CAD-Based Porous Scaffold Design of Intervertebral Discs in Tissue Engineering

With the development and maturity of three-dimensional (3D) printing technology over the past decade, 3D printing has been widely investigated and applied in the field of tissue engineering to repair damaged tissues or organs, such as muscles, skin, and bones, Although a number of automated fabrication methods have been developed to create superior bio-scaffolds with specific surface properties and porosity, the major challenges still focus on how to fabricate 3D natural biodegradable scaffolds that have tailor properties such as intricate architecture, porosity, and interconnectivity in order to provide the needed structural integrity, strength, transport, and ideal microenvironment for cell- and tissue-growth. In this dissertation, a robust pipeline of fabricating bio-functional porous scaffolds of intervertebral discs based on different innovative porous design methodologies is illustrated. Firstly, a triply periodic minimal surface (TPMS) based parameterization method, which has overcome the integrity problem of traditional TPMS method, is presented in Chapter 3. Then, an implicit surface modeling (ISM) approach using tetrahedral implicit surface (TIS) is demonstrated and compared with the TPMS method in Chapter 4. In Chapter 5, we present an advanced porous design method with higher flexibility using anisotropic radial basis function (ARBF) and volumetric meshes. Based on all these advanced porous design methods, the 3D model of a bio-functional porous intervertebral disc scaffold can be easily designed and its physical model can also be manufactured through 3D printing. However, due to the unique shape of each intervertebral disc and the intricate topological relationship between the intervertebral discs and the spine, the accurate localization and segmentation of dysfunctional discs are regarded as another obstacle to fabricating porous 3D disc models. To that end, we discuss in Chapter 6 a segmentation technique of intervertebral discs from CT-scanned medical images by using deep convolutional neural networks. Additionally, some examples of applying different porous designs on the segmented intervertebral disc models are demonstrated in Chapter 6

Machine Learning towards General Medical Image Segmentation

The quality of patient care associated with diagnostic radiology is proportionate to a physician\u27s workload. Segmentation is a fundamental limiting precursor to diagnostic and therapeutic procedures. Advances in machine learning aims to increase diagnostic efficiency to replace single applications with generalized algorithms. We approached segmentation as a multitask shape regression problem, simultaneously predicting coordinates on an object\u27s contour while jointly capturing global shape information. Shape regression models inherent point correlations to recover ambiguous boundaries not supported by clear edges and region homogeneity. Its capabilities was investigated using multi-output support vector regression (MSVR) on head and neck (HaN) CT images. Subsequently, we incorporated multiplane and multimodality spinal images and presented the first deep learning multiapplication framework for shape regression, the holistic multitask regression network (HMR-Net). MSVR and HMR-Net\u27s performance were comparable or superior to state-of-the-art algorithms. Multiapplication frameworks bridges any technical knowledge gaps and increases workflow efficiency

3D Deep Learning on Medical Images: A Review

The rapid advancements in machine learning, graphics processing technologies and availability of medical imaging data has led to a rapid increase in use of deep learning models in the medical domain. This was exacerbated by the rapid advancements in convolutional neural network (CNN) based architectures, which were adopted by the medical imaging community to assist clinicians in disease diagnosis. Since the grand success of AlexNet in 2012, CNNs have been increasingly used in medical image analysis to improve the efficiency of human clinicians. In recent years, three-dimensional (3D) CNNs have been employed for analysis of medical images. In this paper, we trace the history of how the 3D CNN was developed from its machine learning roots, give a brief mathematical description of 3D CNN and the preprocessing steps required for medical images before feeding them to 3D CNNs. We review the significant research in the field of 3D medical imaging analysis using 3D CNNs (and its variants) in different medical areas such as classification, segmentation, detection, and localization. We conclude by discussing the challenges associated with the use of 3D CNNs in the medical imaging domain (and the use of deep learning models, in general) and possible future trends in the field.Comment: 13 pages, 4 figures, 2 table

Machine learning in orthopedics: a literature review

In this paper we present the findings of a systematic literature review covering the articles published in the last two decades in which the authors described the application of a machine learning technique and method to an orthopedic problem or purpose. By searching both in the Scopus and Medline databases, we retrieved, screened and analyzed the content of 70 journal articles, and coded these resources following an iterative method within a Grounded Theory approach. We report the survey findings by outlining the articles\u2019 content in terms of the main machine learning techniques mentioned therein, the orthopedic application domains, the source data and the quality of their predictive performance

Multiclass Bone Segmentation of PET/CT Scans for Automatic SUV Extraction

In this thesis I present an automated framework for segmentation of bone structures from dual modality PET/CT scans and further extraction of SUV measurements. The first stage of this framework consists of a variant of the 3D U-Net architecture for segmentation of three bone structures: vertebral body, pelvis, and sternum. The dataset for this model consists of annotated slices from the CT scans retrieved from the study of post-HCST patients and the 18F-FLT radiotracer, which are undersampled volumes due to the low-dose radiation used during the scanning. The mean Dice scores obtained by the proposed model are 0.9162, 0.9163, and 0.8721 for the vertebral body, pelvis, and sternum class respectively. The next step of the proposed framework consists of identifying the individual vertebrae, which is a particularly difficult task due to the low resolution of the CT scans in the axial dimension. To address this issue, I present an iterative algorithm for instance segmentation of vertebral bodies, based on anatomical priors of the spine for detecting the starting point of a vertebra. The spatial information contained in the CT and PET scans is used to translate the resulting masks to the PET image space and extract SUV measurements. I then present a CNN model based on the DenseNet architecture that, for the first time, classifies the spatial distribution of SUV within the marrow cavities of the vertebral bodies as normal engraftment or possible relapse. With an AUC of 0.931 and an accuracy of 92% obtained on real patient data, this method shows good potential as a future automated tool to assist in monitoring the recovery process of HSCT patients

Machine Learning in Orthopedics: A Literature Review

In this paper we present the findings of a systematic literature review covering the articles published in the last two decades in which the authors described the application of a machine learning technique and method to an orthopedic problem or purpose. By searching both in the Scopus and Medline databases, we retrieved, screened and analyzed the content of 70 journal articles, and coded these resources following an iterative method within a Grounded Theory approach. We report the survey findings by outlining the articles' content in terms of the main machine learning techniques mentioned therein, the orthopedic application domains, the source data and the quality of their predictive performance

Low Back Pain (LBP)

Low back pain (LBP) is a major public health problem, being the most commonly reported musculoskeletal disorder (MSD) and the leading cause of compromised quality of life and work absenteeism. Indeed, LBP is the leading worldwide cause of years lost to disability, and its burden is growing alongside the increasing and aging population. The etiology, pathogenesis, and occupational risk factors of LBP are still not fully understood. It is crucial to give a stronger focus to reducing the consequences of LBP, as well as preventing its onset. Primary prevention at the occupational level remains important for highly exposed groups. Therefore, it is essential to identify which treatment options and workplace-based intervention strategies are effective in increasing participation at work and encouraging early return-to-work to reduce the consequences of LBP. The present Special Issue offers a unique opportunity to update many of the recent advances and perspectives of this health problem. A number of topics will be covered in order to attract high-quality research papers, including the following major areas: prevalence and epidemiological data, etiology, prevention, assessment and treatment approaches, and health promotion strategies for LBP. We have received a wide range of submissions, including research on the physical, psychosocial, environmental, and occupational perspectives, also focused on workplace interventions

Identifying the Severity of Adolescent Idiopathic Scoliosis During Gait by Using Machine Learning

La scoliose idiopathique de l'adolescent (SIA) est une déformation de la colonne vertébrale dans les trois plans de l’espace objectivée par un angle de Cobb ≥ 10°. Celle-ci affecte les adolescents âgés entre 10 et 16 ans. L’étiologie de la scoliose demeure à ce jour inconnue malgré des recherches approfondies. Différentes hypothèses telles que l’implication de facteurs génétiques, hormonaux, biomécaniques, neuromusculaires ou encore des anomalies de croissance ont été avancées. Chez ces adolescents, l'ampleur de la déformation de la colonne vertébrale est objectivée par mesure manuelle de l’angle de Cobb sur radiographies antéropostérieures. Cependant, l’imprécision inter / intra observateur de cette mesure, ainsi que de l’exposition fréquente (biannuelle) aux rayons X que celle-ci nécessite pour un suivi adéquat, sont un domaine qui préoccupe la communauté scientifique et clinique. Les solutions proposées à cet effet concernent pour beaucoup l'utilisation de méthodes assistées par ordinateur, telles que des méthodes d'apprentissage machine utilisant des images radiographiques ou des images du dos du corps humain. Ces images sont utilisées pour classer la sévérité de la déformation vertébrale ou pour identifier l'angle de Cobb. Cependant, aucune de ces méthodes ne s’est avérée suffisamment précise pour se substituer l’utilisation des radiographies. Parallèlement, les recherches ont démontré que la scoliose modifie le schéma de marche des personnes qui en souffrent et par conséquent également les efforts intervertébraux. C’est pourquoi, l'objectif de cette thèse est de développer un modèle non invasif d’identification de la sévérité de la scoliose grâce aux mesures des efforts intervertébraux mesurés durant la marche. Pour atteindre cet objectif, nous avons d'abord comparé les efforts intervertébraux calculés par un modèle dynamique multicorps, en utilisant la dynamique inverse, chez 15 adolescents atteints de SIA avec différents types de courbes et de sévérités et chez 12 adolescents asymptomatiques (à titre comparatif). Par cette comparaison, nous avons pu objectiver que les efforts intervertébraux les plus discriminants pour prédire la déformation vertébrale étaient la force et le couple antéro-postérieur et la force médio-latérale. Par la suite, nous nous sommes concentrés sur la classification de la sévérité de la déformation vertébrale de 30 AIS ayant une courbure thoraco-lombaire / lombaire. Pour ce faire, nous avons testé différents modèles de classification. L'angle de Cobb a été identifié en exécutant différents modèles de régression. Les caractéristiques (features) servant à alimenter les algorithmes d'entraînement ont été choisies en fonction des efforts intervertébraux les plus pertinents à la déformation vertébrale au niveau de la charnière lombo-sacrée (vertèbres allantes de L5-S1). Les précisions les plus élevées pour la classification exécutant différents algorithmes ont été obtenues par un algorithme de classification d'ensemble comprenant les “K-nearest neighbors”, “Support vector machine”, “Random forest”, “multilayer perceptron”, et un modèle de “neural networks” avec une précision de 91.4% et 93.6%, respectivement. De même, le modèle de régression par “Decision tree” parmi les autres modèles a obtenu le meilleur résultat avec une erreur absolue moyenne égale à 4.6° de moyenne de validation croisée de 10 fois. En conclusion, nous pouvons dire que cette étude démontre une relation entre la déformation de la colonne vertébrale et les efforts intervertébraux mesurés lors de la marche. L'angle de Cobb a été identifié à l'aide d'une méthode sans rayonnement avec une précision prometteuse égale à 4.6°. Il s’agit d’une amélioration majeure par rapport aux méthodes précédemment proposées ainsi que par rapport à la mesure classique réalisée par des spécialistes présentant une erreur entre 5° et 10° (ceci en raison de la variation intra/inter observateur). L’algorithme que nous vous présentons peut être utilisé comme un outil d'évaluation pour suivre la progression de la scoliose. Il peut être considéré comme une alternative à la radiographie. Des travaux futurs devraient tester l'algorithme et l’adapter pour d’autres formes de SIA, telles que les scolioses lombaire ou thoracolombaire.----------ABSTRACT Adolescent idiopathic scoliosis (AIS) is a 3D deformation of the spine and rib cage greater than 10° that affects adolescents between the ages of 10 and 16 years old. The true etiology is unknown despite extensive research and investigation. However, different theories such as genetic and hormonal factors, growth abnormalities or biomechanical and neuromuscular reasons have been proposed as possible causes. The magnitude of spinal deformity in AIS is measured by the Cobb angle in degrees as the gold standard through the X-rays by specialists. The inter/intra observer error and the cumulative exposure to radiation, however, are sources of increasing concern among researchers with regards to the accuracy of manual measurement. Proposed solutions have therefore, focused on using computer-assisted methods such as Machine Learning using X-ray images, and/or trunk images to classify the severity of spinal deformity or to identify the Cobb angle. However, none of the proposed methods have shown the level of accuracy required for use as an alternative to X-rays. Meanwhile, scoliosis has been recognized as a pathology that modifies the gait pattern, subsequently impinging upon intervertebral efforts. The present thesis aims to develop a radiation-free model to identify the severity of idiopathic scoliosis in adolescents based on the intervertebral efforts during gait. To accomplish this objective, we compared the intervertebral efforts computed using a multibody dynamics model, by way of inverse dynamics, among 15 adolescents with AIS having different curve types and severities, as well as 12 typically developed adolescents. This resulted in the identification of the most relevant intervertebral efforts influenced by spinal deformity: mediolateral (ML) force; anteroposterior (AP) force; and torque. Additionally, we focused on the classification of the severity of spinal deformity among 30 AIS with thoracolumbar/lumbar curvature, testing different classification models. Lastly, the Cobb angle was identified running regression models. The features to feed training algorithms were chosen based on the most relevant intervertebral efforts to the spinal deformity on the lumbosacral (L5-S1) joint. The highest accuracies for the classification were obtained by the ensemble classifier algorithm, including “K-nearest neighbors”, “support vector machine”, “random forest”, and “multilayer perceptron”, as well as a neural network model with an accuracy of 91.4% and 93.6%, respectively. Likewise, the “decision tree regression” model achieved the best result with a mean absolute error equal to 4.6 degrees of an averaged 10-fold cross-validation. This study shows a relation between spinal deformity and the produced intervertebral efforts during gait. The Cobb angle was identified using a radiation-free method with a promising accuracy, providing a mean absolute error of 4.6°. Compared to measurement variations, ranging between 5° and 10° in the manual Cobb angle measurements by specialists, the proposed model provided reliable accuracy. This algorithm can be used as an assessment tool, alternative to the X-ray radiography, to follow up the progression of scoliosis. As future work, the algorithm should be tested and modified on AIS with other types of spine curvature than lumbar/thoracolumbar

Machine learning-based automated segmentation with a feedback loop for 3D synchrotron micro-CT

Die Entwicklung von Synchrotronlichtquellen der dritten Generation hat die Grundlage für die Untersuchung der 3D-Struktur opaker Proben mit einer Auflösung im Mikrometerbereich und höher geschaffen. Dies führte zur Entwicklung der Röntgen-Synchrotron-Mikro-Computertomographie, welche die Schaffung von Bildgebungseinrichtungen zur Untersuchung von Proben verschiedenster Art förderte, z.B. von Modellorganismen, um die Physiologie komplexer lebender Systeme besser zu verstehen. Die Entwicklung moderner Steuerungssysteme und Robotik ermöglichte die vollständige Automatisierung der Röntgenbildgebungsexperimente und die Kalibrierung der Parameter des Versuchsaufbaus während des Betriebs. Die Weiterentwicklung der digitalen Detektorsysteme führte zu Verbesserungen der Auflösung, des Dynamikbereichs, der Empfindlichkeit und anderer wesentlicher Eigenschaften. Diese Verbesserungen führten zu einer beträchtlichen Steigerung des Durchsatzes des Bildgebungsprozesses, aber auf der anderen Seite begannen die Experimente eine wesentlich größere Datenmenge von bis zu Dutzenden von Terabyte zu generieren, welche anschließend manuell verarbeitet wurden. Somit ebneten diese technischen Fortschritte den Weg für die Durchführung effizienterer Hochdurchsatzexperimente zur Untersuchung einer großen Anzahl von Proben, welche Datensätze von besserer Qualität produzierten. In der wissenschaftlichen Gemeinschaft besteht daher ein hoher Bedarf an einem effizienten, automatisierten Workflow für die Röntgendatenanalyse, welcher eine solche Datenlast bewältigen und wertvolle Erkenntnisse für die Fachexperten liefern kann. Die bestehenden Lösungen für einen solchen Workflow sind nicht direkt auf Hochdurchsatzexperimente anwendbar, da sie für Ad-hoc-Szenarien im Bereich der medizinischen Bildgebung entwickelt wurden. Daher sind sie nicht für Hochdurchsatzdatenströme optimiert und auch nicht in der Lage, die hierarchische Beschaffenheit von Proben zu nutzen. Die wichtigsten Beiträge der vorliegenden Arbeit sind ein neuer automatisierter Analyse-Workflow, der für die effiziente Verarbeitung heterogener Röntgendatensätze hierarchischer Natur geeignet ist. Der entwickelte Workflow basiert auf verbesserten Methoden zur Datenvorverarbeitung, Registrierung, Lokalisierung und Segmentierung. Jede Phase eines Arbeitsablaufs, die eine Trainingsphase beinhaltet, kann automatisch feinabgestimmt werden, um die besten Hyperparameter für den spezifischen Datensatz zu finden. Für die Analyse von Faserstrukturen in Proben wurde eine neue, hochgradig parallelisierbare 3D-Orientierungsanalysemethode entwickelt, die auf einem neuartigen Konzept der emittierenden Strahlen basiert und eine präzisere morphologische Analyse ermöglicht. Alle entwickelten Methoden wurden gründlich an synthetischen Datensätzen validiert, um ihre Anwendbarkeit unter verschiedenen Abbildungsbedingungen quantitativ zu bewerten. Es wurde gezeigt, dass der Workflow in der Lage ist, eine Reihe von Datensätzen ähnlicher Art zu verarbeiten. Darüber hinaus werden die effizienten CPU/GPU-Implementierungen des entwickelten Workflows und der Methoden vorgestellt und der Gemeinschaft als Module für die Sprache Python zur Verfügung gestellt. Der entwickelte automatisierte Analyse-Workflow wurde erfolgreich für Mikro-CT-Datensätze angewandt, die in Hochdurchsatzröntgenexperimenten im Bereich der Entwicklungsbiologie und Materialwissenschaft gewonnen wurden. Insbesondere wurde dieser Arbeitsablauf für die Analyse der Medaka-Fisch-Datensätze angewandt, was eine automatisierte Segmentierung und anschließende morphologische Analyse von Gehirn, Leber, Kopfnephronen und Herz ermöglichte. Darüber hinaus wurde die entwickelte Methode der 3D-Orientierungsanalyse bei der morphologischen Analyse von Polymergerüst-Datensätzen eingesetzt, um einen Herstellungsprozess in Richtung wünschenswerter Eigenschaften zu lenken