Automatic matching of homologous histological sections

The role of neuroanatomical atlases is undergoing a significant redefinition as digital atlases become available. These have the potential to serve as more than passive guides and to hold the role of directing segmentation and multimodal fusion of experimental data. Key elements needed to support these new tasks are registration algorithms. For images derived from histological procedures, the need is for techniques to map the two-dimensional (2-D) images of the sectional material into the reference atlas which may be a full three-dimensional (3-D) data set or one consisting of a series of 2-D images. A variety of 2-D-2-D registration methods are available to align experimental images with the atlas once the corresponding plane of section through the atlas has been identified. Methods to automate the identification of the homologous plane, however, have not been previously reported. Here, the authors use the external section contour to drive the identification and registration procedure. For this purpose, the authors model the contours by B-splines because of their attractive properties the most important of which are: (1) smoothness and continuity; (2) local controllability which implies that local changes in shape are confined to the B-spline parameters local to that change; (3) shape invariance under affine transformation, which means that the affine transformed curve is still a B-spline whose control points are related to the object control points through the transformation. The authors present a fast algorithm for estimating the control points of the B-spline which is robust to nonuniform sampling, noise, and local deformations. Curve matching is achieved by using a similarity measure that depends directly on the parameters of the B-spline. Performance tests are reported using histological material from rat brains     

3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake.

We introduce a three-dimensional (3-D) parametric active contour algorithm for the shape estimation of DNA molecules from stereo cryo-electron micrographs. We estimate the shape by matching the projections of a 3-D global shape model with the micrographs; we choose the global model as a 3-D filament with a B-spline skeleton and a specified radial profile. The active contour algorithm iteratively updates the B-spline coefficients, which requires us to evaluate the projections and match them with the micrographs at every iteration. Since the evaluation of the projections of the global model is computationally expensive, we propose a fast algorithm based on locally approximating it by elongated blob-like templates. We introduce the concept of projection-steerability and derive a projection-steerable elongated template. Since the two-dimensional projections of such a blob at any 3-D orientation can be expressed as a linear combination of a few basis functions, matching the projections of such a 3-D template involves evaluating a weighted sum of inner products between the basis functions and the micrographs. The weights are simple functions of the 3-D orientation and the inner-products are evaluated efficiently by separable filtering. We choose an internal energy term that penalizes the average curvature magnitude. Since the exact length of the DNA molecule is known a priori, we introduce a constraint energy term that forces the curve to have this specified length. The sum of these energies along with the image energy derived from the matching process is minimized using the conjugate gradients algorithm. We validate the algorithm using real, as well as simulated, data and show that it performs well.     

Automatic construction of multiple-object three-dimensional statistical shape models: application to cardiac modeling

A novel method is introduced for the generation of landmarks for three-dimensional (3-D) shapes and the construction of the corresponding 3-D statistical shape models. Automatic landmarking of a set of manual segmentations from a class of shapes is achieved by 1) construction of an atlas of the class, 2) automatic extraction of the landmarks from the atlas, and 3) subsequent propagation of these landmarks to each example shape via a volumetric nonrigid registration technique using multiresolution B-spline deformations. This approach presents some advantages over previously published methods: it can treat multiple-part structures and requires less restrictive assumptions on the structure's topology. In this paper, we address the problem of building a 3-D statistical shape model of the left and right ventricle of the heart from 3-D magnetic resonance images. The average accuracy in landmark propagation is shown to be below 2.2 mm. This application demonstrates the robustness and accuracy of the method in the presence of large shape variability and multiple objects.     

Spatial shape error concealment for object-based image and video coding

In this paper, an original spatial shape error-concealment technique, to be used in the context of object-based image and video coding schemes, is proposed. In this technique, it is assumed that the shape of the corrupted object at hand is in the form of a binary alpha plane, in which some of the shape data is missing due to channel errors. From this alpha plane, a contour corresponding to the border of the object can be extracted. However, due to errors, some parts of the contour will be missing and, therefore, the contour will be broken. The proposed technique relies on the interpolation of the missing contours with Bézier curves, which is done based on the available surrounding contours. After all the missing parts of the contour have been interpolated, the concealed alpha plane can be easily reconstructed from the fully recovered contour and used instead of the erroneous one improving the final subjective impact.     

基于变形模板技术的目标轮廓跟踪算法

为了适应目标旋转、尺度、场景光照等变化,利用B样条曲线表达目标轮廓,结合变形模板技术对运动目标的轮廓进行跟踪.在跟踪过程中,沿着模板曲线的法线方向检测目标轮廓,提高了检测效率.根据同一曲线上相邻点间的相关性,对检测所得的轮廓点集的坐标序列进行中值滤波,有效降低噪声干扰.将检测到的轮廓点集在形状空间匹配,使目标轮廓的形变限制在一定范围之内,有效抑制噪声和背景边缘特征的干扰.仿真试验表明,该算法能够有效得到目标轮廓,且具有较好的实时性.     

An integrated region-, boundary-, shape-based active contour for multiple object overlap resolution in histological imagery

Active contours and active shape models (ASM) have been widely employed in image segmentation. A major limitation of active contours, however, is in their 1) inability to resolve boundaries of intersecting objects and to 2) handle occlusion. Multiple overlapping objects are typically segmented out as a single object. On the other hand, ASMs are limited by point correspondence issues since object landmarks need to be identified across multiple objects for initial object alignment. ASMs are also are constrained in that they can usually only segment a single object in an image. In this paper, we present a novel synergistic boundary and region-based active contour model that incorporates shape priors in a level set formulation with automated initialization based on watershed. We demonstrate an application of these synergistic active contour models using multiple level sets to segment nuclear and glandular structures on digitized histopathology images of breast and prostate biopsy specimens. Unlike previous related approaches, our model is able to resolve object overlap and separate occluded boundaries of multiple objects simultaneously. The energy functional of the active contour is comprised of three terms. The first term is the prior shape term, modeled on the object of interest, thereby constraining the deformation achievable by the active contour. The second term, a boundary-based term detects object boundaries from image gradients. The third term drives the shape prior and the contour towards the object boundary based on region statistics. The results of qualitative and quantitative evaluation on 100 prostate and 14 breast cancer histology images for the task of detecting and segmenting nuclei and lymphocytes reveals that the model easily outperforms two state of the art segmentation schemes (geodesic active contour and Rousson shape-based model) and on average is able to resolve up to 91% of overlapping/occluded structures in the images.     

Segmentation and tracking in echocardiographic sequences: activecontours guided by optical flow estimates

This paper presents a method for segmentation and tracking of cardiac structures in ultrasound image sequences. The developed algorithm is based on the active contour framework. This approach requires initial placement of the contour close to the desired position in the image, usually an object outline. Best contour shape and position are then calculated, assuming that at this configuration a global energy function, associated with a contour, attains its minimum. Active contours can be used for tracking by selecting a solution from a previous frame as an initial position in a present frame. Such an approach, however, fails for large displacements of the object of interest. This paper presents a technique that incorporates the information on pixel velocities (optical flow) into the estimate of initial contour to enable tracking of fast-moving objects. The algorithm was tested on several ultrasound image sequences, each covering one complete cardiac cycle. The contour successfully tracked boundaries of mitral valve leaflets, aortic root and endocardial borders of the left ventricle. The algorithm-generated outlines were compared against manual tracings by expert physicians. The automated method resulted in contours that were within the boundaries of intraobserver variability     

Plotting satellite antenna radiation patterns

Approaches for visualizing satellite antenna radiation patterns are presented. Gain-level contours drawn over a geographical map give the clearest quantitative information. A three-dimensional surface plot displays the qualitative shape of the radiation pattern more naturally. Giving a 3-D effect to level contours allows quantitative and qualitative information to be combined, but it can only be used to complement the other plots. These methods of visualization all use plotters to produce their images. The hidden-point algorithm for 3-D contour plots is described     

B-spline explicit active surfaces: an efficient framework for real-time 3-D region-based segmentation

A new formulation of active contours based on explicit functions has been recently suggested. This novel framework allows real-time 3-D segmentation since it reduces the dimensionality of the segmentation problem. In this paper, we propose a B-spline formulation of this approach, which further improves the computational efficiency of the algorithm. We also show that this framework allows evolving the active contour using local region-based terms, thereby overcoming the limitations of the original method while preserving computational speed. The feasibility of real-time 3-D segmentation is demonstrated using simulated and medical data such as liver computer tomography and cardiac ultrasound images.     

A discrete dynamic contour model

A discrete dynamic model for defining contours in 2-D images is developed. The structure of this model is a set of connected vertices. With a minimum of interaction, an initial contour model can be defined, which is then automatically modified by an energy minimizing process. The internal energy of the model depends on local contour curvature, while the external energy is derived from image features. Solutions are presented to avoid undesirable deformation effects, like shrinking and vertex clustering, which are common in existing active contour models. The deformation process stops when a local minimum of the energy function is reached. The final shape of the model is a reproducible approximation of the desired contour. Results of applying the method to computer-generated images, as well as clinical images, are presented.     

Matching shapes with self-intersections:application to leaf classification

We address the problem of two-dimensional (2-D) shape representation and matching in presence of self-intersection for large image databases. This may occur when part of an object is hidden behind another part and results in a darker section in the gray level image of the object. The boundary contour of the object must include the boundary of this part which is entirely inside the outline of the object. The Curvature Scale Space (CSS) image of a shape is a multiscale organization of its inflection points as it is smoothed. The CSS-based shape representation method has been selected for MPEG-7 standardization. We study the effects of contour self-intersection on the Curvature Scale Space image. When there is no self-intersection, the CSS image contains several arch shape contours, each related to a concavity or a convexity of the shape. Self intersections create contours with minima as well as maxima in the CSS image. An efficient shape representation method has been introduced in this paper which describes a shape using the maxima as well as the minima of its CSS contours. This is a natural generalization of the conventional method which only includes the maxima of the CSS image contours. The conventional matching algorithm has also been modified to accommodate the new information about the minima. The method has been successfully used in a real world application to find, for an unknown leaf, similar classes from a database of classified leaf images representing different varieties of chrysanthemum. For many classes of leaves, self-intersection is inevitable during the scanning of the image. Therefore the original contributions of this paper is the generalization of the Curvature Scale Space representation to the class of 2-D contours with self-intersection, and its application to the classification of Chrysanthemum leaves.     

A neural network-based stochastic active contour model (NNS-SNAKE)for contour finding of distinct features

Contour finding of distinct features in 2-D/3-D images is essential for image analysis and computer vision. To overcome the potential problems associated with existing contour finding algorithms, we propose a framework, called the neural network-based stochastic active contour model (NNS-SNAKE), which integrates a neural network classifier for systematic knowledge building, an active contour model (also known as the "Snake") for automated contour finding using energy functions, and the Gibbs sampler to help the snake to find the most probable contour using a stochastic decision mechanism. Successful application of the NNS-SNAKE to extraction of several types of contours on magnetic resonance (MR) images is presented.     

Personalized tooth shape estimation from radiograph and cast

Three-dimensional geometric information of teeth is usually needed in pre- and postoperative diagnoses of orthodontic dentistry. The computerized tomography can provide comprehensive 3-D teeth geometries. However, there is still a discussion on computed tomography (CT) as a routine in orthodontic dentistry due to radiation dose. Moreover, the CT is useless when a dentist needs to extract 3-D structures from old archive files with only radiographs and casts, where patient's teeth changed ever since. In this paper, we propose a reconstruction framework for patient-specific teeth based on an integration of 2-D radiographs and digitized casts. The reconstruction is under a template-fitting framework. The shape and orientation of teeth templates are tuned in accordance with patient's radiographs. Specially, the tooth root morphology is controlled by 2-D contours in radiographs. With ray tracing and a contour plane assumption, 2-D root contours in radiographs are projected back to 3-D space, and guide tooth root deformations. Moreover, the template's crown is deformed nonrigidly to fit digitized casts that bear patient's crown details. The system allows 3-D tooth reconstruction with patient-specific geometric details from just casts and 2-D radiographs.     

Guiding ziplock snakes with a priori information

In this paper, we present a method to combine a grammatical model that encodes a priori shape information with the ziplock snakes presented by Neuenschwander et al. (1997). A competing mechanism is adopted to take advantage of the shape models without inducing excessive computation. The resulting model-based ziplock snakes have many advantages over the original model: they can accurately locate contour features, produce more refined results, and deal with multiple contours, missing image cues, and noise.     

A contour-based approach to multisensor image registration

Image registration is concerned with the establishment of correspondence between images of the same scene. One challenging problem in this area is the registration of multispectral/multisensor images. In general, such images have different gray level characteristics, and simple techniques such as those based on area correlations cannot be applied directly. On the other hand, contours representing region boundaries are preserved in most cases. The authors present two contour-based methods which use region boundaries and other strong edges as matching primitives. The first contour matching algorithm is based on the chain-code correlation and other shape similarity criteria such as invariant moments. Closed contours and the salient segments along the open contours are matched separately. This method works well for image pairs in which the contour information is well preserved, such as the optical images from Landsat and Spot satellites. For the registration of the optical images with synthetic aperture radar (SAR) images, the authors propose an elastic contour matching scheme based on the active contour model. Using the contours from the optical image as the initial condition, accurate contour locations in the SAR image are obtained by applying the active contour model. Both contour matching methods are automatic and computationally quite efficient. Experimental results with various kinds of image data have verified the robustness of the algorithms, which have outperformed manual registration in terms of root mean square error at the control points.     

3-D model localization using high-resolution reconstruction ofmonocular image sequences

In this paper, we present a complete system for the recognition and localization of a three-dimensional (3-D) model from a sequence of monocular images with known motion. The originality of this system is twofold. First, it uses a purely 3-D approach, starting from the 3-D reconstruction of the scene and ending by the 3-D matching of the model. Second, unlike most monocular systems, we do not use token tracking to match successive images. Rather, subpixel contour matching is used to recover more precisely complete 3-D contours. In contrast with the token tracking approaches, which yield a representation of the 3-D scene based on disconnected segments or points, this approach provides us with a denser and higher level representation of the scene. The reconstructed contours are fused along successive images using a simple result derived from the Kalman filter theory. The fusion process increases the localization precision and the robustness of the 3-D reconstruction. Finally, corners are extracted from the 3-D contours. They are used to generate hypotheses of the model position, using a hypothesize-and-verify algorithm that is described in detail. This algorithm yields a robust recognition and precise localization of the model in the scene. Results are presented on infrared image sequences with different resolutions, demonstrating the precision of the localization as well as the robustness and the low computational complexity of the algorithms.     

Three-dimensional myocardial strain reconstruction from tagged MRI using a cylindrical B-spline model

In this paper, we present a new method for reconstructing three-dimensional (3-D) left ventricular myocardial strain from tagged magnetic resonance (MR) image data with a 3-D B-spline deformation model. The B-spline model is based on a cylindrical coordinate system that more closely fits the morphology of the myocardium than previously proposed Cartesian B-spline models and does not require explicit regularization. Our reconstruction method first fits a spatial coordinate B-spline displacement field to the tag line data. This displacement field maps each tag line point in the deformed myocardium back to its reference position (end-diastole). The spatial coordinate displacement field is then converted to material coordinates with another B-spline fit. Finally, strain is computed by analytically differentiating the material coordinate B-spline displacement field with respect to space. We tested our method with strains reconstructed from an analytically defined mathematical left ventricular deformation model and ten human imaging studies. Our results demonstrate that a quadratic cylindrical B-spline with a fixed number of control points can accurately fit a physiologically realistic range of deformations. The average 3-D reconstruction computation time is 20 seconds per time frame on a 450 MHz Sun Ultra80 workstation.     

Medical image segmentation using minimal path deformable models with implicit shape priors.

This paper presents a new method for segmentation of medical images by extracting organ contours, using minimal path deformable models incorporated with statistical shape priors. In our approach, boundaries of structures are considered as minimal paths, i.e., paths associated with the minimal energy, on weighted graphs. Starting from the theory of minimal path deformable models, an intelligent "worm" algorithm is proposed for segmentation, which is used to evaluate the paths and finally find the minimal path. Prior shape knowledge is incorporated into the segmentation process to achieve more robust segmentation. The shape priors are implicitly represented and the estimated shapes of the structures can be conveniently obtained. The worm evolves under the joint influence of the image features, its internal energy, and the shape priors. The contour of the structure is then extracted as the worm trail. The proposed segmentation framework overcomes the short-comings of existing deformable models and has been successfully applied to segmenting various medical images.