A UNIFIED ENERGY APPROACH FOR B-SPLINE SNAKE IN MEDICAL IMAGE SEGMENTATION

 The parametric snake is one of the preferred approaches in feature extraction from images because of their simplicity and efficiency. However the method has also limitations. In this paper an explicit snake that represented using BSpline applied for image segmentation is considered. In this paper, we identify some of these problems and propose efficient solutions to get around them. The proposed method is inspired by classical snake from Kass with some adaption for parametric curve. The paper also proposes new definitions of energy terms in the model to bring the snake performance more robust and efficient for image segmentation. This energy term unify the edge based and region based energy derived from the image data. The main objective of developed work is to develop an automatic method to segment the anatomical organs from medical images which is very hard and tedious to be performed manually. After this segmentation, the anatomical object can be further measured and analyzed to diagnose the anomaly in that organ. The results have shown that the proposed method has been proven qualitatively successful in segmenting different types of medical images.

Combining spatial support information and shape-based method for tomographic imaging inside a microwave cylindrical scanner

International audienceA nonlinear inverse scattering problem is solved to retrieve the permittivity maps inside a microwave cylindrical scanner of circular cross-section. In this article, we show how we can improve this minimization scheme by taking advantage of several a priori pieces of information. In particular, a global representation based on a Zernike basis expansion is introduced in order to restrain the class of solutions to functions which have circular spatial support, as is the case with the encountered geometrical configuration. The level-set function formalism is also exploited as the targets are known to be homogeneous by parts. We will show how we can combine the spatial support information and the binary nature of the scatterer, with limited changes of the inversion algorithm. Both synthetic and experimental results will be presented in order to highlight the importance of combining all the pieces of available information

Non-Euclidean Image-Adaptive Radial Basis Functions for 3D Interactive Segmentation

© 2009 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.DOI: 10.1109/ICCV.2009.5459245In the context of variational image segmentation, we propose a new finite-dimensional implicit surface representation. The key idea is to span a subset of implicit functions with linear combinations of spatially-localized kernels that follow image features. This is achieved by replacing the Euclidean distance in conventional Radial Basis Functions with non-Euclidean, image-dependent distances. For the minimization of an objective region-based criterion, this representation yields more accurate results with fewer control points than its Euclidean counterpart. If the user positions these control points, the non-Euclidean distance enables to further specify our localized kernels for a target object in the image. Moreover, an intuitive control of the result of the segmentation is obtained by casting inside/outside labels as linear inequality constraints. Finally, we discuss several algorithmic aspects needed for a responsive interactive workflow. We have applied this framework to 3D medical imaging and built a real-time prototype with which the segmentation of whole organs is only a few clicks away

Variational B-spline level-set method for fast image segmentation

International audienc

Variational B-Spline Level-Set Method for Fast Image Segmentation

In the field of image segmentation, most of level-set-based active contour approaches are based on a discrete representation of the associated implicit function. We present in this paper a different formulation where the level-set is modelled as a continuous parametric function expressed on a B-spline basis. Starting from the Mumford-Shah energy functional, we show that this formulation allows computing the solution as a restriction of the variational problem on the space spanned by the B-splines. As a consequence, the minimization of the functional is directly obtained in terms of the B-splines parameters. We also show that each step of this minimization may be expressed through a convolution operation. Because the B-spline functions are separable, this convolution may in turn be performed as a sequence of simple 1D convolutions, which yields a very efficient algorithm. The behaviour of this approach is illustrated on biomedical images from various fields

Interactive Segmentation of 3D Medical Images with Implicit Surfaces

To cope with a variety of clinical applications, research in medical image processing has led to a large spectrum of segmentation techniques that extract anatomical structures from volumetric data acquired with 3D imaging modalities. Despite continuing advances in mathematical models for automatic segmentation, many medical practitioners still rely on 2D manual delineation, due to the lack of intuitive semi-automatic tools in 3D. In this thesis, we propose a methodology and associated numerical schemes enabling the development of 3D image segmentation tools that are reliable, fast and interactive. These properties are key factors for clinical acceptance. Our approach derives from the framework of variational methods: segmentation is obtained by solving an optimization problem that translates the expected properties of target objects in mathematical terms. Such variational methods involve three essential components that constitute our main research axes: an objective criterion, a shape representation and an optional set of constraints. As objective criterion, we propose a unified formulation that extends existing homogeneity measures in order to model the spatial variations of statistical properties that are frequently encountered in medical images, without compromising efficiency. Within this formulation, we explore several shape representations based on implicit surfaces with the objective to cover a broad range of typical anatomical structures. Firstly, to model tubular shapes in vascular imaging, we introduce convolution surfaces in the variational context of image segmentation. Secondly, compact shapes such as lesions are described with a new representation that generalizes Radial Basis Functions with non-Euclidean distances, which enables the design of basis functions that naturally align with salient image features. Finally, we estimate geometric non-rigid deformations of prior templates to recover structures that have a predictable shape such as whole organs. Interactivity is ensured by restricting admissible solutions with additional constraints. Translating user input into constraints on the sign of the implicit representation at prescribed points in the image leads us to consider inequality-constrained optimization

Image analysis and statistical modeling for applications in cytometry and bioprocess control

Today, signal processing has a central role in many of the advancements in systems biology. Modern signal processing is required to provide efficient computational solutions to unravel complex problems that are either arduous or impossible to obtain using conventional approaches. For example, imaging-based high-throughput experiments enable cells to be examined at even subcellular level yielding huge amount of image data. Cytometry is an integral part of such experiments and involves measurement of different cell parameters which requires extraction of quantitative experimental values from cell microscopy images. In order to do that for such large number of images, fast and accurate automated image analysis methods are required. In another example, modeling of bioprocesses and their scale-up is a challenging task where different scales have different parameters and often there are more variables than the available number of observations thus requiring special methodology. In many biomedical cell microscopy studies, it is necessary to analyze the images at single cell or even subcellular level since owing to the heterogeneity of cell populations the population-averaged measurements are often inconclusive. Moreover, the emergence of imaging-based high-content screening experiments, especially for drug design, has put single cell analysis at the forefront since it is required to study the dynamics of single-cell gene expressions for tracking and quantification of cell phenotypic variations. The ability to perform single cell analysis depends on the accuracy of image segmentation in detecting individual cells from images. However, clumping of cells at both nuclei and cytoplasm level hinders accurate cell image segmentation. Part of this thesis work concentrates on developing accurate automated methods for segmentation of bright field as well as multichannel fluorescence microscopy images of cells with an emphasis on clump splitting so that cells are separated from each other as well as from background. The complexity in bioprocess development and control crave for the usage of computational modeling and data analysis approaches for process optimization and scale-up. This is also asserted by the fact that obtaining a priori knowledge needed for the development of traditional scale-up criteria may at times be difficult. Moreover, employment of efficient process modeling may provide the added advantage of automatic identification of influential control parameters. Determination of the values of the identified parameters and the ability to predict them at different scales help in process control and in achieving their scale-up. Bioprocess modeling and control can also benefit from single cell analysis where the latter could add a new dimension to the former once imaging-based in-line sensors allow for monitoring of key variables governing the processes. In this thesis we exploited signal processing techniques for statistical modeling of bioprocess and its scale-up as well as for development of fully automated methods for biomedical cell microscopy image segmentation beginning from image pre-processing and initial segmentation to clump splitting and image post-processing with the goal to facilitate the high-throughput analysis. In order to highlight the contribution of this work, we present three application case studies where we applied the developed methods to solve the problems of cell image segmentation and bioprocess modeling and scale-up