Dynamic low-level context for the detection of mild traumatic brain injury.

Mild traumatic brain injury (mTBI) appears as low contrast lesions in magnetic resonance (MR) imaging. Standard automated detection approaches cannot detect the subtle changes caused by the lesions. The use of context has become integral for the detection of low contrast objects in images. Context is any information that can be used for object detection but is not directly due to the physical appearance of an object in an image. In this paper, new low-level static and dynamic context features are proposed and integrated into a discriminative voxel-level classifier to improve the detection of mTBI lesions. Visual features, including multiple texture measures, are used to give an initial estimate of a lesion. From the initial estimate novel proximity and directional distance, contextual features are calculated and used as features for another classifier. This feature takes advantage of spatial information given by the initial lesion estimate using only the visual features. Dynamic context is captured by the proposed posterior marginal edge distance context feature, which measures the distance from a hard estimate of the lesion at a previous time point. The approach is validated on a temporal mTBI rat model dataset and shown to have improved dice score and convergence compared to other state-of-the-art approaches. Analysis of feature importance and versatility of the approach on other datasets are also provided

Modeling Brain Circuitry over a Wide Range of Scales

If we are ever to unravel the mysteries of brain function at its most fundamental level, we will need a precise understanding of how its component neurons connect to each other. Electron Microscopes (EM) can now provide the nanometer resolution that is needed to image synapses, and therefore connections, while Light Microscopes (LM) see at the micrometer resolution required to model the 3D structure of the dendritic network. Since both the topology and the connection strength are integral parts of the brain's wiring diagram, being able to combine these two modalities is critically important. In fact, these microscopes now routinely produce high-resolution imagery in such large quantities that the bottleneck becomes automated processing and interpretation, which is needed for such data to be exploited to its full potential. In this paper, we briefly review the Computer Vision techniques we have developed at EPFL to address this need. They include delineating dendritic arbors from LM imagery, segmenting organelles from EM, and combining the two into a consistent representation

Statistical Medial Model dor Cardiac Segmentation and Morphometry

In biomedical image analysis, shape information can be utilized for many purposes. For example, irregular shape features can help identify diseases; shape features can help match different instances of anatomical structures for statistical comparison; and prior knowledge of the mean and possible variation of an anatomical structure\u27s shape can help segment a new example of this structure in noisy, low-contrast images. A good shape representation helps to improve the performance of the above techniques. The overall goal of the proposed research is to develop and evaluate methods for representing shapes of anatomical structures. The medial model is a shape representation method that models a 3D object by explicitly defining its skeleton (medial axis) and deriving the object\u27s boundary via inverse-skeletonization . This model represents shape compactly, and naturally expresses descriptive global shape features like thickening , bending , and elongation . However, its application in biomedical image analysis has been limited, and it has not yet been applied to the heart, which has a complex shape. In this thesis, I focus on developing efficient methods to construct the medial model, and apply it to solve biomedical image analysis problems. I propose a new 3D medial model which can be efficiently applied to complex shapes. The proposed medial model closely approximates the medial geometry along medial edge curves and medial branching curves by soft-penalty optimization and local correction. I further develop a scheme to perform model-based segmentation using a statistical medial model which incorporates prior shape and appearance information. The proposed medial models are applied to a series of image analysis tasks. The 2D medial model is applied to the corpus callosum which results in an improved alignment of the patterns of commissural connectivity compared to a volumetric registration method. The 3D medial model is used to describe the myocardium of the left and right ventricles, which provides detailed thickness maps characterizing different disease states. The model-based myocardium segmentation scheme is tested in a heterogeneous adult MRI dataset. Our segmentation experiments demonstrate that the statistical medial model can accurately segment the ventricular myocardium and provide useful parameters to characterize heart function

Ear Contour Detection and Modeling Using Statistical Shape Models

Ear detection is an actively growing area of research because of its applications in human head tracking and biometric recognition. In head tracking, it is used to augment face detectors and to perform pose estimation. In biometric systems, it is used both as an independent modality and in multi-modal biometric recognition. The ear shape is the preferred feature used to perform detection because of its unique structure in both 2D color images and 3D range images. Ear shape models have also been used in literature to perform ear detection, but at a cost of a loss in information about the exact ear structure. In this thesis, we seek to address these issues in existing methods by a combination of techniques including Viola Jones Haar Cascades, Active Shape Models (ASM) and Dijkstra\u27s shortest path algorithm to devise a shape model of the ear using geometric parameters and mark an accurate contour around the ear using only 2D color images. The Viola Jones Haar Cascades classifier is used to mark a rectangular region around the ear in a left side profile image. Then a set of key landmark points around the ear including the ear outer helix, the ear anti-helix and the ear center is extracted using the ASM. This set of landmarks is then fed into Dijkstra\u27s shortest path algorithm which traces out the strongest edge between adjacent landmarks, to extract the entire ear outer contour, while maintaining a high computational efficiency

Doctor of Philosophy

dissertationScene labeling is the problem of assigning an object label to each pixel of a given image. It is the primary step towards image understanding and unifies object recognition and image segmentation in a single framework. A perfect scene labeling framework detects and densely labels every region and every object that exists in an image. This task is of substantial importance in a wide range of applications in computer vision. Contextual information plays an important role in scene labeling frameworks. A contextual model utilizes the relationships among the objects in a scene to facilitate object detection and image segmentation. Using contextual information in an effective way is one of the main questions that should be answered in any scene labeling framework. In this dissertation, we develop two scene labeling frameworks that rely heavily on contextual information to improve the performance over state-of-the-art methods. The first model, called the multiclass multiscale contextual model (MCMS), uses contextual information from multiple objects and at different scales for learning discriminative models in a supervised setting. The MCMS model incorporates crossobject and interobject information into one probabilistic framework, and thus is able to capture geometrical relationships and dependencies among multiple objects in addition to local information from each single object present in an image. The second model, called the contextual hierarchical model (CHM), learns contextual information in a hierarchy for scene labeling. At each level of the hierarchy, a classifier is trained based on downsampled input images and outputs of previous levels. The CHM then incorporates the resulting multiresolution contextual information into a classifier to segment the input image at original resolution. This training strategy allows for optimization of a joint posterior probability at multiple resolutions through the hierarchy. We demonstrate the performance of CHM on different challenging tasks such as outdoor scene labeling and edge detection in natural images and membrane detection in electron microscopy images. We also introduce two novel classification methods. WNS-AdaBoost speeds up the training of AdaBoost by providing a compact representation of a training set. Disjunctive normal random forest (DNRF) is an ensemble method that is able to learn complex decision boundaries and achieves low generalization error by optimizing a single objective function for each weak classifier in the ensemble. Finally, a segmentation framework is introduced that exploits both shape information and regional statistics to segment irregularly shaped intracellular structures such as mitochondria in electron microscopy images

A Survey on Ear Biometrics

Recognizing people by their ear has recently received significant attention in the literature. Several reasons account for this trend: first, ear recognition does not suffer from some problems associated with other non contact biometrics, such as face recognition; second, it is the most promising candidate for combination with the face in the context of multi-pose face recognition; and third, the ear can be used for human recognition in surveillance videos where the face may be occluded completely or in part. Further, the ear appears to degrade little with age. Even though, current ear detection and recognition systems have reached a certain level of maturity, their success is limited to controlled indoor conditions. In addition to variation in illumination, other open research problems include hair occlusion; earprint forensics; ear symmetry; ear classification; and ear individuality. This paper provides a detailed survey of research conducted in ear detection and recognition. It provides an up-to-date review of the existing literature revealing the current state-of-art for not only those who are working in this area but also for those who might exploit this new approach. Furthermore, it offers insights into some unsolved ear recognition problems as well as ear databases available for researchers

Histopathological image analysis : a review

Over the past decade, dramatic increases in computational power and improvement in image analysis algorithms have allowed the development of powerful computer-assisted analytical approaches to radiological data. With the recent advent of whole slide digital scanners, tissue histopathology slides can now be digitized and stored in digital image form. Consequently, digitized tissue histopathology has now become amenable to the application of computerized image analysis and machine learning techniques. Analogous to the role of computer-assisted diagnosis (CAD) algorithms in medical imaging to complement the opinion of a radiologist, CAD algorithms have begun to be developed for disease detection, diagnosis, and prognosis prediction to complement the opinion of the pathologist. In this paper, we review the recent state of the art CAD technology for digitized histopathology. This paper also briefly describes the development and application of novel image analysis technology for a few specific histopathology related problems being pursued in the United States and Europe