Automatic segmentation of the left ventricle cavity and myocardium in MRI data

A novel approach for the automatic segmentation has been developed to extract the epi-cardium and endo-cardium boundaries of the left ventricle (lv) of the heart. The developed segmentation scheme takes multi-slice and multi-phase magnetic resonance (MR) images of the heart, transversing the short-axis length from the base to the apex. Each image is taken at one instance in the heart's phase. The images are segmented using a diffusion-based filter followed by an unsupervised clustering technique and the resulting labels are checked to locate the (lv) cavity. From cardiac anatomy, the closest pool of blood to the lv cavity is the right ventricle cavity. The wall between these two blood-pools (interventricular septum) is measured to give an approximate thickness for the myocardium. This value is used when a radial search is performed on a gradient image to find appropriate robust segments of the epi-cardium boundary. The robust edge segments are then joined using a normal spline curve. Experimental results are presented with very encouraging qualitative and quantitative results and a comparison is made against the state-of-the art level-sets method

Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Towards multiple 3D bone surface identification and reconstruction using few 2D X-ray images for intraoperative applications

This article discusses a possible method to use a small number, e.g. 5, of conventional 2D X-ray images to reconstruct multiple 3D bone surfaces intraoperatively. Each bone’s edge contours in X-ray images are automatically identified. Sparse 3D landmark points of each bone are automatically reconstructed by pairing the 2D X-ray images. The reconstructed landmark point distribution on a surface is approximately optimal covering main characteristics of the surface. A statistical shape model, dense point distribution model (DPDM), is then used to fit the reconstructed optimal landmarks vertices to reconstruct a full surface of each bone separately. The reconstructed surfaces can then be visualised and manipulated by surgeons or used by surgical robotic systems

Decomposition using Maximum Autocorrelation Factors

This article presents methods for the analysis and decomposition of multivariate datasets where a given ordering/structure of the observations or the variables exist. Examples of such data sets are remote sensing imagery where observations (pixels) each consisting of a reflectance spectrum are organised in a two-dimensional grid. Another example is biological shape analysis. Here each observation (e.g. human bone, cerebral ventricle) is represented by a number of landmarks the coordinates of which are the variables. Here we do not have an ordering of the observations (individuals). However, normally we have an ordering of landmarks (variables) along the contour of the objects. In this context a landmark is a point with anatomical or geometrical meaning across observations. A further example is reflectance spectra from samples, where the samples do not exhibit any order but the variables do. For the case with observation ordering the maximum autocorrelation factor (MAF) transform was proposed for multivariate imagery in [1]. this corresponds to a R-mode analyse of the data matrix. We propose to extend this concept to situations with variable ordering. This corresponds to a Q-mode analysis of the datamatrix. We denote this methods Q-MAF decomposition. It turns out that in many situations the new variables resulting from the MAF and the Q-MAF analyses can be interpreted as a frequency analysis. However, contrary to Fourier decomposition these new variables are located in frequency as well as location (space, time, wavelength etc).

Projecting Active Contours with Diminutive Sequence Optimality

Active contours are widely used in image segmentation. To cope with missing or misleading features in image frames taken in contexts such as spatial and surveillance, researchers have commence various ways to model the preceding of shapes and use the prior to constrict active contours. However, the shape prior is frequently learnt from a large set of annotated data, which is not constantly accessible in practice. In addition, it is often doubted that the existing shapes in the training set will be sufficient to model the new instance in the testing image. In this paper we propose to use the diminutive sequence of image frames to learn the missing contour of the input images. The central median minimization is a simple and effective way to impose the proposed constraint on existing active contour models. Moreover, we extend a fast algorithm to solve the projected model by using the hastened proximal method. The Experiments done using image frames acquired from surveillance, which demonstrated that the proposed method can consistently improve the performance of active contour models and increase the robustness against image defects such as missing boundaries

Aquatics reconstruction software: the design of a diagnostic tool based on computer vision algorithms

Computer vision methods can be applied to a variety of medical and surgical applications, and many techniques and algorithms are available that can be used to recover 3D shapes and information from images range and volume data. Complex practical applications, however, are rarely approachable with a single technique, and require detailed analysis on how they can be subdivided in subtasks that are computationally treatable and that, at the same time, allow for the appropriate level of user-interaction. In this paper we show an example of a complex application where, following criteria of efficiency, reliability and user friendliness, several computer vision techniques have been selected and customized to build a system able to support diagnosis and endovascular treatment of Abdominal Aortic Aneurysms. The system reconstructs the geometrical representation of four different structures related to the aorta (vessel lumen, thrombus, calcifications and skeleton) from CT angiography data. In this way it supports the three dimensional measurements required for a careful geometrical evaluation of the vessel, that is fundamental to decide if the treatment is necessary and to perform, in this case, its planning. The system has been realized within the European trial AQUATICS (IST-1999-20226 EUTIST-M WP 12), and it has been widely tested on clinical data

A PDE Method to Segment Image Linear Objects with Application to Lens Distortion Removal

In this paper, we propose a partial differential equation based method to segment image objects, which have a given parametric shape based on energy functional. The energy functional is composed of a term that detects object boundaries and a term that constrains the contour to find a shape compatible with the parametric shape. While the shape constraints guiding the PDE may be determined from object's shape statistical models, we demonstrate the proposed approach on the extraction of objects with explicit shape parameterization, such as linear image segments. Several experiments are reported on synthetic and real images to evaluate our approach. We also demonstrate the successful application of the proposed method to the problem of removing camera lens distortion, which can be significant in medium to wide-angle lenses