Aquatics reconstruction software: the design of a diagnostic tool based on computer vision algorithms

Computer vision methods can be applied to a variety of medical and surgical applications, and many techniques and algorithms are available that can be used to recover 3D shapes and information from images range and volume data. Complex practical applications, however, are rarely approachable with a single technique, and require detailed analysis on how they can be subdivided in subtasks that are computationally treatable and that, at the same time, allow for the appropriate level of user-interaction. In this paper we show an example of a complex application where, following criteria of efficiency, reliability and user friendliness, several computer vision techniques have been selected and customized to build a system able to support diagnosis and endovascular treatment of Abdominal Aortic Aneurysms. The system reconstructs the geometrical representation of four different structures related to the aorta (vessel lumen, thrombus, calcifications and skeleton) from CT angiography data. In this way it supports the three dimensional measurements required for a careful geometrical evaluation of the vessel, that is fundamental to decide if the treatment is necessary and to perform, in this case, its planning. The system has been realized within the European trial AQUATICS (IST-1999-20226 EUTIST-M WP 12), and it has been widely tested on clinical data

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

Geometric Shape Features Extraction Using a Steady State Partial Differential Equation System

A unified method for extracting geometric shape features from binary image data using a steady state partial differential equation (PDE) system as a boundary value problem is presented in this paper. The PDE and functions are formulated to extract the thickness, orientation, and skeleton simultaneously. The main advantages of the proposed method is that the orientation is defined without derivatives and thickness computation is not imposed a topological constraint on the target shape. A one-dimensional analytical solution is provided to validate the proposed method. In addition, two-dimensional numerical examples are presented to confirm the usefulness of the proposed method.Comment: 31 pages, 10 figure

Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods

This paper is the first of a three-part series that investigates the architecture of cancellous (‘spongy’) bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and has previously been used to infer locomotor biomechanics in extinct tetrapod vertebrates, especially primates. Despite great promise, cancellous bone architecture has remained little utilized for investigating locomotion in many other extinct vertebrate groups, such as dinosaurs. Documentation and quantification of architectural patterns across a whole bone, and across multiple bones, can provide much information on cancellous bone architectural patterns and variation across species. Additionally, this also lends itself to analysis of the musculoskeletal biomechanical factors involved in a direct, mechanistic fashion. On this premise, computed tomographic and image analysis techniques were used to describe and analyse the three-dimensional architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs for the first time. A comprehensive survey across many extant and extinct species is produced, identifying several patterns of similarity and contrast between groups. For instance, more stemward non-avian theropods (e.g. ceratosaurs and tyrannosaurids) exhibit cancellous bone architectures more comparable to that present in humans, whereas species more closely related to birds (e.g. paravians) exhibit architectural patterns bearing greater similarity to those of extant birds. Many of the observed patterns may be linked to particular aspects of locomotor biomechanics, such as the degree of hip or knee flexion during stance and gait. A further important observation is the abundance of markedly oblique trabeculae in the diaphyses of the femur and tibia of birds, which in large species produces spiralling patterns along the endosteal surface. Not only do these observations provide new insight into theropod anatomy and behaviour, they also provide the foundation for mechanistic testing of locomotor hypotheses via musculoskeletal biomechanical modelling

Modeling and Extraction of Transport Parameters to Simulate Drug Delivery in the Murine Cochlea

The usage of 1D and 3D models to simulate drug transport through the inner ear is a prominent method in cochlear fluid pharmacokinetics. However, the data used to create these models, is often based on invasive sampling methods that limit the spatial resolution given the size of the cochlear compartments within which solute can be measured. In this work by leveraging 3-D registered micro-Computed Tomography (μCT) scans of the murine cochlea that have been taken as iodinated contrast agent is delivered to it, we extract transport parameters and simulate a forward 1D model that allows variable and pulsatile delivery profiles over time and can be extended to the use of other drugs. Our 1D model may be used to simulate transport of a compound within the primary scalae or compartments of the cochlea namely: scala tympani (ST), scala vestibuli (SV) and scala media (SM). We investigate extracting transport parameters of the 1D model for the iodinated contrast agent (Iopamidol), such as the concentration dependent diffusion coefficient, along with permeabilities across membranes that represent transfer between the primary scalae and clearance out to blood. Flow rates that change over time are also learned, to account for leakage due to experimental set up. Dimensions of cochlear structures considered in the model, and empirical concentration profiles are extracted non-invasively over regional cross sections of a set of registered μCT scans of the mouse cochlea while an Iodinated contrast agent (Iopamidol) is delivered to it. Given initial estimates of the transport parameters, we use a simple iterative gradient descent approach to minimize the mean-squared error between our predicted concentrations from the 1D model and those derived empirically. We put forth a method to illustrate that once these parameters are learned for the contrast agent, they can be adjusted to simulate the delivery of other compounds, and can also be used to study various infusion paradigms to maintain a suitable therapeutic window for optimal, effective and safe administration of a drug. The results are important in the development of such paradigms for the prevention and treatment of acute and chronic types of hearing loss

Vascular Complexity Evaluation Using a Skeletonization Approach and 3D LED-Based Photoacoustic Images

Vasculature analysis is a fundamental aspect in the diagnosis, treatment, outcome evaluation and follow-up of several diseases. The quantitative characterization of the vascular network can be a powerful means for earlier pathologies revealing and for their monitoring. For this reason, non-invasive and quantitative methods for the evaluation of blood vessels complexity is a very important issue. Many imaging techniques can be used for visualizing blood vessels, but many modalities are limited by high costs, the need of exogenous contrast agents, the use of ionizing radiation, a very limited acquisition depth, and/or long acquisition times. Photoacoustic imaging has recently been the focus of much research and is now emerging in clinical applications. This imaging modality combines the qualities of good contrast and the spectral specificity of optical imaging and the high penetration depth and the spatial resolution of acoustic imaging. The optical absorption properties of blood also make it an endogenous contrast agent, allowing a completely non-invasive visualization of blood vessels. Moreover, more recent LED-based photoacoustic imaging systems are more affordable, safe and portable when compared to a laser-based systems. In this chapter we will confront the issue of vessel extraction techniques and how quantitative vascular parameters can be computed on 3D LED-based photoacoustic images using an in vitro vessel phantom model

A proposed method for evaluation of morphological changes in the condyle and glenoid fossa by cone beam computed tomography

The difficulty with three-dimensional analyses remains with the myriad of data that is possible to derive from a volume. The goal of this study is to report 3D changes in the temporomandibular joint in a reliable and quantifiable way. The approach included plotting specific referents on the mandibular condyle and tracking them in magnitude (mm) and direction (°) on a reference plane after superimposing the cone beams three-dimensionally on the inferior alveolar nerve canal and the lower contour of the third molar tooth germ. Two sets of measurements were compared for reliability and each measurement showed varied correlation. Linear measurements tended to be more reliable than component and angular measurements. Angular measurements were generally the least reliable. The varied reliability results are likely due to the difficulty in superimposing limited field of view (FOV) cone beam radiographs because of inadequate structures that are able to be superimposed

Automatic knee joint space measurement from plain radiographs

Abstract. Knee osteoarthritis is a common joint disease and one of the leading causes of disability. The disease is characterized by loss of articular cartilage and bone remodeling. Tissue deformations eventually lead to joint space narrowing which can be detected from plain radiographs. Joint space narrowing is typically measured by an experienced radiologist manually, which can be time consuming and error prone process. The aim of this study was to develop and evaluate a fully automatic joint space width measurement method for bilateral knee radiographs. The knee joint was localized from the x-ray images using template matching and the joint space was delineated using active shape model (ASM). Two different automatic joint space measurement methods were tested and the results were validated against manual measurements performed by an experienced researcher. The first joint space width measurements were done by binarizing the joint space and measuring the local thickness of the binary mask using disk fitting. The second method classified bone pixels to tibia and femur. Classification was based on the ASM delineation. Nearest neighbors between femur and tibia were then used to find the joint space width. An automatic method for tibial region of interest (ROI) selection was also implemented. The algorithms used in this thesis were also made publicly available online. The automatically obtained joint space widths were in line with manual measurements. Higher accuracy was obtained using the disk fitting algorithm. Automatic Tibial ROI selection was accurate, although the orientation of the joint was ignored in this study. An open source software with a simple graphical user interface and visualization tools was also developed. Computationally efficient and easily explainable methods were utilized in order to improve accessibility and transparency of computer assisted diagnosis of knee osteoarthritis.Tiivistelmä. Polvinivelrikko on eräs yleisimpiä niveltauteja sekä yksi merkittävimmistä liikuntavammojen aiheuttajista. Nivelrikolle ominaisia piirteitä ovat nivelruston vaurioituminen ja muutokset nivelrustonalaisessa luussa. Kudosten muutokset ja vauriot johtavat lopulta niveltilan kaventumiseen, mikä voidaan havaita röntgenkuvista. Tavallisesti kokenut radiologi tekee niveltilan mittaukset manuaalisesti, mikä vaatii usein paljon aikaa ja on lisäksi virhealtis prosessi. Tämän tutkielman tavoitteena oli kehittää täysin automaattinen niveltilan mittausmenetelmä bilateraalisille polven röntgenkuville. Polvinivel paikallistettiin röntgenkuvista muotoon perustuvalla hahmontunnistuksella ja nivelväli rajattiin käyttämällä aktiivista muodon sovitusta (active shape model, ASM). Nivelvälin mittaukseen käytettiin kahta eri menetelmää, joita verrattiin kokeneen tutkijan tekemiin manuaalisiin mittauksiin. Ensimmäinen nivelvälin mittausmenetelmä sovitti ympyränmuotoisia maskeja niveltilasta tehtyyn binäärimaskiin. Toinen mittausmenetelmä luokitteli luuhun kuuluvat pikselit sääri- ja reisiluuhun. Luokittelu perustui aikaisemmin tehtyyn automaattiseen nivelvälin rajaukseen. Nivelvälin mittaukseen käytettiin lähimpiä naapuripikseleitä sääri- ja reisiluusta. Työssä kehitettiin myös menetelmä automaattiseen sääriluun mielenkiintoalueiden (region of interest, ROI) valintaan. Käytetyt algoritmit ovat julkisesti saatavilla verkossa. Automaattiset nivelväli mittaukset vastasivat manuaalisia mittauksia hyvin. Parempi tarkkuus saatiin käyttämällä ympyrän sovitusta hyödyntävää algoritmia nivelvälin mittaukseen. Sääriluun mielenkiintoalueet onnistuttiin määrittämään automaattisesti, tosin nivelen orientaatiota ei huomioitu tässä työssä. Lisäksi kehitettiin avoimen lähdekoodin ohjelmisto yksinkertaisella graafisella käyttöliittymällä ja visualisointityökaluilla. Työssä käytettiin laskennallisesti tehokkaita ja helposti selitettäviä menetelmiä, mikä edesauttaa tietokoneavusteisen menetelmien käyttöä polvinivelrikon tutkimuksessa

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results