Reconstruction of 3D Surface Maps from Anterior Segment Optical Coherence Tomography Images Using Graph Theory and Genetic Algorithms

Automatic segmentation of anterior segment optical coherence tomography images provides an important tool to aid management of ocular diseases. Previous studies have mainly focused on 2D segmentation of these images. A novel technique capable of producing 3D maps of the anterior segment is presented here. This method uses graph theory and dynamic programming with shape constraint to segment the anterior and posterior surfaces in individual 2D images. Genetic algorithms are then used to align 2D images to produce a full 3D representation of the anterior segment. In order to validate the results of the 2D segmentation comparison is made to manual segmentation over a set of 39 images. For the 3D reconstruction a data set of 17 eyes is used. These have each been imaged twice so a repeatability measurement can be made. Good agreement was found with manual segmentation for the 2D segmentation method achieving a Dice similarity coefficient of 0.96, which is comparable to the inter-observer agreement. Good repeatability of results was demonstrated with the 3D registration method. A mean difference of 1.77 pixels was found between the anterior surfaces found from repeated scans of the same eye

Angle-Closure Detection in Anterior Segment OCT based on Multi-Level Deep Network

Irreversible visual impairment is often caused by primary angle-closure glaucoma, which could be detected via Anterior Segment Optical Coherence Tomography (AS-OCT). In this paper, an automated system based on deep learning is presented for angle-closure detection in AS-OCT images. Our system learns a discriminative representation from training data that captures subtle visual cues not modeled by handcrafted features. A Multi-Level Deep Network (MLDN) is proposed to formulate this learning, which utilizes three particular AS-OCT regions based on clinical priors: the global anterior segment structure, local iris region, and anterior chamber angle (ACA) patch. In our method, a sliding window based detector is designed to localize the ACA region, which addresses ACA detection as a regression task. Then, three parallel sub-networks are applied to extract AS-OCT representations for the global image and at clinically-relevant local regions. Finally, the extracted deep features of these sub-networks are concatenated into one fully connected layer to predict the angle-closure detection result. In the experiments, our system is shown to surpass previous detection methods and other deep learning systems on two clinical AS-OCT datasets.Comment: 9 pages, accepted by IEEE Transactions on Cybernetic

Anterior Chamber Angle Shape Analysis and Classification of Glaucoma in SS-OCT Images

Optical coherence tomography is a high resolution, rapid, and noninvasive diagnostic tool for angle closure glaucoma. In this paper, we present a new strategy for the classification of the angle closure glaucoma using morphological shape analysis of the iridocorneal angle. The angle structure configuration is quantified by the following six features: (1) mean of the continuous measurement of the angle opening distance; (2) area of the trapezoidal profile of the iridocorneal angle centered at Schwalbe's line; (3) mean of the iris curvature from the extracted iris image; (4) complex shape descriptor, fractal dimension, to quantify the complexity, or changes of iridocorneal angle; (5) ellipticity moment shape descriptor; and (6) triangularity moment shape descriptor. Then, the fuzzy k nearest neighbor (fkNN) classifier is utilized for classification of angle closure glaucoma. Two hundred and sixty-four swept source optical coherence tomography (SS-OCT) images from 148 patients were analyzed in this study. From the experimental results, the fkNN reveals the best classification accuracy (99.11±0.76%) and AUC (0.98±0.012) with the combination of fractal dimension and biometric parameters. It showed that the proposed approach has promising potential to become a computer aided diagnostic tool for angle closure glaucoma (ACG) disease

Machine learning methods for the characterization and classification of complex data

This thesis work presents novel methods for the analysis and classification of medical images and, more generally, complex data. First, an unsupervised machine learning method is proposed to order anterior chamber OCT (Optical Coherence Tomography) images according to a patient's risk of developing angle-closure glaucoma. In a second study, two outlier finding techniques are proposed to improve the results of above mentioned machine learning algorithm, we also show that they are applicable to a wide variety of data, including fraud detection in credit card transactions. In a third study, the topology of the vascular network of the retina, considering it a complex tree-like network is analyzed and we show that structural differences reveal the presence of glaucoma and diabetic retinopathy. In a fourth study we use a model of a laser with optical injection that presents extreme events in its intensity time-series to evaluate machine learning methods to forecast such extreme events.El presente trabajo de tesis desarrolla nuevos métodos para el análisis y clasificación de imágenes médicas y datos complejos en general. Primero, proponemos un método de aprendizaje automático sin supervisión que ordena imágenes OCT (tomografía de coherencia óptica) de la cámara anterior del ojo en función del grado de riesgo del paciente de padecer glaucoma de ángulo cerrado. Luego, desarrollamos dos métodos de detección automática de anomalías que utilizamos para mejorar los resultados del algoritmo anterior, pero que su aplicabilidad va mucho más allá, siendo útil, incluso, para la detección automática de fraudes en transacciones de tarjetas de crédito. Mostramos también, cómo al analizar la topología de la red vascular de la retina considerándola una red compleja, podemos detectar la presencia de glaucoma y de retinopatía diabética a través de diferencias estructurales. Estudiamos también un modelo de un láser con inyección óptica que presenta eventos extremos en la serie temporal de intensidad para evaluar diferentes métodos de aprendizaje automático para predecir dichos eventos extremos.Aquesta tesi desenvolupa nous mètodes per a l’anàlisi i la classificació d’imatges mèdiques i dades complexes. Hem proposat, primer, un mètode d’aprenentatge automàtic sense supervisió que ordena imatges OCT (tomografia de coherència òptica) de la cambra anterior de l’ull en funció del grau de risc del pacient de patir glaucoma d’angle tancat. Després, hem desenvolupat dos mètodes de detecció automàtica d’anomalies que hem utilitzat per millorar els resultats de l’algoritme anterior, però que la seva aplicabilitat va molt més enllà, sent útil, fins i tot, per a la detecció automàtica de fraus en transaccions de targetes de crèdit. Mostrem també, com en analitzar la topologia de la xarxa vascular de la retina considerant-la una xarxa complexa, podem detectar la presència de glaucoma i de retinopatia diabètica a través de diferències estructurals. Finalment, hem estudiat un làser amb injecció òptica, el qual presenta esdeveniments extrems en la sèrie temporal d’intensitat. Hem avaluat diferents mètodes per tal de predir-los.Postprint (published version

NOVEL METHODS OF MERIDIONAL AND CIRCUMFERENTIAL ANTERIOR CHAMBER ANGLE IMAGING

Ph.DDOCTOR OF PHILOSOPH

Automatic segmentation of anterior segment optical coherence tomography images

Automatic segmentation of anterior segment optical coherence tomography (AS OCT) images provides an important tool to aid management of ocular diseases. Having precise details about the topography and thickness of an individual eye enables treatments to be tailored to a specific problem. OCT is an imaging technique that can be used to acquire volumetric data of the anterior segment of the human eye. Fast automatic segmentation of this data, which is not available, means clinically useful information can be obtained without the need for time consuming error-prone manual analysis of the images. This thesis presents newly developed automatic segmentation techniques of OCT images. Segmentation of 2D OCT images is first performed. One of the main challenges segmenting 2D OCT images is the presence of regions of the image that generally have a low signal to noise ratio. This is overcome by the use of shape based terms. A number of different methods, such as level set, graph cut, and graph theory, are developed to do this. The segmentation techniques are validated by comparison to expert manual segmentation and previously published segmentation techniques. The best method, graph theory with shape, was able to achieve segmentation comparable to manual segmentation. Good agreement is found with manual segmentation for the best 2D segmentation method, graph theory with shape, achieving a Dice similarity coefficient of 0.96, which is comparable to inter-observer agreement. It performed significantly better than previously published techniques. The 2D segmentation techniques are then extended to 3D segmentation of OCT images. The challenge here is motion artefact or poor alignment between each 2D images comprising the 3D images. Different segmentation strategies are investigated including direct segmentation by level set or graph cut approaches, and segmentation with registration. In particular the latter requires the introduction of a registration step to align multiple 2D images to produce a 3D representation to overcome the presence of involuntary motion artefacts. This method produces the best performance. In particular, it uses graph theory and dynamic programming to segment the anterior and posterior surfaces in individual 2D images with shape constraint. Genetic algorithms are then used to align 2D images to produce a full 3D representation of the anterior segment based on landmarks or geometric constraints. For the 3D segmentation, a data set of 17 eyes is used for validation. These have each been imaged twice so a repeatability measurement can be made. Good repeatability of results is demonstrated with the 3D alignment method. A mean difference of 1.77 pixels is found between the same surfaces of the repeated scans of the same eye. Overall, a new automation method is developed that can produce maps of the anterior and posterior surfaces of the cornea from a 3D images of the anterior segment of a human eye. This will be a valuable tool that can be used for patient specific biomechanical modelling of the human eye