Automated analysis of nerve-cell images using active contour models

The number of nerve fibers (axons) in a nerve, the axon size, and shape can all be important neuroanatomical features in understanding different aspects of nerves in the brain. However, the number of axons in a nerve is typically in the order of tens of thousands and a study of a particular aspect of the nerve often involves many nerves. Potentially meaningful studies are often prohibited by the huge number involved when manual measurements have to be employed. A method that automates the analysis of axons from electron-micrographic images is presented. It begins with a rough identification of all the axon centers by use of an elliptical Hough transform procedure. Boundaries of each axons are then extracted based on active contour model, or snakes, approach where physical properties of the axons and the given image data are used in an optimization scheme to guide the snakes to converge to axon boundaries for accurate sheath measurement. However, false axon detection is still common due to poor image quality and the presence of other irrelevant cell features, thus a conflict resolution scheme is developed to eliminate false axons to further improve the performance of detection. The developed method has been tested on a number of nerve images and its results are presented.     

A Fully Global Approach to Image Segmentation via Coupled Curve Evolution Equations

In this paper, we develop a novel region-based approach to snakes designed to optimally separate the values of certain image statistics over a known number of region types. Multiple sets of contours deform according to a coupled set of curve evolution equations derived from a single global cost functional. The resulting active contour model, in contrast to many other edge and region based models, is fully global in that the evolution of each curve depends at all times upon every pixel in the image and is directly coupled to the evolution of every other curve regardless of their mutual proximity. As such evolving contours enjoy a very wide “field of view,” endowing the algorithm with a robustness to initial contour placement above and beyond the significant improvement exhibited by other region based snakes over earlier edge based snakes.     

Object detection with feature stability over scale space

This paper proposes a novel segmentation method based on the scale space techniques endowed with a feature stability approach. The novelty of the paper is the lifetime of the space-scale blobs measured not only by their presence and disappearance but by the stability of the features characterizing the objects of interest as well. Our numerical experiments show that the algorithm outperforms the conventional space scale algorithm applied to variable size and variable shape objects. The proposed algorithm can be used as a preprocessing step in object or pattern recognition applications to produce seeds for more accurate image segmentation methods such as the snakes or the level set techniques.     

Fusion of physically-based registration and deformation modelingfor nonrigid motion analysis

In our previous work, we used finite element models to determine nonrigid motion parameters and recover unknown local properties of objects given correspondence data recovered with snakes or other tracking models. In this paper, we present a novel multiscale approach to recovery of nonrigid motion from sequences of registered intensity and range images. The main idea of our approach is that a finite element (FEM) model incorporating material properties of the object can naturally handle both registration and deformation modeling using a single model-driving strategy. The method includes a multiscale iterative algorithm based on analysis of the undirected Hausdorff distance to recover correspondences. The method is evaluated with respect to speed and accuracy. Noise sensitivity issues are addressed. Advantages of the proposed approach are demonstrated using man-made elastic materials and human skin motion. Experiments with regular grid features are used for performance comparison with a conventional approach (separate snakes and FEM models). It is shown, however, that the new method does not require a sampling/correspondence template and can adapt the model to available object features. Usefulness of the method is presented not only in the context of tracking and motion analysis, but also for a burn scar detection application.     

Tracking leukocytes in vivo with shape and size constrained active contours

Inflammatory disease is initiated by leukocytes (white blood cells) rolling along the inner surface lining of small blood vessels called postcapillary venules. Studying the number and velocity of rolling leukocytes is essential to understanding and successfully treating inflammatory diseases. Potential inhibitors of leukocyte recruitment can be screened by leukocyte rolling assays and successful inhibitors validated by intravital microscopy. In this paper, we present an active contour or snake-based technique to automatically track the movement of the leukocytes. The novelty of the proposed method lies in the energy functional that constrains the shape and size of the active contour. This paper introduces a significant enhancement over existing gradient-based snakes in the form of a modified gradient vector flow. Using the gradient vector flow, we can track leukocytes rolling at high speeds that are not amenable to tracking with the existing edge-based techniques. We also propose a new energy-based implicit sampling method of the points on the active contour that replaces the computationally expensive explicit method. To enhance the performance of this shape and size constrained snake model, we have coupled it with Kalman filter so that during coasting (when the leukocytes are completely occluded or obscured), the tracker may infer the location of the center of the leukocyte. Finally, we have compared the performance of the proposed snake tracker with that of the correlation and centroid-based trackers. The proposed snake tracker results in superior performance measures, such as reduced error in locating the leukocyte under tracking and improvements in the percentage of frames successfully tracked. For screening and drug validation, the tracker shows promise as an automated data collection tool.     

Validation of an optical flow method for tag displacementestimation

We present a validation study of an optical-flow method for the rapid estimation of myocardial displacement in magnetic resonance tagged cardiac images. This registration and change visualization (RCV) software uses a hierarchical estimation technique to compute the flow field that describes the warping of an image of one cardiac phase into alignment with the next. This method overcomes the requirement of constant pixel intensity in standard optical-flow methods by preprocessing the input images to reduce any intensity bias which results from the reduction in stripe contrast throughout the cardiac cycle. To validate the method, SPAMM-tagged images were acquired of a silicon gel phantom with simulated rotational motion. The pixel displacement was estimated with the RCV method and the error in pixel tracking was <4% 1000 ms after application of the tags, and after 30 degrees of rotation. An additional study was performed using a SPAMM-tagged multiphase slice of a canine left ventricle. The true displacement was determined using a previously validated active contour model (snakes). The error between methods was 6.7% at end systole. The RCV method has the advantage of tracking all pixels in the image in a substantially shorter period than the snakes method.     

Nonparametric snakes.

Active contours, or so-called snakes, require some parameters to determine the form of the external force or to adjust the tradeoff between the internal forces and the external forces acting on the active contour. However, the optimal values of these parameters cannot be easily identified in a general sense. The usual way to find these required parameters is to run the algorithm several times for a different set of parameters, until a satisfactory performance is obtained. Our nonparametric formulation translates the problem of seeking these unknown parameters into the problem of seeking a good edge probability density estimate. Density estimation is a well-researched field, and our nonparametric formulation allows using well-known concepts of density estimation to get rid of the exhaustive parameter search. Indeed, with the use of kernel density estimation these parameters can be defined locally, whereas, in the original snake approach, all the shape parameters are defined globally. We tested the proposed method on synthetic and real images and obtained comparatively better results.     

A novel method for automatic face segmentation, facial feature extraction and tracking

The present paper describes a novel method for the segmentation of faces, extraction of facial features and tracking of the face contour and features over time. Robust segmentation of faces out of complex scenes is done based on color and shape information. Additionally, face candidates are verified by searching for facial features in the interior of the face. As interesting facial features we employ eyebrows, eyes, nostrils, mouth and chin. We consider incomplete feature constellations as well. If a face and its features are detected once reliably, we track the face contour and the features over time. Face contour tracking is done by using deformable models like snakes. Facial feature tracking is performed by block matching. The success of our approach was verified by evaluating 38 different color image sequences, containing features as beard, glasses and changing facial expressions.     

Snakes with an ellipse-reproducing property

We present a new class of continuously defined parametric snakes using a special kind of exponential splines as basis functions. We have enforced our bases to have the shortest possible support subject to some design constraints to maximize efficiency. While the resulting snakes are versatile enough to provide a good approximation of any closed curve in the plane, their most important feature is the fact that they admit ellipses within their span. Thus, they can perfectly generate circular and elliptical shapes. These features are appropriate to delineate cross sections of cylindrical-like conduits and to outline bloblike objects. We address the implementation details and illustrate the capabilities of our snake with synthetic and real data.     

B-spline snakes: a flexible tool for parametric contour detection

We present a novel formulation for B-spline snakes that can be used as a tool for fast and intuitive contour outlining. We start with a theoretical argument in favor of splines in the traditional formulation by showing that the optimal, curvature-constrained snake is a cubic spline, irrespective of the form of the external energy field. Unfortunately, such regularized snakes suffer from slow convergence speed because of a large number of control points, as well as from difficulties in determining the weight factors associated to the internal energies of the curve. We therefore propose an alternative formulation in which the intrinsic scale of the spline model is adjusted a priori; this leads to a reduction of the number of parameters to be optimized and eliminates the need for internal energies (i.e., the regularization term). In other words, we are now controlling the elasticity of the spline implicitly and rather intuitively by varying the spacing between the spline knots. The theory is embedded into a multiresolution formulation demonstrating improved stability in noisy image environments. Validation results are presented, comparing the traditional snake using internal energies and the proposed approach without internal energies, showing the similar performance of the latter. Several biomedical examples of applications are included to illustrate the versatility of the method.     

An integrated system for the segmentation of atherosclerotic carotid plaque.

In this paper, we propose and evaluate an integrated system for the segmentation of atherosclerotic plaque in ultrasound imaging of the carotid artery based on normalization, speckle reduction filtering, and four different snakes segmentation methods. These methods are the Williams and Shah, Balloon, Lai and Chin, and the gradient vector flow (GVF) snake. The performance of the four different plaque snakes segmentation methods was tested on 80 longitudinal ultrasound images of the carotid artery using receiver operating characteristic (ROC) analysis and the manual delineations of an expert. All four methods were very satisfactory and similar in all measures evaluated, with no significant differences between them; however, the Lai and Chin snakes segmentation method gave slightly better results. Concluding, it is proposed that the integrated system investigated in this study could be used successfully for the automated segmentation of the carotid plaque.     

Coupled B-snake grids and constrained thin-plate splines foranalysis of 2-D tissue deformations from tagged MRI

Magnetic resonance imaging (MRI) is unique in its ability to noninvasively and selectively alter tissue magnetization and create tagged patterns within a deforming body such as the heart muscle. The resulting patterns define a time-varying curvilinear coordinate system on the tissue, which the authors track with coupled B-snake grids. B-spline bases provide local control of shape, compact representation, and parametric continuity. Efficient spline warps are proposed which warp an area in the plane such that two embedded snake grids obtained from two tagged frames are brought into registration, interpolating a dense displacement vector field. The reconstructed vector field adheres to the known displacement information at the intersections, forces corresponding snakes to be warped into one another, and for all other points in the plane, where no information is available, a C¹ continuous vector field is interpolated. The implementation proposed in this paper improves on the authors' previous variational-based implementation and generalizes warp methods to include biologically relevant contiguous open curves, in addition to standard landmark points. The methods are validated with a cardiac motion simulator, in addition to in-vivo tagging data sets     

Large deflection dynamics and control for planar continuum robots

This paper focuses on a class of robot manipulators termed "continuum" robots - robots that exhibit behavior similar to tentacles, trunks, and snakes. In previous work, we studied details of the mechanical design, kinematics, path-planning and small-deflection dynamics for continuum robots such as the Clemson "tentacle manipulator". In this paper, we discuss the dynamics of a planar continuum backbone section, incorporating a large-deflection dynamic model. Based on these dynamics, we formulate a vibration-damping setpoint controller, and include experimental results to illustrate the efficacy of the proposed controller.     

Snakuscules.

A snakuscule (a minuscule snake) is the simplest active contour that we were able to design while keeping the quintessence of traditional snakes: an energy term governed by the data, and a regularization term. Our construction is an area-based snake, as opposed to curve-based snakes. It is parameterized by just two points, thus further easing requirements on the optimizer. Despite their ultimate simplicity, snakuscules retain enough versatility to be employed for solving various problems such as cell counting and segmentation of approximately circular features. In this paper, we detail the design process of a snakuscule and illustrate its usefulness through practical examples. We claim that our didactic intentions are well served by the simplicity of snakuscules.     

Automatic Quantification of Joint Space Narrowing and Erosions in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic disease that affects and potentially destroys the joints of the appendicular skeleton. The precise and reproducible quantification of the progression of joint space narrowing and the erosive bone destructions caused by RA is crucial during treatment and in imaging biomarkers in clinical trials. Current manual scoring methods exhibit high interreader variability, even after intensive training, and thus, impede the efficient monitoring of the disease. We propose a fully automatic quantitative assessment of the radiographic changes that result from RA, to increase the accuracy, reproducibility, and speed of image interpretation. Initial joint location estimates are obtained by local linear mappings based on texture features. Bone contours are delineated by active shape models comprised of statistical models of bone shape and local texture. These models are refined by snakes which increase the accuracy and allow for a fitting of pathological deviations from the training population. The method then measures joint space widths and detects erosions on the bone contour. Joint space widths are measured with a coefficient of variation of 2%–7% for repeated measurements and erosion detection exhibits an area under the receiver operating characteristic (ROC) curve of 0.89. Model landmarks serve as a reference system along the contour. These landmarks enable the definition of joint regions and more specific follow-up monitoring. The automatic quantification allows for a remote analysis, relevant for multicenter clinical trials, and reduces the workload of clinical experts since parts of the process can be managed by nonexpert personnel.      

Kinematic and dynamic description of non-standard snake-like locomotion systems

The paper deals with terrestrial locomotion systems. Worms and snakes are living paragons for the development of biological inspired crawling robots. We set up certain models of worm- and snake-like locomotion systems and present purely analytical investigations in this paper. We try to follow an analytical framework, i.e., analyzing kinematics at first. Later on, we switch to dynamics and control of these models, to get hints for a technical development. The systems are modeled as chains of mass points. The mass points are interconnected via massless links with time-varying link-length. In contrast to the literature, the snake systems exhibit passive joints, but active links and rotatable skids. The combination of shape variation (via active links) together with the ground contact (via ideal spikes guaranteeing a one-sided velocity restriction) results in a global movement of the systems — undulatory locomotion. In dynamics, these link functions should be adjusted via, e.g., a force actuator between each mass point. Because it is impossible to determine a-priori these force outputs generating a desired gait, we apply an adaptive controller which adjusts these force outputs on-line on its own and λ-tracks a certain gait to achieve a movement of the whole system.     

Probabilistic contour extraction based on shape prior model

Various methods have been proposed for contour ex-traction.One approachis to group edge points into con-tinuous contours fromthe seed points[1].Froma proba-bilistic point of view,contours can beregardedas config-urations of a stochastic process driven by both a dynam-ics and a statistical data model ,so that the groupingturns out to be esti mating the states of the stochasticprocess .P啨rezet al .achieved the esti mation by using aparticle filtering approach,named Jet Stream[1].Themethod exhi…     

Flexible skew-symmetric shape model for shape representation, classification, and sampling.

Skewness of shape data often arises in applications (e.g., medical image analysis) and is usually overlooked in statistical shape models. In such cases, a Gaussian assumption is unrealistic and a formulation of a general shape model which accounts for skewness is in order. In this paper, we present a novel statistical method for shape modeling, which we refer to as the flexible skew-symmetric shape model (FSSM). The model is sufficiently flexible to accommodate a departure from Gaussianity of the data and is fairly general to learn a "mean shape" (template), with a potential for classification and random generation of new realizations of a given shape. Robustness to skewness results from deriving the FSSM from an extended class of flexible skew-symmetric distributions. In addition, we demonstrate that the model allows us to extract principal curves in a point cloud. The idea is to view a shape as a realization of a spatial random process and to subsequently learn a shape distribution which captures the inherent variability of realizations, provided they remain, with high probability, within a certain neighborhood range around a mean. Specifically, given shape realizations, FSSM is formulated as a joint bimodal distribution of angle and distance from the centroid of an aggregate of random points. Mean shape is recovered from the modes of the distribution, while the maximum likelihood criterion is employed for classification.     

Application of active contours for photochromic tracer flowextraction

This paper addresses the implementation of image processing and computer vision techniques to automate tracer flow extraction in images obtained by the photochromic dye technique. This task is important in modeled arterial blood flow studies. Currently, it is performed via manual application of B-spline curve fitting. However, this is a tedious and error-prone procedure and its results are nonreproducible. In the proposed approach, active contours, snakes, are employed in a new curve-fitting method for tracer flow extraction in photochromic images. An algorithm implementing snakes is introduced to automate extraction. Utilizing correlation matching, the algorithm quickly locates and localizes all flow traces in the images. The feasibility of the method for tracer flow extraction is demonstrated. Moreover, results regarding the automation algorithm are presented showing its accuracy and effectiveness. The proposed approach for tracer flow extraction has potential for real-system application     

基于形状及空间关系的场景相似性检索

为解决空间数据检索效率低、准确性差的问题,本文提出由空间对象形状描述模型、空间关系描述模型、场景相似性自适应计算模型构成的场景相似性检索方法.空间对象形状描述模型精准检索满足样例对象形状约束的数据库对象,提高空间对象形状的识别精度.空间关系描述模型检索满足样例场景关系约束的数据库场景,提高空间关系的描述精度.场景相似性自适应计算模型对满足形状及关系约束的完全匹配、局部匹配场景进行打分、排序,增加检索结果相似性打分的合理性.模拟场景、真实场景的实验表明本场景相似性检索方法具有良好的检索性能.