SEGMENT3D: A Web-based Application for Collaborative Segmentation of 3D images used in the Shoot Apical Meristem

The quantitative analysis of 3D confocal microscopy images of the shoot apical meristem helps understanding the growth process of some plants. Cell segmentation in these images is crucial for computational plant analysis and many automated methods have been proposed. However, variations in signal intensity across the image mitigate the effectiveness of those approaches with no easy way for user correction. We propose a web-based collaborative 3D image segmentation application, SEGMENT3D, to leverage automatic segmentation results. The image is divided into 3D tiles that can be either segmented interactively from scratch or corrected from a pre-existing segmentation. Individual segmentation results per tile are then automatically merged via consensus analysis and then stitched to complete the segmentation for the entire image stack. SEGMENT3D is a comprehensive application that can be applied to other 3D imaging modalities and general objects. It also provides an easy way to create supervised data to advance segmentation using machine learning models

Unsupervised brain anomaly detection in MR images

Brain disorders are characterized by morphological deformations in shape and size of (sub)cortical structures in one or both hemispheres. These deformations cause deviations from the normal pattern of brain asymmetries, resulting in asymmetric lesions that directly affect the patient’s condition. Unsupervised methods aim to learn a model from unlabeled healthy images, so that an unseen image that breaks priors of this model, i.e., an outlier, is considered an anomaly. Consequently, they are generic in detecting any lesions, e.g., coming from multiple diseases, as long as these notably differ from healthy training images. This thesis addresses the development of solutions to leverage unsupervised machine learning for the detection/analysis of abnormal brain asymmetries related to anomalies in magnetic resonance (MR) images. First, we propose an automatic probabilistic-atlas-based approach for anomalous brain image segmentation. Second, we explore an automatic method for the detection of abnormal hippocampi from abnormal asymmetries based on deep generative networks and a one-class classifier. Third, we present a more generic framework to detect abnormal asymmetries in the entire brain hemispheres. Our approach extracts pairs of symmetric regions — called supervoxels — in both hemispheres of a test image under study. One-class classifiers then analyze the asymmetries present in each pair. Experimental results on 3D MR-T1 images from healthy subjects and patients with a variety of lesions show the effectiveness and robustness of the proposed unsupervised approaches for brain anomaly detection

Mobile Wound Assessment and 3D Modeling from a Single Image

The prevalence of camera-enabled mobile phones have made mobile wound assessment a viable treatment option for millions of previously difficult to reach patients. We have designed a complete mobile wound assessment platform to ameliorate the many challenges related to chronic wound care. Chronic wounds and infections are the most severe, costly and fatal types of wounds, placing them at the center of mobile wound assessment. Wound physicians assess thousands of single-view wound images from all over the world, and it may be difficult to determine the location of the wound on the body, for example, if the wound is taken at close range. In our solution, end-users capture an image of the wound by taking a picture with their mobile camera. The wound image is segmented and classified using modern convolution neural networks, and is stored securely in the cloud for remote tracking. We use an interactive semi-automated approach to allow users to specify the location of the wound on the body. To accomplish this we have created, to the best our knowledge, the first 3D human surface anatomy labeling system, based off the current NYU and Anatomy Mapper labeling systems. To interactively view wounds in 3D, we have presented an efficient projective texture mapping algorithm for texturing wounds onto a 3D human anatomy model. In so doing, we have demonstrated an approach to 3D wound reconstruction that works even for a single wound image

Shape segmentation and retrieval based on the skeleton cut space

3D vormverzamelingen groeien snel in veel toepassingsgebieden. Om deze effectief te kunnen gebruiken bij modelleren, simuleren, of 3D contentontwikkeling moet men 3D vormen verwerken. Voorbeelden hiervan zijn het snijden van een vorm in zijn natuurlijke onderdelen (ook bekend als segmentatie), en het vinden van vormen die lijken op een gegeven model in een grote vormverzameling (ook bekend als opvraging). Dit proefschrift presenteert nieuwe methodes voor 3D vormsegmentatie en vormopvraging die gebaseerd zijn op het zogenaamde oppervlakskelet van een 3D vorm. Hoewel allang bekend, dergelijke skeletten kunnen alleen sinds kort snel, robuust, en bijna automatisch berekend worden. Deze ontwikkelingen stellen ons in staat om oppervlakskeletten te gebruiken om vormen te karakteriseren en analyseren zodat operaties zoals segmentatie en opvraging snel en automatisch gedaan kunnen worden. We vergelijken onze nieuwe methodes met moderne methodes voor dezelfde doeleinden en laten zien dat ons aanpak kwalitatief betere resultaten kan produceren. Ten slotte presenteren wij een nieuwe methode om oppervlakskeletten te extraheren die is veel simpeler dan, en heeft vergelijkbare snelheid met, de beste technieken in zijn klasse. Samenvattend, dit proefschrift laat zien hoe men een complete workflow kan implementeren voor het segmenteren en opvragen van 3D vormen gebruik makend van oppervlakskeletten alleen

Análise visual aplicada à análise de imagens

Orientadores: Alexandre Xavier Falcão, Alexandru Cristian Telea, Pedro Jussieu de Rezende, Johannes Bernardus Theodorus Maria RoerdinkTese (doutorado) - Universidade Estadual de Campinas, Instituto de Computação e Universidade de GroningenResumo: Análise de imagens é o campo de pesquisa preocupado com a extração de informações a partir de imagens. Esse campo é bastante importante para aplicações científicas e comerciais. O objetivo principal do trabalho apresentado nesta tese é permitir interatividade com o usuário durante várias tarefas relacionadas à análise de imagens: segmentação, seleção de atributos, e classificação. Neste contexto, permitir interatividade com o usuário significa prover mecanismos que tornem possível que humanos auxiliem computadores em tarefas que são de difícil automação. Com respeito à segmentação de imagens, propomos uma nova técnica interativa que combina superpixels com a transformada imagem-floresta. A vantagem principal dessa técnica é permitir rápida segmentação interativa de imagens grandes, além de permitir extração de características potencialmente mais ricas. Os experimentos sugerem que nossa técnica é tão eficaz quanto a alternativa baseada em pixels. No contexto de seleção de atributos e classificação, propomos um novo sistema de visualização interativa que combina exploração do espaço de atributos (baseada em redução de dimensionalidade) com avaliação automática de atributos. Esse sistema tem como objetivo revelar informações que levem ao desenvolvimento de conjuntos de atributos eficazes para classificação de imagens. O mesmo sistema também pode ser aplicado para seleção de atributos para segmentação de imagens e para classificação de padrões, apesar dessas tarefas não serem nosso foco. Apresentamos casos de uso que mostram como esse sistema pode prover certos tipos de informação qualitativa sobre sistemas de classificação de imagens que seriam difíceis de obter por outros métodos. Também mostramos como o sistema interativo proposto pode ser adaptado para a exploração de resultados computacionais intermediários de redes neurais artificiais. Essas redes atualmente alcançam resultados no estado da arte em muitas aplicações de classificação de imagens. Através de casos de uso envolvendo conjuntos de dados de referência, mostramos que nosso sistema pode prover informações sobre como uma rede opera que levam a melhorias em sistemas de classificação. Já que os parâmetros de uma rede neural artificial são tipicamente adaptados iterativamente, a visualização de seus resultados intermediários pode ser vista como uma tarefa dependente de tempo. Com base nessa perspectiva, propomos uma nova técnica de redução de dimensionalidade dependente de tempo que permite a redução de mudanças desnecessárias nos resultados causadas por pequenas mudanças nos dados. Experimentos preliminares mostram que essa técnica é eficaz em manter a coerência temporal desejadaAbstract: We define image analysis as the field of study concerned with extracting information from images. This field is immensely important for commercial and interdisciplinary applications. The overarching goal behind the work presented in this thesis is enabling user interaction during several tasks related to image analysis: image segmentation, feature selection, and image classification. In this context, enabling user interaction refers to providing mechanisms that allow humans to assist machines in tasks that are difficult to automate. Such tasks are very common in image analysis. Concerning image segmentation, we propose a new interactive technique that combines superpixels with the image foresting transform. The main advantage of our proposed technique is enabling faster interactive segmentation of large images, although it also enables potentially richer feature extraction. Our experiments show that our technique is at least as effective as its pixel-based counterpart. In the context of feature selection and image classification, we propose a new interactive visualization system that combines feature space exploration (based on dimensionality reduction) with automatic feature scoring. This visualization system aims to provide insights that lead to the development of effective feature sets for image classification. The same system can also be applied to select features for image segmentation and (general) pattern classification, although these tasks are not our focus. We present use cases that show how this system may provide a kind of qualitative feedback about image classification systems that would be very difficult to obtain by other (non-visual) means. We also show how our proposed interactive visualization system can be adapted to explore intermediary computational results of artificial neural networks. Such networks currently achieve state-of-the-art results in many image classification applications. Through use cases involving traditional benchmark datasets, we show that our system may enable insights about how a network operates that lead to improvements along the classification pipeline. Because the parameters of an artificial neural network are typically adapted iteratively, visualizing its intermediary computational results can be seen as a time-dependent task. Motivated by this, we propose a new time-dependent dimensionality reduction technique that enables the reduction of apparently unnecessary changes in results due to small changes in the data (temporal coherence). Preliminary experiments show that this technique is effective in enforcing temporal coherenceDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação2012/24121-9;FAPESPCAPE

Visualisation of curved tubular structures in medical databases: An application to virtual colonoscopy

Medical conditions affecting the colon are problematic to diagnose due to the difficulty in examining this particular internal organ. To date, the most widely used approach is to perform a colonoscopy; a procedure in which a small camera is inserted into the colon to examine its surface. This procedure is unpleasant and potentially dangerous for the patient, and is expensive and time consuming for the hospital. As a result, patients at risk of developing the conditions are not always screened as often as would be desirable. Over the last few years a new approach known as virtual colonoscopy has been gaining popularity. The method uses information from a CT scan to reconstruct a 3D model of the colon which can then be examined without the patient needing to undergo a colonoscopy. This approach is now commonly used when screening for polyps (an indication of colon cancer) but can not be so easily used on conditions such as Inflammatory Bowel Disease (IBD) where information beyond the shape of the surface is required. This thesis forms part of a larger project which aims to diagnose conditions such as IBD by using image processing algorithms on CT data and presenting the results to the user in an easy to interpret way. Specifically we are concerned with this visualisation stage of the system and so have developed a new visualisation approach which we call Volumetric CPR. This can be used to supplement the more traditional virtual flythrough visualisation and is applicable to IBD detection as well as screening for polyps. Our technique builds on the concept of Curved Planar Reformation (CPR), which has proved to be a practical and widely used tool for the visualisation of curved tubular structures within the human body. It has been useful in medical procedures involving the examination of blood vessels and the spine. However, it is more difficult to use it for structures such as the colon because abnormalities are smaller relative to the size of the structure and may not have such distinct density and shape characteristics. Our new approach improves on this situation by using volume rendering for hollow regions of the structure and standard CPR, for the surrounding tissue. This effectively combines grey scale contextual information with detailed colour information from the area of interest. The approach is successfully used with each of the standard CPR types and the resulting images are promising as an alternative for virtual colonoscopy. We also demonstrate how systems can effectively utilize this new visualisation in order to convey maximum information to the user. We show how overlays can be used to present surface coverage data and how sophisticated lighting models can improve the users understanding of the 3D structure. We also present details of how to integrate our visualisation into existing systems and work flows

Visual analytics of multidimensional time-dependent trails:with applications in shape tracking

Lots of data collected for both scientific and non-scientific purposes have similar characteristics: changing over time with many different properties. For example, consider the trajectory of an airplane travelling from one location to the other. Not only does the airplane itself move over time, but its heading, height and speed are changing at the same time. During this research, we investigated different ways to collect and visualze data with these characteristics. One practical application being for an automated milking device which needs to be able to determine the position of a cow's teats. By visualizing all data which is generated during the tracking process we can acquire insights in the working of the tracking system and identify possibilites for improvement which should lead to better recognition of the teats by the machine. Another important result of the research is a method which can be used to efficiently process a large amount of trajectory data and visualize this in a simplified manner. This has lead to a system which can be used to show the movement of all airplanes around the world for a period of multiple weeks

User-centered design and evaluation of interactive segmentation methods for medical images

Segmentation of medical images is a challenging task that aims to identify a particular structure present on the image. Among the existing methods involving the user at different levels, from a fully-manual to a fully-automated task, interactive segmentation methods provide assistance to the user during the task to reduce the variability in the results and allow occasional corrections of segmentation failures. Therefore, they offer a compromise between the segmentation efficiency and the accuracy of the results. It is the user who judges whether the results are satisfactory and how to correct them during the segmentation, making the process subject to human factors. Despite the strong influence of the user on the outcomes of a segmentation task, the impact of such factors has received little attention, with the literature focusing the assessment of segmentation processes on computational performance. Yet, involving the user performance in the analysis is more representative of a realistic scenario. Our goal is to explore the user behaviour in order to improve the efficiency of interactive image segmentation processes. This is achieved through three contributions. First, we developed a method which is based on a new user interaction mechanism to provide hints as to where to concentrate the computations. This significantly improves the computation efficiency without sacrificing the quality of the segmentation. The benefits of using such hints are twofold: (i) because our contribution is based on user interaction, it generalizes to a wide range of segmentation methods, and (ii) it gives comprehensive indications about where to focus the segmentation search. The latter advantage is used to achieve the second contribution. We developed an automated method based on a multi-scale strategy to: (i) reduce the user’s workload and, (ii) improve the computational time up to tenfold, allowing real-time segmentation feedback. Third, we have investigated the effects of such improvements in computations on the user’s performance. We report an experiment that manipulates the delay induced by the computation time while performing an interactive segmentation task. Results reveal that the influence of this delay can be significantly reduced with an appropriate interaction mechanism design. In conclusion, this project provides an effective image segmentation solution that has been developed in compliance with user performance requirements. We validated our approach through multiple user studies that provided a step forward into understanding the user behaviour during interactive image segmentation