D surface models were created, analyzed and computed using shape analysis methods. Results: There is inter-strain variation in condyle morphologies among inbred strains and at each age group. For A/J condylar growth the greatest differences in morphologic change occurs between 3-5 weeks and 6-8 weeks of age with little change thereafter. For the C3H/HeJ strain condylar growth and morphology continued to change beyond 6-8 weeks of age. The anterior and the posterior surfaces of the condyles tended to vary greatest in morphology. Conclusions: Condyles of A/J inbred of mice reach a morphologic plateau around 6-8 weeks of age whereas C3H/HeJ inbred of mice condyles continue morphologic change and growth after 6-8 weeks. Inbred mice despite being isogenic still present shape differences in anatomical structures such as the condyle.Master of Scienc

exploring patterns of morphological integration in the crania of papio hamadryas ursinus and homo sapiens

A Theses submitted to the faculty of science, university of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of doctor of philosophyMorphological integration is the pattern of correlation or covariation among parts due to genetic, developmental and functional processes, and is essential for the viability of an organism. Integration among processes is not uniform but forms distinct modules allowing for their independent evolvability and is thus central to the study of biological evolution. The incongruence between phylogenies estimated using the genotype and the cranial morphology in both the Papionini primates as well as the Hominidae possibly result from the disregard of character integration. Regarding the degree of morphological integration humans display extremely low levels of integration among the primates, while the baboon possesses extremely high levels. This thesis set out to address three broad aims regarding integration of the baboon and human cranium; namely 1) to study the effect of allometry on measures of integration, and when allometry and sexual dimorphism had been accounted for, 2) to assess the patterning of morphological integration into morphological modules; and finally, 3) to assess differences in the pattern of covariation between the cranial base, cranial vault and facial skeleton in humans and baboons. Although allometric growth is divided into neural and somatic, the findings suggest that the effect of allometry conceals more detailed patterns of morphological integration likely resulting from genetic and developmental processes, and should therefore be accounted for in studies of morphological integration. It is unlikely that allometry among cranial regions constrains evolutionary diversity, but rather offers a path of least resistance. The second aim offered up novel methods of exploring the pattern of morphological covariation using clustering and network methods that supported current hypotheses and proposed that the oral and basicranial regions are comprised of additional modules; however, rigorous scientific scrutiny is required for its support. iv The third aim involved the analysis of integration between the cranial base, cranial vault, and facial skeleton. The results supported the proposal that humans and nonhuman primates share a similar pattern of integration likely reflecting shared developmental processes among the primates, but with key differences probably relating to functional demands. Integration between these three cranial regions primarily involve their relative positioning and proportions. The broad pattern of integration likely reflects the role of the cranium as the supporting framework around the organs and functional capsules, the “real” modules, which accommodate one another epigenetically as they develop. The recognition of both independent modules and their pervasive integration are important and depend primarily on the nature of the investigation.GR201

The petrous portion of the human temporal bone: potential for forensic individuation

In this dissertation I evaluate the potential of the morphology of the petrous portion of the human temporal bone as seen on axial CT scans of the head as a means to generate identifications of fragmentary human skeletal remains. The specific goals are threefold: (1) To investigate variability in the shape of the petrous portion of the human temporal bone using two-dimensional morphometric analysis; (2) to evaluate the reliability of the resultant method in forensic identification; and (3) to consider the results within the framework of Bayesian theory in light of recent rulings regarding the admissibility of forensic testimony. The data used in this research were collected from axial CT images of the cranium. Two sets of images were collected for each of the 115 individuals in the sample so that Euclidean distance comparisons could be made between images of the same individual and images from different individuals. I collected two-dimensional coordinate data from 36 landmarks on each of the CT images and calculated the distances between each of the coordinate points to generate the data used in the statistical analyses. I pared down this set of measurements using two different models (referred to as the biological and PCFA models). The measurement sets of both models were then compared to one another using nearest neighbor analysis, to test their relative efficiency in matching replicate images to one another. The results of both models were highly accurate. Three incorrect nearest neighbor matches resulted from the biological model and 5 from the PCFA model. The errors appear to have been the result of variation in the axial plane between the first and second scans. The results of the nearest neighbor comparisons were then considered within the context of Bayes' Theorem by calculating likelihood ratios and posterior probabilities. The likelihood ratios and posterior probabilities were very high for both models, indicating that: 1) there is significant individual variability in the measurements of the petrous portion used in this research, and 2) this variation represents a high level of potential accuracy in the application of this method in the identification of forensic remains