Методика выделения топологических признаков на трехмерных изображениях

Представлена новая методика получения и анализа топологических характеристик для последующей классификации на трехмерных изображениях. Для получения топологических структур использовались трехмерные дистанционные карты, анализ применялся с помощью рассмотрения совместных свойств скелета, границы и выпуклой оболочки объекта.Представлена нова методика отримання та аналізу топологічних характеристик для подальшої класифікації на тривимірних зображеннях. Для отримання топологічних структур використовувалися тривимірні дистанційні карти, аналіз застосовувався з допомогою розгляду спільних властивостей скелета, межі та опуклої оболонки об’єкту.The paper is devoted to the problem of obtaining and analyzing the topological features for the subsequent classification of three-dimensional images. To obtain the topological structures, we used three-dimensional distance maps, the analysis applied by considering the joint properties of the skeleton, the boundary and the convex hul of the object

Методика выделения топологических признаков на трехмерных изображениях

Представлена новая методика получения и анализа топологических характеристик для последующей классификации на трехмерных изображениях. Для получения топологических структур использовались трехмерные дистанционные карты, анализ применялся с помощью рассмотрения совместных свойств скелета, границы и выпуклой оболочки объекта.Представлена нова методика отримання та аналізу топологічних характеристик для подальшої класифікації на тривимірних зображеннях. Для отримання топологічних структур використовувалися тривимірні дистанційні карти, аналіз застосовувався з допомогою розгляду спільних властивостей скелета, межі та опуклої оболонки об’єкту.The paper is devoted to the problem of obtaining and analyzing the topological features for the subsequent classification of three-dimensional images. To obtain the topological structures, we used three-dimensional distance maps, the analysis applied by considering the joint properties of the skeleton, the boundary and the convex hul of the object

3D Object Comparison Based on Shape Descriptors

No abstract availabl

Visualizing and Tracking Evolving Features in 3D Unstructured and Adaptive Datasets

The massive amounts of time-varying datasets being generated demand new visualization and quantification techniques. Visualization alone is not sufficient. Without proper measurement information/computations real science cannot be done. Our focus is this work was to combine visualization with quantification of the data to allow for advanced querying and searching. As part of this proposal, we have developed a feature extraction adn tracking methodology which allows researcher to identify features of interest and follow their evolution over time. The implementation is distributed and operates over data In-situ: where it is stored and when it was computed

A K-MEANS CLUSTERING BASED SHAPE RETRIEVAL TECHNIQUE FOR 3D MESH MODELS

Due to the large size of shape databases, importance of effective and robust method in shape retrieval has been increased. Researchers mainly focus on finding descriptors which is suitable for rigid models. Retrieval of non-rigid models is a still challenging field which needs to be studied more. For non-rigid models, descriptors that are designed should be insensitive to different poses. For non-rigid model retrieval, we propose a new method which first divides a model into clusters using geodesic distance metric and then computes the descriptor using these clusters. Mesh segmentation is performed using a skeleton-based K-means clustering method.  Each cluster is represented by an area based descriptor which is invariant to scale and orientation. Finally, similar objects for the input model are retrieved. Articulated objects from human to animals are used for this study’s experiments for the validation of the proposed retrieval algorithm

Shape analysis in shape space

This study aims to classify different deformations based on the shape space concept. A shape space is a quotient space in which each point corresponds to a class of shapes. The shapes of each class are transformed to each other by a transformation group preserving a geometrical property in which we are interested. Therefore, each deformation is a curve on the high dimensional shape space manifold, and one can classify the deformations by comparison of their corresponding deformation curves in shape space. Towards this end, two classification methods are proposed. In the first method, a quasi conformal shape space is constructed based on a novel quasi-conformal metric, which preserves the curvature changes at each vertex during the deformation. Besides, a classification framework is introduced for deformation classification. The results on synthetic and real datasets show the effectiveness of the metric to estimate the intrinsic geometry of the shape space manifold, and its ability to classify and interpolate different deformations. In the second method, we introduce the medial surface shape space which classifies the deformations based on the medial surface and thickness of the shape. This shape space is based on the log map and uses two novel measures, average of the normal vectors and mean of the positions, to determine the distance between each pair of shapes on shape space. We applied these methods to classify the left ventricle deformations. The experimental results shows that the first method can remarkably classify the normal and abnormal subjects but this method cannot spot the location of the abnormality. In contrast, the second method can discriminate healthy subjects from patients with cardiomyopathy, and also can spot the abnormality on the left ventricle, which makes it a valuable assistant tool for diagnostic purposes

Sketching-based Skeleton Extraction

Articulated character animation can be performed by manually creating and rigging a skeleton into an unfolded 3D mesh model. Such tasks are not trivial, as they require a substantial amount of training and practice. Although methods have been proposed to help automatic extraction of skeleton structure, they may not guarantee that the resulting skeleton can help to produce animations according to user manipulation. We present a sketching-based skeleton extraction method to create a user desired skeleton structure which is used in 3D model animation. This method takes user sketching as an input, and based on the mesh segmentation result of a 3D mesh model, generates a skeleton for articulated character animation. In our system, we assume that a user will properly sketch bones by roughly following the mesh model structure. The user is expected to sketch independently on different regions of a mesh model for creating separate bones. For each sketched stroke, we project it into the mesh model so that it becomes the medial axis of its corresponding mesh model region from the current viewer perspective. We call this projected stroke a “sketched bone”. After pre-processing user sketched bones, we cluster them into groups. This process is critical as user sketching can be done from any orientation of a mesh model. To specify the topology feature for different mesh parts, a user can sketch strokes from different orientations of a mesh model, as there may be duplicate strokes from different orientations for the same mesh part. We need a clustering process to merge similar sketched bones into one bone, which we call a “reference bone”. The clustering process is based on three criteria: orientation, overlapping and locality. Given the reference bones as the input, we adopt a mesh segmentation process to assist our skeleton extraction method. To be specific, we apply the reference bones and the seed triangles to segment the input mesh model into meaningful segments using a multiple-region growing mechanism. The seed triangles, which are collected from the reference bones, are used as the initial seeds in the mesh segmentation process. We have designed a new segmentation metric [1] to form a better segmentation criterion. Then we compute the Level Set Diagrams (LSDs) on each mesh part to extract bones and joints. To construct the final skeleton, we connect bones extracted from all mesh parts together into a single structure. There are three major steps involved: optimizing and smoothing bones, generating joints and forming the skeleton structure. After constructing the skeleton model, we have proposed a new method, which utilizes the Linear Blend Skinning (LBS) technique and the Laplacian mesh deformation technique together to perform skeleton-driven animation. Traditional LBS techniques may have self-intersection problem in regions around segmentation boundaries. Laplacian mesh deformation can preserve the local surface details, which can eliminate the self-intersection problem. In this case, we make use of LBS result as the positional constraint to perform a Laplacian mesh deformation. By using the Laplacian mesh deformation method, we maintain the surface details in segmentation boundary regions. This thesis outlines a novel approach to construct a 3D skeleton model interactively, which can also be used in 3D animation and 3D model matching area. The work is motivated by the observation that either most of the existing automatic skeleton extraction methods lack well-positioned joints specification or the manually generated methods require too much professional training to create a good skeleton structure. We dedicate a novel approach to create 3D model skeleton based on user sketching which specifies articulated skeleton with joints. The experimental results show that our method can produce better skeletons in terms of joint positions and topological structure

Caractérisation géométrique par la logique floue et simulation de la résorption cellulairement assistée de substituts poreux pour tissus osseux par microtomographie à rayons X

The objective of this thesis is to provide an improved characterization of porous scaffolds. A more focused objective is to provide a computational model simulating the cell mediated resorption process of resorbable bone substitutes. The thesis is structured in three scientific manuscripts. The first manuscript used fuzzy-based image treatment methods to analyse images generated by micro-computed tomography. From the literature, it is known that the fuzzy-based method helps to improve the accuracy of the characterization, in particular for scaffolds featuring a relatively small pore size. In addition, a new algorithm was introduced to determine both pore and interconnection sizes. The surface area of bone substitutes was quantified by using marching cube algorithm. Besides, the so-called Lattice Boltzmann method was used to characterize the permeability of the investigated scaffolds. Scaffolds made of [béta]-tricalcium phosphate ([béta]-Ca[subscript 3](PO[subscript 4])[subscript 2]) and presenting a constant porosity and four variable pore sizes were examined. The average pore size (diameter) of the four bone substitute groups (denominated with a letter from group A to D) was measured to be 170.3«1.7, 217.3«5.2, 415.8«18.8 and 972.3«10.9 [micro]m. Despite this significant change in pore size, the pore interconnection size only increased slightly, in the range of 61.7 to 85.2 [micro]m. The average porosity of the four groups was 52.3«1.5 %. The surface density of scaffolds decreased from 11.5 to 3.3 mm[superscript -1], when the pore size increased. The results revealed that the permeability of scaffolds is in the same order of magnitude and increased from 1.1?10[superscript -10] to 4.1?10[superscript -10] m[superscript 2] with increasing the pore size. The second manuscript was devoted to the use of subvoxelization algorithm and high-resolution scanner, in an attempt to further improve the accuracy of the results, in particular, of the small pore scaffolds. As expected, an increase of the image resolution from 15 to 7.5 [micro]m significantly eased the segmentation process and hence improved scaffold characterization. Subvoxelization also improved the results specifically in terms of interconnection sizes. Specifically, much smaller interconnection sizes were yielded after applying the subvoxelization process. For example, the mean interconnection size of small pore size groups, group A and B, dropped from 63 to 20 and 30 [micro]m, respectively. Furthermore, due to more details obtained from subvoxelization and high-resolution scanning, additional effects so called"boundary effects" were observed. The boundary effects can yield misleading results in terms of interconnection sizes. The means to reduce these effects were proposed. The third manuscript focused on the simulation and understanding of cell mediated resorption of bone graft substitutes. A computer model was developed to simulate the resorption process of four bone substitute groups. [mu]CT data and new"image processing" tools such as labelling and skeletonization were combined in an algorithm to perform the steps of resorption simulation algorithm. The proposed algorithm was verified by comparing simulation results with the analytical results of a simple geometry and biological in vivo data of bone substitutes. A correlation coefficient between the simulation results and both analytical and experimental data, was found to be larger than 0.9. Local resorption process revealed faster resorption in external region specifically at earlier resorption time. This finding is in agreement with the in vivo results. Two definitions were introduced to estimate the resorption rate; volume resorption rate and linear resorption rate. The volume resorption rate was proportional to accessible surface and decreased when the pore size increased, while the linear resorption rate was proportional to thickness of material and increased with increasing the pore size. In addition, the simulation results revealed no effect of resorption direction on resorption behaviour of substitutes. However, the resorption rate of small pore size samples was decreased with increasing the minimum interconnection size required for cell ingrowth, to 100 [micro]m. This thesis combined novel"image processing" tools and subvoxelization method to improve the characterization of porous bone substitutes used in the bone repair process. The improved characterization allowed a more accurate simulation process. The simulation data were consistent with previously obtained biological data of the same group and allows understanding the local resorption process. The available tools and results are expected to help with the design of optimal substitute for bone repair."--Résumé abrégé par UMI

Three-dimensional body scanning: methods and applications for anthropometry

In questa tesi descriviamo i metodi informatici e gli esperimenti eseguiti per l\u2019applicazione della tecnologia whole body 3D scanner in supporto dell\u2019antropometria. I body scanner restituiscono in uscita una nuvola di punti, solitamente trasformata in mesh triangolare mediante l\u2019uso di algoritmi specifici per supportare la visualizzazione 3D della superficie e l\u2019estrazione di misure e landmarks antropometrici significativi. L\u2019antropometria digitale \ue8 gi\ue0 stata utilizzata con successo in vari studi per valutare importanti parametri medici. L\u2019analisi antropometrica digitale \ue8 solitamente eseguita utilizzando soluzioni software fornite dai costruttori che sono chiuse e specifiche per il prodotto, che richiedono attenzione nell\u2019acquisizione e dei forti limiti sulla posa assunta dal soggetto. Questo pu\uf2 portare a dei problemi nella comparazione di dati acquisiti in diversi luoghi, nella realizzazione di studi multicentrici su larga scala e nell\u2019applicazione di metodi avanzati di shape analysis sui modelli acquisiti. L\u2019obiettivo del nostro lavoro \ue8 di superare questi problemi selezionando e personalizzando strumenti di processing geometrico capaci di creare un sistema aperto ed indipendente dallo strumento per l\u2019analisi di dati da body scanner. Abbiamo inoltre sviluppato e validato dei metodi per estrarre automaticamente dei punti caratteristici, segmenti corporei e misure significative che possono essere utilizzate nella ricerca antropometrica e metabolica. Nello specifico, presentiamo tre esperimenti. Nel primo, utilizzando uno specifico software per l\u2019antropometria digitale, abbiamo valutato la performance dello scanner Breuckmann BodySCAN nelle misure antropometriche. I soggetti degli esperimenti sono 12 giovani adulti che sono stati sottoposti procedure di antropometria manuale e digitale tridimensionale (25 misurazioni) indossando abbigliamento intimo attillato. Le misure duplicate effettuate da un\u2019antropometrista esperto mostrano una correlazione r=0.975-0.999; la loro media \ue8 significativamente (secondo il test t di Student) diversa su 4 delle 25 misure. Le misure digitali effettuate in duplicato da un antropometrista esperto e da due antropometristi non esperti, mostrano indici di correlazione individuali r che variano nel range 0.975-0.999 e medie che che erano significativamente diverse in una misurazione su 25. La maggior parte delle misure effettuate dall\u2019antropometrista esperto, manuali e digitali, mostrano una correlazione significativa (coefficiente di correlazione intra-classe che variano nell\u2019intervallo 0.855-0.995, p<0.0001). Concludiamo che lo scanner Breuckmann BodySCAN \ue8 uno strumento affidabile ed efficace per le misure antropometriche. In un secondo esperimento, compariamo alcune caratteristiche geometriche facilmente misurabili ottenute dalle scansioni di femmine obese (BMI>30) con i parametri di composizione corporea (misurata con una DXA) dei soggetti stessi, per investigare quali misure dei descrittori di forma correlavano meglio con il grasso del torso e corporeo. I risultati ottenuti mostrano che alcuni dei parametri geometrici testati presentano una elevata correlazione, mentre altri non correlano fortemente con il grasso corporeo. Questi risultati supportano il ruolo dell\u2019antropometria digitale nell\u2019indagine sulle caratteristiche fisiche rilevanti per la salute, ed incoraggiano la realizzazione di ulteriori studi che analizzino la relazione tra descrittori di forma e composizione corporea. Infine, presentiamo un nuovo metodo per caratterizzare le superfici tridimensionali mediante il calcolo di una funzione chiamata \u201cArea projection transform\u201d, la quale misura la possibilit\ue0 dei punti dello spazio 3D di essere il centro di simmetria radiale della forma a predeterminati raggi. La trasformata pu\uf2 essere usata per rilevare e caratterizzare in maniera robusta i regioni salienti (approssimativamente parti sferiche e cilindriche) ed \ue8, quindi, adatta ad applicazioni come la detection di caratteristiche anatomiche. In particolare, mostriamo che \ue8 possibile costruire grafi che uniscono questi punti seguendo i valori massimali della MAPT (Radial Simmetry Graphs) e che questi grafi possono essere usati per estrarre rilevanti propriet\ue0 della forma o definire corrispondenze puntuali robuste nei confronti di problematiche quali parti mancanti, rumore topologico e deformazioni articolate. Concludiamo che le potenziali applicazioni della tecnologia della scansione tridimensionale applicata all\u2019antropometria sono innumerevoli, limitate solo dall\u2019abilit\ue0 della conoscienza scientifica di connettere il fenomeno biologico con le appropriate descrizioni matematiche/geometriche.In this thesis we describe the developed computer method and experiments performed in order to apply whole body 3D scanner technology in support to anthropometry. The output of whole body scanners is a cloud of points, usually transformed in a triangulated mesh through the use of specific algorithms in order to support the 3D visualization of the surface and the extraction of meaningful anthropometric landmarks and measurements. Digital anthropometry has been already used in various studies to assess important health-related parameters. Digital anthropometric analysis is usually performed using device-specific and closed software solutions provided by scanner manufacturers, and requires often a careful acquisition, with strong constraints on subject pose. This may create problems in comparing data acquired in different places and performing large-scale multi-centric studies as well as in applying advanced shape analysis tools on the captured models. The aim of our work is to overcome these problems by selecting and customizing geometrical processing tools able to create an open and device-independent method for the analysis of body scanner data. We also developed and validated methods to extract automatically feature points, body segments and relevant measurements that can be used in anthropometric and metabolic research. In particular we present three experiments. In the first, using specific digital anthropometry software, we evaluated the Breuckmann BodySCAN for performance in anthropometric measurement. Subjects of the experiment were 12 young adults underwent both manual and 3D digital anthropometry (25 measurements) wearing close-fitting underwear. Duplicated manual measurement taken by one experienced anthropometrist showed correlation r 0.975-0.999; their means were significantly different in four out of 25 measurements by Student\u2019s t test. Duplicate digital measurements taken by one experienced anthropometrist and two na\uefve anthropometrists showed individual correlation coefficients r ranging 0.975-0.999 and means were significantly different in one out of 25 measurements. Most measurements taken by the experienced anthropometrist in the manual and digital mode showed significant correlation (intraclass correlation coefficient ranging 0.855-0.995, p<0.0001). We conclude that the Breuckmann BodyScan is reliable and effective tool for digital anthropometry. In a second experiment, we compare easily detectable geometrical features obtained from 3D scans of female obese (BMI > 30) subjects with body composition (measured with a DXA device) of the same subjects, in order to investigate which measurements on shape descriptors better correlate with torso and body fat. The results obtained show that some of the tested geometrical parameters have a relevant correlation, while other ones do not strongly correlate with body fat. These results support the role of digital anthropometry in investigating health-related physical characteristics and encourage the realization of further studies analyzing the relationships between shape descriptors and body composition. Finally, we present a novel method to characterize 3D surfaces through the computation of a function called Area Projection Transform, measuring the likelihood of points in the 3D space to be center of radial symmetry at selected scales (radii). The transform can be used to detect and characterize robustly salient regions (approximately spherical and cylindrical parts) and it is, therefore, suitable for applications like anatomical features detection. In particular, we show that it is possible to build graphs joining these points following maximal values of the MAPT (Radial Symmetry Graphs) and that these graphs can be used to extract relevant shape properties or to establish point correspondences on models robustly against holes, topological noise and articulated deformations. It is concluded that whole body scanning technology application to anthropometry are potentially countless, limited only by the ability of science to connect the biological phenomenon with the appropriate mathematical/geometrical descriptions

ANALYSIS AND VISUALIZATION OF FLOW FIELDS USING INFORMATION-THEORETIC TECHNIQUES AND GRAPH-BASED REPRESENTATIONS

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner. My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow patterns and how to pick good viewpoints to observe flow fields become critical. We treat streamline selection and viewpoint selection as symmetric problems and solve them simultaneously using the dual information channel [81]. To the best of my knowledge, this is the first attempt in flow visualization to combine these two selection problems in a unified approach. This work selects streamline in a view-independent manner and the selected streamlines will not change for all viewpoints. My another work [56] uses an information-theoretic approach to evaluate the importance of each streamline under various sample viewpoints and presents a solution for view-dependent streamline selection that guarantees coherent streamline update when the view changes gradually. When projecting 3D streamlines to 2D images for viewing, occlusion and clutter become inevitable. To address this challenge, we design FlowGraph [57, 58], a novel compound graph representation that organizes field line clusters and spatiotemporal regions hierarchically for occlusion-free and controllable visual exploration. We enable observation and exploration of the relationships among field line clusters, spatiotemporal regions and their interconnection in the transformed space. Most viewpoint selection methods only consider the external viewpoints outside of the flow field. This will not convey a clear observation when the flow field is clutter on the boundary side. Therefore, we propose a new way to explore flow fields by selecting several internal viewpoints around the flow features inside of the flow field and then generating a B-Spline curve path traversing these viewpoints to provide users with closeup views of the flow field for detailed observation of hidden or occluded internal flow features [54]. This work is also extended to deal with unsteady flow fields. Besides flow field visualization, some other topics relevant to visualization also attract my attention. In iGraph [31], we leverage a distributed system along with a tiled display wall to provide users with high-resolution visual analytics of big image and text collections in real time. Developing pedagogical visualization tools forms my other research focus. Since most cryptography algorithms use sophisticated mathematics, it is difficult for beginners to understand both what the algorithm does and how the algorithm does that. Therefore, we develop a set of visualization tools to provide users with an intuitive way to learn and understand these algorithms