Three-Dimensional GPU-Accelerated Active Contours for Automated Localization of Cells in Large Images

Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. This becomes particularly challenging for extremely large images, since manual intervention and processing time can make segmentation intractable. In this paper, we present an efficient and highly parallel formulation for symmetric three-dimensional (3D) contour evolution that extends previous work on fast two-dimensional active contours. We provide a formulation for optimization on 3D images, as well as a strategy for accelerating computation on consumer graphics hardware. The proposed software takes advantage of Monte-Carlo sampling schemes in order to speed up convergence and reduce thread divergence. Experimental results show that this method provides superior performance for large 2D and 3D cell segmentation tasks when compared to existing methods on large 3D brain images

Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors

Segmentation of biomedical images is essential for studying and characterizing anatomical structures, detection and evaluation of pathological tissues. Segmentation has been further shown to enhance the reconstruction performance in many tomographic imaging modalities by accounting for heterogeneities of the excitation field and tissue properties in the imaged region. This is particularly relevant in optoacoustic tomography, where discontinuities in the optical and acoustic tissue properties, if not properly accounted for, may result in deterioration of the imaging performance. Efficient segmentation of optoacoustic images is often hampered by the relatively low intrinsic contrast of large anatomical structures, which is further impaired by the limited angular coverage of some commonly employed tomographic imaging configurations. Herein, we analyze the performance of active contour models for boundary segmentation in cross-sectional optoacoustic tomography. The segmented mask is employed to construct a two compartment model for the acoustic and optical parameters of the imaged tissues, which is subsequently used to improve accuracy of the image reconstruction routines. The performance of the suggested segmentation and modeling approach are showcased in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin

Super-resolution-based snake model—an unsupervised method for large-scale building extraction using airborne LiDAR Data and optical image

Automatic extraction of buildings in urban and residential scenes has become a subject of growing interest in the domain of photogrammetry and remote sensing, particularly since the mid-1990s. Active contour model, colloquially known as snake model, has been studied to extract buildings from aerial and satellite imagery. However, this task is still very challenging due to the complexity of building size, shape, and its surrounding environment. This complexity leads to a major obstacle for carrying out a reliable large-scale building extraction, since the involved prior information and assumptions on building such as shape, size, and color cannot be generalized over large areas. This paper presents an efficient snake model to overcome such a challenge, called Super-Resolution-based Snake Model (SRSM). The SRSM operates on high-resolution Light Detection and Ranging (LiDAR)-based elevation images—called z-images—generated by a super-resolution process applied to LiDAR data. The involved balloon force model is also improved to shrink or inflate adaptively, instead of inflating continuously. This method is applicable for a large scale such as city scale and even larger, while having a high level of automation and not requiring any prior knowledge nor training data from the urban scenes (hence unsupervised). It achieves high overall accuracy when tested on various datasets. For instance, the proposed SRSM yields an average area-based Quality of 86.57% and object-based Quality of 81.60% on the ISPRS Vaihingen benchmark datasets. Compared to other methods using this benchmark dataset, this level of accuracy is highly desirable even for a supervised method. Similarly desirable outcomes are obtained when carrying out the proposed SRSM on the whole City of Quebec (total area of 656 km2), yielding an area-based Quality of 62.37% and an object-based Quality of 63.21%

Accurate and reliable segmentation of the optic disc in digital fundus images

We describe a complete pipeline for the detection and accurate automatic segmentation of the optic disc in digital fundus images. This procedure provides separation of vascular information and accurate inpainting of vessel-removed images, symmetry-based optic disc localization, and fitting of incrementally complex contour models at increasing resolutions using information related to inpainted images and vessel masks. Validation experiments, performed on a large dataset of images of healthy and pathological eyes, annotated by experts and partially graded with a quality label, demonstrate the good performances of the proposed approach. The method is able to detect the optic disc and trace its contours better than the other systems presented in the literature and tested on the same data. The average error in the obtained contour masks is reasonably close to the interoperator errors and suitable for practical applications. The optic disc segmentation pipeline is currently integrated in a complete software suite for the semiautomatic quantification of retinal vessel properties from fundus camera images (VAMPIRE)

Traffic monitoring using image processing : a thesis presented in partial fulfillment of the requirements for the degree of Master of Engineering in Information and Telecommunications Engineering at Massey University, Palmerston North, New Zealand

Traffic monitoring involves the collection of data describing the characteristics of vehicles and their movements. Such data may be used for automatic tolls, congestion and incident detection, law enforcement, and road capacity planning etc. With the recent advances in Computer Vision technology, videos can be analysed automatically and relevant information can be extracted for particular applications. Automatic surveillance using video cameras with image processing technique is becoming a powerful and useful technology for traffic monitoring. In this research project, a video image processing system that has the potential to be developed for real-time application is developed for traffic monitoring including vehicle tracking, counting, and classification. A heuristic approach is applied in developing this system. The system is divided into several parts, and several different functional components have been built and tested using some traffic video sequences. Evaluations are carried out to show that this system is robust and can be developed towards real-time applications

A ribbon of twins for extracting vessel boundaries

This paper presents an efficient model for automatic detection and extraction of blood vessels in ocular fundus images. The model is formed using a combination of the concept of ribbon snakes and twin snakes. On each edge, the twin concept is introduced by using two snakes, one inside and one outside the boundary. The ribbon concept integrates the pair of twins on the two vessel edges into a single ribbon. The twins maintain the consistency of the vessel width, particularly on very blurred, thin and noisy vessels. The model exhibits excellent performance in extracting the boundaries of vessels, with improved robustness compared to alternative models in the presence of occlusion, poor contrast or noise. Results are presented which demonstrate the performance of the discussed edge extraction method, and show a significant improvement compared to classical snake formulations

DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images

Copyright @ Skounakis et al.This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. AVAILABILITY: THE PLATFORM, A MANUAL AND TUTORIAL VIDEOS ARE AVAILABLE AT: http://biomodeling.ics.forth.gr. It is free to use under the GNU General Public License