Generalizable automated pixel-level structural segmentation of medical and biological data

Over the years, the rapid expansion in imaging techniques and equipments has driven the demand for more automation in handling large medical and biological data sets. A wealth of approaches have been suggested as optimal solutions for their respective imaging types. These solutions span various image resolutions, modalities and contrast (staining) mechanisms. Few approaches generalise well across multiple image types, contrasts or resolution. This thesis proposes an automated pixel-level framework that addresses 2D, 2D+t and 3D structural segmentation in a more generalizable manner, yet has enough adaptability to address a number of specific image modalities, spanning retinal funduscopy, sequential fluorescein angiography and two-photon microscopy. The pixel-level segmentation scheme involves: i ) constructing a phase-invariant orientation field of the local spatial neighbourhood; ii ) combining local feature maps with intensity-based measures in a structural patch context; iii ) using a complex supervised learning process to interpret the combination of all the elements in the patch in order to reach a classification decision. This has the advantage of transferability from retinal blood vessels in 2D to neural structures in 3D. To process the temporal components in non-standard 2D+t retinal angiography sequences, we first introduce a co-registration procedure: at the pairwise level, we combine projective RANSAC with a quadratic homography transformation to map the coordinate systems between any two frames. At the joint level, we construct a hierarchical approach in order for each individual frame to be registered to the global reference intra- and inter- sequence(s). We then take a non-training approach that searches in both the spatial neighbourhood of each pixel and the filter output across varying scales to locate and link microvascular centrelines to (sub-) pixel accuracy. In essence, this \link while extract" piece-wise segmentation approach combines the local phase-invariant orientation field information with additional local phase estimates to obtain a soft classification of the centreline (sub-) pixel locations. Unlike retinal segmentation problems where vasculature is the main focus, 3D neural segmentation requires additional exibility, allowing a variety of structures of anatomical importance yet with different geometric properties to be differentiated both from the background and against other structures. Notably, cellular structures, such as Purkinje cells, neural dendrites and interneurons, all display certain elongation along their medial axes, yet each class has a characteristic shape captured by an orientation field that distinguishes it from other structures. To take this into consideration, we introduce a 5D orientation mapping to capture these orientation properties. This mapping is incorporated into the local feature map description prior to a learning machine. Extensive performance evaluations and validation of each of the techniques presented in this thesis is carried out. For retinal fundus images, we compute Receiver Operating Characteristic (ROC) curves on existing public databases (DRIVE & STARE) to assess and compare our algorithms with other benchmark methods. For 2D+t retinal angiography sequences, we compute the error metrics ("Centreline Error") of our scheme with other benchmark methods. For microscopic cortical data stacks, we present segmentation results on both surrogate data with known ground-truth and experimental rat cerebellar cortex two-photon microscopic tissue stacks.Open Acces

Noise-Enhanced and Human Visual System-Driven Image Processing: Algorithms and Performance Limits

This dissertation investigates the problem of image processing based on stochastic resonance (SR) noise and human visual system (HVS) properties, where several novel frameworks and algorithms for object detection in images, image enhancement and image segmentation as well as the method to estimate the performance limit of image segmentation algorithms are developed. Object detection in images is a fundamental problem whose goal is to make a decision if the object of interest is present or absent in a given image. We develop a framework and algorithm to enhance the detection performance of suboptimal detectors using SR noise, where we add a suitable dose of noise into the original image data and obtain the performance improvement. Micro-calcification detection is employed in this dissertation as an illustrative example. The comparative experiments with a large number of images verify the efficiency of the presented approach. Image enhancement plays an important role and is widely used in various vision tasks. We develop two image enhancement approaches. One is based on SR noise, HVS-driven image quality evaluation metrics and the constrained multi-objective optimization (MOO) technique, which aims at refining the existing suboptimal image enhancement methods. Another is based on the selective enhancement framework, under which we develop several image enhancement algorithms. The two approaches are applied to many low quality images, and they outperform many existing enhancement algorithms. Image segmentation is critical to image analysis. We present two segmentation algorithms driven by HVS properties, where we incorporate the human visual perception factors into the segmentation procedure and encode the prior expectation on the segmentation results into the objective functions through Markov random fields (MRF). Our experimental results show that the presented algorithms achieve higher segmentation accuracy than many representative segmentation and clustering algorithms available in the literature. Performance limit, or performance bound, is very useful to evaluate different image segmentation algorithms and to analyze the segmentability of the given image content. We formulate image segmentation as a parameter estimation problem and derive a lower bound on the segmentation error, i.e., the mean square error (MSE) of the pixel labels considered in our work, using a modified Cramér-Rao bound (CRB). The derivation is based on the biased estimator assumption, whose reasonability is verified in this dissertation. Experimental results demonstrate the validity of the derived bound

Coronary Artery Segmentation and Motion Modelling

Conventional coronary artery bypass surgery requires invasive sternotomy and the use of a cardiopulmonary bypass, which leads to long recovery period and has high infectious potential. Totally endoscopic coronary artery bypass (TECAB) surgery based on image guided robotic surgical approaches have been developed to allow the clinicians to conduct the bypass surgery off-pump with only three pin holes incisions in the chest cavity, through which two robotic arms and one stereo endoscopic camera are inserted. However, the restricted field of view of the stereo endoscopic images leads to possible vessel misidentification and coronary artery mis-localization. This results in 20-30% conversion rates from TECAB surgery to the conventional approach. We have constructed patient-specific 3D + time coronary artery and left ventricle motion models from preoperative 4D Computed Tomography Angiography (CTA) scans. Through temporally and spatially aligning this model with the intraoperative endoscopic views of the patient's beating heart, this work assists the surgeon to identify and locate the correct coronaries during the TECAB precedures. Thus this work has the prospect of reducing the conversion rate from TECAB to conventional coronary bypass procedures. This thesis mainly focus on designing segmentation and motion tracking methods of the coronary arteries in order to build pre-operative patient-specific motion models. Various vessel centreline extraction and lumen segmentation algorithms are presented, including intensity based approaches, geometric model matching method and morphology-based method. A probabilistic atlas of the coronary arteries is formed from a group of subjects to facilitate the vascular segmentation and registration procedures. Non-rigid registration framework based on a free-form deformation model and multi-level multi-channel large deformation diffeomorphic metric mapping are proposed to track the coronary motion. The methods are applied to 4D CTA images acquired from various groups of patients and quantitatively evaluated

Efficient data structures for piecewise-smooth video processing

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 95-102).A number of useful image and video processing techniques, ranging from low level operations such as denoising and detail enhancement to higher level methods such as object manipulation and special effects, rely on piecewise-smooth functions computed from the input data. In this thesis, we present two computationally efficient data structures for representing piecewise-smooth visual information and demonstrate how they can dramatically simplify and accelerate a variety of video processing algorithms. We start by introducing the bilateral grid, an image representation that explicitly accounts for intensity edges. By interpreting brightness values as Euclidean coordinates, the bilateral grid enables simple expressions for edge-aware filters. Smooth functions defined on the bilateral grid are piecewise-smooth in image space. Within this framework, we derive efficient reinterpretations of a number of edge-aware filters commonly used in computational photography as operations on the bilateral grid, including the bilateral filter, edgeaware scattered data interpolation, and local histogram equalization. We also show how these techniques can be easily parallelized onto modern graphics hardware for real-time processing of high definition video. The second data structure we introduce is the video mesh, designed as a flexible central data structure for general-purpose video editing. It represents objects in a video sequence as 2.5D "paper cutouts" and allows interactive editing of moving objects and modeling of depth, which enables 3D effects and post-exposure camera control. In our representation, we assume that motion and depth are piecewise-smooth, and encode them sparsely as a set of points tracked over time. The video mesh is a triangulation over this point set and per-pixel information is obtained by interpolation. To handle occlusions and detailed object boundaries, we rely on the user to rotoscope the scene at a sparse set of frames using spline curves. We introduce an algorithm to robustly and automatically cut the mesh into local layers with proper occlusion topology, and propagate the splines to the remaining frames. Object boundaries are refined with per-pixel alpha mattes. At its core, the video mesh is a collection of texture-mapped triangles, which we can edit and render interactively using graphics hardware. We demonstrate the effectiveness of our representation with special effects such as 3D viewpoint changes, object insertion, depthof- field manipulation, and 2D to 3D video conversion.by Jiawen Chen.Ph.D

Advanced image processing techniques for detection and quantification of drusen

Dissertation presented to obtain the degree of Doctor of Philosophy in Electrical Engineering, speciality on Perceptional Systems, by the Universidade Nova de Lisboa, Faculty of Sciences and TechnologyDrusen are common features in the ageing macula, caused by accumulation of extracellular materials beneath the retinal surface, visible in retinal fundus images as yellow spots. In the ophthalmologists’ opinion, the evaluation of the total drusen area, in a sequence of images taken during a treatment, will help to understand the disease progression and effectiveness. However, this evaluation is fastidious and difficult to reproduce when performed manually. A literature review on automated drusen detection showed that the works already published were limited to techniques of either adaptive or global thresholds which showed a tendency to produce a significant number of false positives. The purpose for this work was to propose an alternative method to automatically quantify drusen using advanced digital image processing techniques. This methodology is based on a detection and modelling algorithm to automatically quantify drusen. It includes an image pre-processing step to correct the uneven illumination by using smoothing splines fitting and to normalize the contrast. To quantify drusen a detection and modelling algorithm is adopted. The detection uses a new gradient based segmentation algorithm that isolates drusen and provides basic drusen characterization to the modelling stage. These are then fitted by Gaussian functions, to produce a model of the image, which is used to compute the affected areas. To validate the methodology, two software applications, one for semi-automated (MD3RI) and other for automated detection of drusen (AD3RI), were implemented. The first was developed for Ophthalmologists to manually analyse and mark drusen deposits, while the other implemented algorithms for automatic drusen quantification.Four studies to assess the methodology accuracy involving twelve specialists have taken place. These compared the automated method to the specialists and evaluated its repeatability. The studies were analysed regarding several indicators, which were based on the total affected area and on a pixel-to-pixel analysis. Due to the high variability among the graders involved in the first study, a new evaluation method, the Weighed Matching Analysis, was developed to improve the pixel-to-pixel analysis by using the statistical significance of the observations to differentiate positive and negative pixels. From the results of these studies it was concluded that the methodology proposed is capable to automatically measure drusen in an accurate and reproducible process. Also, the thesis proposes new image processing algorithms, for image pre-processing, image segmentation,image modelling and images comparison, which are also applicable to other image processing fields

Contrast enhancement and exposure correction using a structure-aware distribution fitting

Realce de contraste e correção de exposição são úteis em aplicações domésticas e técnicas, no segundo caso como uma etapa de pré-processamento para outras técnicas ou para ajudar a observação humana. Frequentemente, uma transformação localmente adaptativa é mais adequada para a tarefa do que uma transformação global. Por exemplo, objetos e regiões podem ter níveis de iluminação muito diferentes, fenômenos físicos podem comprometer o contraste em algumas regiões mas não em outras, ou pode ser desejável ter alta visibilidade de detalhes em todas as partes da imagem. Para esses casos, métodos de realce de imagem locais são preferíveis. Embora existam muitos métodos de realce de contraste e correção de exposição disponíveis na literatura, não há uma solução definitiva que forneça um resultado satisfatório em todas as situações, e novos métodos surgem a cada ano. Em especial, os métodos tradicionais baseados em equalização adaptativa de histograma sofrem dos efeitos checkerboard e staircase e de excesso de realce. Esta dissertação propõe um método para realce de contraste e correção de exposição em imagens chamado Structure-Aware Distribution Stretching (SADS). O método ajusta regionalmente à imagem um modelo paramétrico de distribuição de probabilidade, respeitando a estrutura da imagem e as bordas entre as regiões. Isso é feito usando versões regionais das expressões clássicas de estimativa dos parâmetros da distribuição, que são obtidas substituindo a mé- dia amostral presente nas expressões originais por um filtro de suavização que preserva as bordas. Após ajustar a distribuição, a função de distribuição acumulada (CDF) do modelo ajustado e a inversa da CDF da distribuição desejada são aplicadas. Uma heurística ciente de estrutura que detecta regiões suaves é proposta e usada para atenuar as transformações em regiões planas. SADS foi comparado a outros métodos da literatura usando métricas objetivas de avaliação de qualidade de imagem (IQA) sem referência e com referência completa nas tarefas de realce de contraste e correção de exposição simultâneos e na tarefa de defogging/dehazing. Os experimentos indicam um desempenho geral superior do SADS em relação aos métodos comparados para os conjuntos de imagens usados, de acordo com as métricas IQA adotadas.Contrast enhancement and exposure correction are useful in domestic and technical applications, the latter as a preprocessing step for other techniques or for aiding human observation. Often, a locally adaptive transformation is more suitable for the task than a global transformation. For example, objects and regions may have very different levels of illumination, physical phenomena may compromise the contrast at some regions but not at others, or it may be desired to have high visibility of details in all parts of the image. For such cases, local image enhancement methods are preferable. Although there are many contrast enhancement and exposure correction methods available in the literature, there is no definitive solution that provides a satisfactory result in all situations, and new methods emerge each year. In special, traditional adaptive histogram equalization-based methods suffer from checkerboard and staircase effects and from over enhancement. This dissertation proposes a method for contrast enhancement and exposure correction in images named Structure-Aware Distribution Stretching (SADS). The method fits a parametric model of probability distribution to the image regionally while respecting the image structure and edges between regions. This is done using regional versions of the classical expressions for estimating the parameters of the distribution, which are obtained by replacing the sample mean present in the original expressions by an edge-preserving smoothing filter. After fitting the distribution, the cumulative distribution function (CDF) of the adjusted model and the inverse of the CDF of the desired distribution are applied. A structure-aware heuristic to indicate smooth regions is proposed and used to attenuate the transformations in flat regions. SADS was compared with other methods from the literature using objective no-reference and full-reference image quality assessment (IQA) metrics in the tasks of simultaneous contrast enhancement and exposure correction and in the task of defogging/dehazing. The experiments indicate a superior overall performance of SADS with respect to the compared methods for the image sets used, according to the IQA metrics adopted

Enhanced iris recognition: Algorithms for segmentation, matching and synthesis

This thesis addresses the issues of segmentation, matching, fusion and synthesis in the context of irises and makes a four-fold contribution. The first contribution of this thesis is a post matching algorithm that observes the structure of the differences in feature templates to enhance recognition accuracy. The significance of the scheme is its robustness to inaccuracies in the iris segmentation process. Experimental results on the CASIA database indicate the efficacy of the proposed technique. The second contribution of this thesis is a novel iris segmentation scheme that employs Geodesic Active Contours to extract the iris from the surrounding structures. The proposed scheme elicits the iris texture in an iterative fashion depending upon both the local and global conditions of the image. The performance of an iris recognition algorithm on both the WVU non-ideal and CASIA iris database is observed to improve upon application of the proposed segmentation algorithm. The third contribution of this thesis is the fusion of multiple instances of the same iris and multiple iris units of the eye, i.e., the left and right iris at the match score level. Using simple sum rule, it is demonstrated that both multi-instance and multi-unit fusion of iris can lead to a significant improvement in matching accuracy. The final contribution is a technique to create a large database of digital renditions of iris images that can be used to evaluate the performance of iris recognition algorithms. This scheme is implemented in two stages. In the first stage, a Markov Random Field model is used to generate a background texture representing the global iris appearance. In the next stage a variety of iris features, viz., radial and concentric furrows, collarette and crypts, are generated and embedded in the texture field. Experimental results confirm the validity of the synthetic irises generated using this technique

Analysis of Retinal Image Data to Support Glaucoma Diagnosis

Fundus kamera je široce dostupné zobrazovací zařízení, které umožňuje relativně rychlé a nenákladné vyšetření zadního segmentu oka – sítnice. Z těchto důvodů se mnoho výzkumných pracovišť zaměřuje právě na vývoj automatických metod diagnostiky nemocí sítnice s využitím fundus fotografií. Tato dizertační práce analyzuje současný stav vědeckého poznání v oblasti diagnostiky glaukomu s využitím fundus kamery a navrhuje novou metodiku hodnocení vrstvy nervových vláken (VNV) na sítnici pomocí texturní analýzy. Spolu s touto metodikou je navržena metoda segmentace cévního řečiště sítnice, jakožto další hodnotný příspěvek k současnému stavu řešené problematiky. Segmentace cévního řečiště rovněž slouží jako nezbytný krok předcházející analýzu VNV. Vedle toho práce publikuje novou volně dostupnou databázi snímků sítnice se zlatými standardy pro účely hodnocení automatických metod segmentace cévního řečiště.Fundus camera is widely available imaging device enabling fast and cheap examination of the human retina. Hence, many researchers focus on development of automatic methods towards assessment of various retinal diseases via fundus images. This dissertation summarizes recent state-of-the-art in the field of glaucoma diagnosis using fundus camera and proposes a novel methodology for assessment of the retinal nerve fiber layer (RNFL) via texture analysis. Along with it, a method for the retinal blood vessel segmentation is introduced as an additional valuable contribution to the recent state-of-the-art in the field of retinal image processing. Segmentation of the blood vessels also serves as a necessary step preceding evaluation of the RNFL via the proposed methodology. In addition, a new publicly available high-resolution retinal image database with gold standard data is introduced as a novel opportunity for other researches to evaluate their segmentation algorithms.