Modelos Deformáveis em Imagem Médica

Modelos deformáveis são actualmente bastante utilizados em imagem médica pois, através da utilização de princípios físicos, simulam de forma bastante satisfatória o comportamento dos objectos reais.Basicamente os modelos deformáveis são inicializados junto dos objectos a considerar, por processos automáticos ou semi-automáticos, e a aproximação para a posição final desejada é conseguida através de um processo de minimização de energia. Esta minimização de energia é verificada quando o modelo atinge o equilíbrio, entre as suas forças internas e as forças externas originadas pelos dados e por eventuais forças impostas pelo utilizador.Neste relatório são apresentados os fundamentos dos modelos deformáveis e indicados alguns exemplos de aplicação em imagem médica, nomeadamente na segmentação, no emparelhamento, no alinhamento e na reconstrução de dados 2D e 3D.Palavras-chave: Contornos activos, imagem médica, modelos deformáveis.Deformable models are currently very used in medical image since, through the use of physical principles, they simulate quite satisfactory the real objects behavior.Basically the deformable models are placed in the image near to the objects to be considered, by automatic or semi-automatic processes, and the approach to the desired final position is obtained through an energy minimization process. This energy minimization is verified when the model reaches the equilibrium, between its internal forces and the external forces originated by the data and eventual forces imposed by the user.In this report are presented the deformable models fundaments and indicated some application examples in medical imaging field, namely in segmentation, matching, alignment and in the reconstruction of 2D and 3D data.Keywords: Active contours, deformable models, medical image

Deep motion tracking from multiview angiographic image sequences for synchronization of cardiac phases

In the diagnosis and interventional treatment of coronary artery disease, the 3D+time reconstruction of the coronary artery on the basis of x-ray angiographic image sequences can provide dynamic structural information. The synchronization of cardiac phases in the sequences is essential for minimizing the influence of cardiorespiratory motion and realizing precise 3D+time reconstruction. Key points are initially extracted from the first image of a sequence. Matching grid points between consecutive images in the sequence are extracted by a multi-layer matching strategy. Then deep motion tracking (DMT) of key points is achieved by local deformation based on the neighboring grid points of key points. The local deformation is optimized by the Random sample consensus (RANSAC) algorithm. Then, a simple harmonic motion (SHM) model is utilized to distinguish cardiac motion from other motion sources (e.g. respiratory, patient movement, etc). Next, the signal which is composed of cardiac motions is filtered by a band-pass filter to reconstruct the cardiac phases. Finally, the synchronization of cardiac phases from different imaging angles is realized by a piece-wise linear transformation. The proposed method was evaluated using clinical x-ray angiographic image sequences from 13 patients. 85% matching points can be accurately computed by the DMT method. The mean peak temporal distance (MPTD) between the reconstructed cardiac phases and the electrocardiograph signal is 0.027 s. The correlation between the cardiac phases of the same patient is over 89%. Compared with three other state-of-the-art methods, the proposed method accurately reconstructs and synchronizes the cardiac phases from different sequences of the same patient. The proposed DMT method is robust and highly effective in synchronizing cardiac phases of angiographic image sequences captured from different imaging angles

Tracking features in image sequences with Kalman filtering, global optimization, mahalanobis distance and a management model

This work addresses the problem of tracking feature points along image sequences. In order to analyze the undergoing movement, an approach based on the Kalman filtering technique has been used, which basically carries out the estimation and correction of the features' movement in every image frame. So as to integrate the measurements obtained from each image into the Kalman filter, a data optimization process has been adopted to achieve the best global correspondence set. The proposed criterion minimizes the cost of global matching, which is based on the Mahalanobis distance. A management model is employed to manage the features being tracked. This model adequately deals with problems related to the occlusion of the tracked features, the appearance of new features, as well as optimizing the computational resources used. Experimental results obtained through the use of the proposed tracking framework are presented

Introdução à Análise de Movimento usando Visão Computacional

Pretende-se com este trabalho fazer uma introdução ao que tem vindo a ser realizado no domínio do seguimento e análise de movimento recorrendo a visão computacional.Assim no primeiro capítulo deste relatório faremos referência aos vários tipos de movimento e analisaremos as fases que compõem um sistema comum de captura e análise de movimento, descrevendo sucintamente alguns trabalhos realizados nesta área.Seguidamente, no segundo capítulo, faremos uma apresentação mais detalhada da área do seguimento e análise de movimento humano de corpo inteiro; nomeadamente, no reconhecimento da pose e do reconhecimento do andar e de gestos.Finalmente, no terceiro e último capítulo, daremos ênfase à análise de imagem médica e exemplificaremos, sumariamente, algumas das suas aplicações.With this work we intend to introduce what has been done in the domain of tracking and motion analysis by using computational vision.Therefore in the first chapter of this report we will refer the various types of motion, and analyse the steps that compose a general system of movement capture and analysis, by succinctly describing some works done in this field.Then, in the second chapter we will do a more detailed study about the area of human entire body tracking and motion analysis; namely, in pose recognition and in the recognition of gait and gestures.Finally, in the third and last chapter, emphasis will be given to the medical images analysis and we will summarily exemplify some of its applications

Differently stained whole slide image registration technique with landmark validation

Abstract. One of the most significant features in digital pathology is to compare and fuse successive differently stained tissue sections, also called slides, visually. Doing so, aligning different images to a common frame, ground truth, is required. Current sample scanning tools enable to create images full of informative layers of digitalized tissues, stored with a high resolution into whole slide images. However, there are a limited amount of automatic alignment tools handling large images precisely in acceptable processing time. The idea of this study is to propose a deep learning solution for histopathology image registration. The main focus is on the understanding of landmark validation and the impact of stain augmentation on differently stained histopathology images. Also, the developed registration method is compared with the state-of-the-art algorithms which utilize whole slide images in the field of digital pathology. There are previous studies about histopathology, digital pathology, whole slide imaging and image registration, color staining, data augmentation, and deep learning that are referenced in this study. The goal is to develop a learning-based registration framework specifically for high-resolution histopathology image registration. Different whole slide tissue sample images are used with a resolution of up to 40x magnification. The images are organized into sets of consecutive, differently dyed sections, and the aim is to register the images based on only the visible tissue and ignore the background. Significant structures in the tissue are marked with landmarks. The quality measurements include, for example, the relative target registration error, structural similarity index metric, visual evaluation, landmark-based evaluation, matching points, and image details. These results are comparable and can be used also in the future research and in development of new tools. Moreover, the results are expected to show how the theory and practice are combined in whole slide image registration challenges. DeepHistReg algorithm will be studied to better understand the development of stain color feature augmentation-based image registration tool of this study. Matlab and Aperio ImageScope are the tools to annotate and validate the image, and Python is used to develop the algorithm of this new registration tool. As cancer is globally a serious disease regardless of age or lifestyle, it is important to find ways to develop the systems experts can use while working with patients’ data. There is still a lot to improve in the field of digital pathology and this study is one step toward it.Eri menetelmin värjättyjen virtuaalinäytelasien rekisteröintitekniikka kiintopisteiden validointia hyödyntäen. Tiivistelmä. Yksi tärkeimmistä digitaalipatologian ominaisuuksista on verrata ja fuusioida peräkkäisiä eri menetelmin värjättyjä kudosleikkeitä toisiinsa visuaalisesti. Tällöin keskenään lähes identtiset kuvat kohdistetaan samaan yhteiseen kehykseen, niin sanottuun pohjatotuuteen. Nykyiset näytteiden skannaustyökalut mahdollistavat sellaisten kuvien luonnin, jotka ovat täynnä kerroksittaista tietoa digitalisoiduista näytteistä, tallennettuna erittäin korkean resoluution virtuaalisiin näytelaseihin. Tällä hetkellä on olemassa kuitenkin vain kourallinen automaattisia työkaluja, jotka kykenevät käsittelemään näin valtavia kuvatiedostoja tarkasti hyväksytyin aikarajoin. Tämän työn tarkoituksena on syväoppimista hyväksikäyttäen löytää ratkaisu histopatologisten kuvien rekisteröintiin. Tärkeimpänä osa-alueena on ymmärtää kiintopisteiden validoinnin periaatteet sekä eri väriaineiden augmentoinnin vaikutus. Lisäksi tässä työssä kehitettyä rekisteröintialgoritmia tullaan vertailemaan muihin kirjallisuudessa esitettyihin algoritmeihin, jotka myös hyödyntävät virtuaalinäytelaseja digitaalipatologian saralla. Kirjallisessa osiossa tullaan siteeraamaan aiempia tutkimuksia muun muassa seuraavista aihealueista: histopatologia, digitaalipatologia, virtuaalinäytelasi, kuvantaminen ja rekisteröinti, näytteen värjäys, data-augmentointi sekä syväoppiminen. Tavoitteena on kehittää oppimispohjainen rekisteröintikehys erityisesti korkearesoluutioisille digitalisoiduille histopatologisille kuville. Erilaisissa näytekuvissa tullaan käyttämään jopa 40-kertaista suurennosta. Kuvat kudoksista on järjestetty eri menetelmin värjättyihin peräkkäisiin kuvasarjoihin ja tämän työn päämääränä on rekisteröidä kuvat pohjautuen ainoastaan kudosten näkyviin osuuksiin, jättäen kuvien tausta huomioimatta. Kudosten merkittävimmät rakenteet on merkattu niin sanotuin kiintopistein. Työn laatumittauksina käytetään arvoja, kuten kohteen suhteellinen rekisteröintivirhe (rTRE), rakenteellisen samankaltaisuuindeksin mittari (SSIM), sekä visuaalista arviointia, kiintopisteisiin pohjautuvaa arviointia, yhteensopivuuskohtia, ja kuvatiedoston yksityiskohtia. Nämä arvot ovat verrattavissa myös tulevissa tutkimuksissa ja samaisia arvoja voidaan käyttää uusia työkaluja kehiteltäessä. DeepHistReg metodi toimii pohjana tässä työssä kehitettävälle näytteen värjäyksen parantamiseen pohjautuvalle rekisteröintityökalulle. Matlab ja Aperio ImageScope ovat ohjelmistoja, joita tullaan hyödyntämään tässä työssä kuvien merkitsemiseen ja validointiin. Ohjelmointikielenä käytetään Pythonia. Syöpä on maailmanlaajuisesti vakava sairaus, joka ei katso ikää eikä elämäntyyliä. Siksi on tärkeää löytää uusia keinoja kehittää työkaluja, joita asiantuntijat voivat hyödyntää jokapäiväisessä työssään potilastietojen käsittelyssä. Digitaalipatologian osa-alueella on vielä paljon innovoitavaa ja tämä työ on yksi askel eteenpäin taistelussa syöpäsairauksia vastaan

Reconstruction and analysis of 4D heart motion from tagged MR images.

Luo Guo.Thesis (M.Phil.)--Chinese University of Hong Kong, 2003.Includes bibliographical references (leaves 97-109).Abstracts in English and Chinese.Abstract --- p.iAcknowledgement --- p.iiiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Motivation --- p.2Chapter 1.2 --- Basics --- p.3Chapter 1.2.1 --- Anatomy of Human Heart --- p.3Chapter 1.2.2 --- The Philosophy of MRI --- p.5Chapter 1.2.3 --- MRI in Practice --- p.7Chapter 1.3 --- Cardiac MR Images Analysis --- p.7Chapter 1.3.1 --- Heart Boundary Segmentation --- p.7Chapter 1.3.2 --- Motion Reconstruction --- p.13Chapter 1.4 --- Summary and Thesis Overview --- p.17Chapter 2 --- Tracking Tags in SPAMM Images --- p.21Chapter 2.1 --- Introduction --- p.21Chapter 2.2 --- The Snake Model --- p.28Chapter 2.3 --- The Improved Snake Model: Tracking Tags Using Snakes --- p.30Chapter 2.3.1 --- Imaging Protocol --- p.30Chapter 2.3.2 --- Model Formulation --- p.31Chapter 2.3.3 --- Numerical Solution --- p.39Chapter 2.4 --- Experimental Results --- p.44Chapter 3 --- B-Spline Based LV Motion Reconstruction --- p.52Chapter 3.1 --- Introduction --- p.52Chapter 3.2 --- LV Shape: Generalized Deformable Ellipsoid --- p.56Chapter 3.3 --- The New Geometric Model: Generalized Prolate Spheroid --- p.58Chapter 3.3.1 --- Generalized Prolate Spheroid --- p.58Chapter 3.3.2 --- Initial Geometric Fitting --- p.59Chapter 3.4 --- Fast Motion Reconstruction: The Enhanced Hi- erarchical Motion Decomposition --- p.65Chapter 3.4.1 --- Hierarchical Motion Decomposition --- p.65Chapter 3.4.2 --- Motion Reconstruction --- p.68Chapter 3.4.3 --- Implementation --- p.76Chapter 3.4.4 --- Time Smoothing --- p.77Chapter 3.5 --- Experimental Results --- p.79Chapter 3.5.1 --- Geometric Fitting --- p.79Chapter 3.5.2 --- Motion Reconstruction --- p.79Chapter 4 --- Conclusion --- p.93Bibliography --- p.10

Image processing using the Walsh transform.

This thesis presents a new algorithm which can be used to register images of the same or different modalities e.g images with multiple channels such as X-rays, temperature, or elevation or simply images of different spectral bands. In particular, a correlation-based scheme is used, but instead of grey values, it correlates numbers formulated by different combinations of the extracted local Walsh coefficients of the images. Each image patch is expanded in terms of Walsh basis functions. Each Walsh basis function can be thought of as measuring a different aspect of local structure, eg horizontal edge, corner, etc. The coefficients of the expansion, therefore, can be thought of as dense local features, estimating at each point the degree of presence of, for example, a horizontal edge, a corner with contrast of a certain type, etc. These coefficients are normalised and used as digits in a chosen number system which allows one to create a unique number for each type of local structure. The choice of the basis of the number system allows one to give different emphasis to different types of local feature (e.g. corners versus edges) and thus the method we present forms a unified framework in terms of which several feature matching methods may be interpreted. The algorithm is compared with wavelet based approaches, using simulated and real images. The images used for the registration experiments are assumed to differ from each other by a rotation and a translation only. Additionally, the method was extended to cope with 3D image sets, while as an add-on, it was also tried in performing image segmentation

Análise de movimento de corpos deformáveis usando visão computacional

O tema desta tese está inserido no domínio da visão por computador e na área da análise de movimento de corpos deformáveis. O seu interesse tem vindo a aumentar consideravelmente nos últimos tempos devido, sobretudo, ao fracasso das tentativas de utilizar as metodologias normalmente associadas aos corpos rígidos para a análise do movimento não rígido, e também ao elevado número de aplicações que existem para tal análise. O enorme potencial de aplicação existente na área da imagem médica, nomeadamente na segmentação, no emparelhamento e na análise e seguimento do movimento de estruturas, é responsável por grande parte do trabalho realizado neste âmbito. Outras aplicações que podem ser referidas são o seguimento de sistemas articulados, a análise do escoamento de fluidos, do movimento de nuvens para a previsão meteorológica, do comportamento de materiais sob a acção de forças, a análise e reconhecimento de faces, de veículos e de caracteres, etc.Ao contrário do que sucede com os objectos rígidos, a representação da forma de um objecto deformável está fortemente relacionada com a análise e seguimento do seu movimento e, para se desenvolverem técnicas para resolver tais problemas, é necessário utilizar determinadas restrições sobre o movimento/forma o que, consequentemente, individualiza as abordagens desenvolvidas e as torna específicas para determinadas classes de problemas.The theme of this thesis is in the computer vision domain and more specifically in the area of motion analysis of deformable bodies. The interest in this field has risen significantly in the last few years due to the failure of adapting existing rigid-body methods and to the very wide range of potential applications. A strong impulse originated in the area of medical imaging for segmenting, matching and tracking body structures, but other application domains have also contributed, namely the tracking of articulate systems, the analysis of fluids flow, the movement of clouds for weather forecasting, the structural analysis of materials, the recognition of faces, vehicles and characters, etc.Unlike rigid objects, the shape representation of deformable objects is strongly related with the analysis and tracking of its motion and thus, in order to develop suitable approaches and techniques for analysis, certain restrictions and constraints on the shape/motion must be specific to the type of task under consideration