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

Segmentation of Football Video Broadcast

In this paper a novel segmentation system for football player detection in broadcasted video is presented. Proposed detection system is a complex solution incorporating a dominant color based segmentation technique of a football playfield, a 3D playfield modeling algorithm based on Hough transform and a dedicated algorithm for player tracking, player detection system based on the combination of Histogram of Oriented Gradients (HOG) descriptors with Principal Component Analysis (PCA) and linear Support Vector Machine (SVM) classification. For the shot classification the several classification technique SVM, artificial neural network and Linear Discriminant Analysis (LDA) are used. Evaluation of the system is carried out using HD (1280×720) resolution test material. Additionally, performance of the proposed system is tested with different lighting conditions (including non-uniform pith lightning and multiple player shadows) and various camera positions. Experimental results presented in this paper show that combination of these techniques seems to be a promising solution for locating and segmenting objects in a broadcasted video

Gait Recognition: Databases, Representations, and Applications

There has been considerable progress in automatic recognition of people by the way they walk since its inception almost 20 years ago: there is now a plethora of technique and data which continue to show that a person’s walking is indeed unique. Gait recognition is a behavioural biometric which is available even at a distance from a camera when other biometrics may be occluded, obscured or suffering from insufficient image resolution (e.g. a blurred face image or a face image occluded by mask). Since gait recognition does not require subject cooperation due to its non-invasive capturing process, it is expected to be applied for criminal investigation from CCTV footages in public and private spaces. This article introduces current progress, a research background, and basic approaches for gait recognition in the first three sections, and two important aspects of gait recognition, the gait databases and gait feature representations are described in the following sections.Publicly available gait databases are essential for benchmarking individual approaches, and such databases should contain a sufficient number of subjects as well as covariate factors to realize statistically reliable performance evaluation and also robust gait recognition. Gait recognition researchers have therefore built such useful gait databases which incorporate subject diversities and/or rich covariate factors.Gait feature representation is also an important aspect for effective and efficient gait recognition. We describe the two main approaches to representation: model-free (appearance-based) approaches and model-based approaches. In particular, silhouette-based model-free approaches predominate in recent studies and many have been proposed and are described in detail.Performance evaluation results of such recent gait feature representations on two of the publicly available gait databases are reported: USF Human ID with rich covariate factors such as views, surface, bag, shoes, time elapse; and OU-ISIR LP with more than 4,000 subjects. Since gait recognition is suitable for criminal investigation applications of the gait recognition to forensics are addressed with real criminal cases in the application section. Finally, several open problems of the gait recognition are discussed to show future research avenues of the gait recognition

Video enhancement : content classification and model selection

The purpose of video enhancement is to improve the subjective picture quality. The field of video enhancement includes a broad category of research topics, such as removing noise in the video, highlighting some specified features and improving the appearance or visibility of the video content. The common difficulty in this field is how to make images or videos more beautiful, or subjectively better. Traditional approaches involve lots of iterations between subjective assessment experiments and redesigns of algorithm improvements, which are very time consuming. Researchers have attempted to design a video quality metric to replace the subjective assessment, but so far it is not successful. As a way to avoid heuristics in the enhancement algorithm design, least mean square methods have received considerable attention. They can optimize filter coefficients automatically by minimizing the difference between processed videos and desired versions through a training. However, these methods are only optimal on average but not locally. To solve the problem, one can apply the least mean square optimization for individual categories that are classified by local image content. The most interesting example is Kondo’s concept of local content adaptivity for image interpolation, which we found could be generalized into an ideal framework for content adaptive video processing. We identify two parts in the concept, content classification and adaptive processing. By exploring new classifiers for the content classification and new models for the adaptive processing, we have generalized a framework for more enhancement applications. For the part of content classification, new classifiers have been proposed to classify different image degradations such as coding artifacts and focal blur. For the coding artifact, a novel classifier has been proposed based on the combination of local structure and contrast, which does not require coding block grid detection. For the focal blur, we have proposed a novel local blur estimation method based on edges, which does not require edge orientation detection and shows more robust blur estimation. With these classifiers, the proposed framework has been extended to coding artifact robust enhancement and blur dependant enhancement. With the content adaptivity to more image features, the number of content classes can increase significantly. We show that it is possible to reduce the number of classes without sacrificing much performance. For the part of model selection, we have introduced several nonlinear filters to the proposed framework. We have also proposed a new type of nonlinear filter, trained bilateral filter, which combines both advantages of the original bilateral filter and the least mean square optimization. With these nonlinear filters, the proposed framework show better performance than with linear filters. Furthermore, we have shown a proof-of-concept for a trained approach to obtain contrast enhancement by a supervised learning. The transfer curves are optimized based on the classification of global or local image content. It showed that it is possible to obtain the desired effect by learning from other computationally expensive enhancement algorithms or expert-tuned examples through the trained approach. Looking back, the thesis reveals a single versatile framework for video enhancement applications. It widens the application scope by including new content classifiers and new processing models and offers scalabilities with solutions to reduce the number of classes, which can greatly accelerate the algorithm design

Assessment of algorithms for mitosis detection in breast cancer histopathology images

The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis counting is laborious, subjective and may suffer from low inter-observer agreement. With the wider acceptance of whole slide images in pathology labs, automatic image analysis has been proposed as a potential solution for these issues. In this paper, the results from the Assessment of Mitosis Detection Algorithms 2013 (AMIDA13) challenge are described. The challenge was based on a data set consisting of 12 training and 11 testing subjects, with more than one thousand annotated mitotic figures by multiple observers. Short descriptions and results from the evaluation of eleven methods are presented. The top performing method has an error rate that is comparable to the inter-observer agreement among pathologists

Transient Study of the Wetting Films in Porous Media Using 3D X-Ray Computed Micro-Tomography: Effect of Imbibition Rate and Pore Geometry

Imbibition in porous media is governed by the complex interplay between viscous and capillary forces, pore structure and fluid properties. Understanding and predicting imbibition is important in many natural and engineered applications; it affects the efficiency of oil production operations, the moisture and contaminant transport in soil science, and the formation of defects in certain types of composite materials. Majority of the studies published on the transient imbibition behavior in a porous medium were conducted in the simplified 2D transparent micromodels or the 2D projection visualization (X-ray or visible light) of the 3D porous medium. However, the pore level transient imbibition studies have not been reported on real three dimensional porous medium. The main challenge arises from the slowness of the present 3D imaging techniques in comparison with the speed of the pore filling events. To overcome these difficulties, we have developed a novel experimental technique using UV-induced polymerization, which allows the fluid phase distributions to be frozen in place during transient imbibition. Pore-scale structure of the front can then be examined in the 3D microscopic details using the X-ray Computed micro-Tomography (XCT). We have also developed a suite of advanced image segmentation programs to segment the grayscale XCT data. Image-based physically representative pore network generation techniques were unitized to quantify the geometry and topology of pore, wetting and nonwetting phase structure. Using UV initiated polymerization technique and image-based quantitative analysis tools; we have studied the effects of capillary number, pore structure and surface roughness on the structure of the transient imbibition front