A geometric model for 3-D confocal image analysis

In this paper, we use partial-differential-equation-based filtering as a preprocessing and post processing strategy for computer-aided cytology. We wish to accurately extract and classify the shapes of nuclei from confocal microscopy images, which is a prerequisite to an accurate quantitative intranuclear (genotypic and phenotypic) and internuclear (tissue structure) analysis of tissue and cultured specimens. First, we study the use of a geometry-driven edge-preserving image smoothing mechanism before nuclear segmentation. We show how this filter outperforms other widely-used filters in that it provides higher edge fidelity. Then we apply the same filter, with a different initial condition, to smooth nuclear surfaces and obtain sub-pixel accuracy. Finally we use another instance of the geometrical filter to correct for misinterpretations of the nuclear surface by the segmentation algorithm. Our prefiltering and post filtering nicely complements our initial segmentation strategy, in that it provides substantial and measurable improvement in the definition of the nuclear surfaces.     

Efficient implementation of accurate geometric transformations for 2-D and 3-D image processing

This paper proposes the use of a polynomial interpolator structure (based on Horner's scheme) which is efficiently realizable in hardware, for high-quality geometric transformation of two- and three-dimensional images. Polynomial-based interpolators such as cubic B-splines and optimal interpolators of shortest support are shown to be exactly implementable in the Horner structure framework. This structure suggests a hardware/software partition which can lead to efficient implementations for multidimensional interpolation.     

Registering coronal histological 2-D sections of a rat brain with coronal sections of a 3-D brain atlas using geometric curve invariants and B-spline representation

A new approach is proposed for registering a set of histological coronal two-dimensional images of a rat brain sectional material with coronal sections of a three-dimensional brain atlas, an intrinsic step and a significant challenge to current efforts in brain mapping and multimodal fusion of experimental data. The alignment problem is based on matching external contours of the brain sections, and operates in the presence of tissue distortion and tears which are routinely encountered, and possible scale, rotation, and shear changes (the affine and weak perspective groups). It is based on a novel set of local absolute affine invariants derived from the set of ordered inflection points on the external contour represented by a cubic B-spline curve. The inflection points are local intrinsic geometric features, which are preserved under both the affine and the weak perspective transformations. The invariants are constructed from the sequence of area patches bounded by the contour and the line connecting two consecutive inflection points, and hence do make direct use of the area (volume) invariance property associated with the affine transformation. These local absolute invariants are very well suited to handle the tissue distortion and tears (occlusion problem).     

3-D SPECT simulations of a complex 3-D mathematical brain model: effects of 3-D geometric detector response, attenuation, scatter, and statistical noise

The quantitative imaging characteristics of ultrahigh-resolution parallel-hole SPECT, including 3-D geometric detector response, attenuation, scatter, and statistical noise, were investigated by simulations based on a complex digitized 3-D brain model of the gray and white matter distributions. The projection data resulting from a uniform distribution of gray and white matter radioactivity, in a ratio of 5:1, were simulated. The results demonstrate significant qualitative and quantitative artifacts in reconstructed human brain images. In the absence of attenuation, scatter, and noise, artifactual variation caused inaccuracies in regional radioactivity quantification. Inclusion of attenuation scatter, and noise in the simulation caused additional artifacts, and resulted in reconstructed images which qualitatively and quantitatively corresponded very closely to reconstructed images of the actual 3-D brain phantom which was constructed from the same set of data as the mathematical 3-D brain model. It is concluded that the major degrading factor in SPECT neuroimaging is the 3-D geometric detector response function.     

Reconstruction of 3-D head geometry from digitized point sets: an evaluation study

In this paper, we evaluate different methods to estimate patient-specific scalp, skull, and brain surfaces from a set of digitized points from the target's scalp surface. The reconstruction problem is treated as a registration problem: An a priori surface model, consisting of the scalp, skull, and brain surfaces, is registered to the digitized surface points. The surface model is generated from segmented magnetic resonance (MR) volume images. We study both affine and free-form deformation (FFD) registration, the use of average models, the averaging of individual registration results, a model selection procedure, and statistical deformation models. The registration algorithms are mainly previously published, and the objective of this paper is to evaluate these methods in this particular application with sparse data. The main interest of this paper is to generate geometric head models for biomedical applications, such as electroencephalography and magnetoencephalographic. However, the methods can also be applied to other anatomical regions and to other application areas. The methods were validated using 15 MR volume images, from which the scalp, skull, and brain were manually segmented. The best results were achieved by averaging the results of the FFD registrations of the database: the mean distance from the manually segmented target surface to a deformed a priori model surface for the studied anatomical objects was 1.68-2.08 mm, depending on the point set used. The results support the use of the evaluated methods for the reconstruction of geometric models in applications with sparse data.     

3-D object recognition using 2-D views

We consider the problem of recognizing 3-D objects from 2-D images using geometric models and assuming different viewing angles and positions. Our goal is to recognize and localize instances of specific objects (i.e., model-based) in a scene. This is in contrast to category-based object recognition methods where the goal is to search for instances of objects that belong to a certain visual category (e.g., faces or cars). The key contribution of our work is improving 3-D object recognition by integrating Algebraic Functions of Views (AFoVs), a powerful framework for predicting the geometric appearance of an object due to viewpoint changes, with indexing and learning. During training, we compute the space of views that groups of object features can produce under the assumption of 3-D linear transformations, by combining a small number of reference views that contain the object features using AFoVs. Unrealistic views (e.g., due to the assumption of 3-D linear transformations) are eliminated by imposing a pair of rigidity constraints based on knowledge of the transformation between the reference views of the object. To represent the space of views that an object can produce compactly while allowing efficient hypothesis generation during recognition, we propose combining indexing with learning in two stages. In the first stage, we sample the space of views of an object sparsely and represent information about the samples using indexing. In the second stage, we build probabilistic models of shape appearance by sampling the space of views of the object densely and learning the manifold formed by the samples. Learning employs the Expectation-Maximization (EM) algorithm and takes place in a "universal," lower-dimensional, space computed through Random Projection (RP). During recognition, we extract groups of point features from the scene and we use indexing to retrieve the most feasible model groups that might have produced them (i.e., hypothesis generation). The likelihood of each hypothesis is then computed using the probabilistic models of shape appearance. Only hypotheses ranked high enough are considered for further verification with the most likely hypotheses verified first. The proposed approach has been evaluated using both artificial and real data, illustrating promising performance. We also present preliminary results illustrating extensions of the AFoVs framework to predict the intensity appearance of an object. In this context, we have built a hybrid recognition framework that exploits geometric knowledge to hypothesize the location of an object in the scene and both geometrical and intesnity information to verify the hypotheses.     

Segmentation of skin lesions in 2-D and 3-D ultrasound images using a spatially coherent generalized Rayleigh mixture model

This paper addresses the problem of jointly estimating the statistical distribution and segmenting lesions in multiple-tissue high-frequency skin ultrasound images. The distribution of multiple-tissue images is modeled as a spatially coherent finite mixture of heavy-tailed Rayleigh distributions. Spatial coherence inherent to biological tissues is modeled by enforcing local dependence between the mixture components. An original Bayesian algorithm combined with a Markov chain Monte Carlo method is then proposed to jointly estimate the mixture parameters and a label-vector associating each voxel to a tissue. More precisely, a hybrid Metropolis-within-Gibbs sampler is used to draw samples that are asymptotically distributed according to the posterior distribution of the Bayesian model. The Bayesian estimators of the model parameters are then computed from the generated samples. Simulation results are conducted on synthetic data to illustrate the performance of the proposed estimation strategy. The method is then successfully applied to the segmentation of in vivo skin tumors in high-frequency 2-D and 3-D ultrasound images.     

Simulation of ST segment changes during subendocardial ischemia using a realistic 3-D cardiac geometry

The mechanisms underlying the ST segment shifts associated with subendocardial ischemia remain unclear. The aim of this paper is to shed further light on the subject through numerical simulations of these shifts. A realistic three-dimensional model of the ventricles, including fiber rotation and anisotropy, is embedded in a nonhomogeneous torso model. A simplification of the bidomain model is used to calculate only the ST segment shift, assuming known values of the transmembrane potential during the plateau and rest phases. A similar simulation is performed in two dimensions. The simulation results suggest that subendocardial ischemia can be located by ST segment shift on the epicardial and torso surfaces. It is shown that ST elevation is associated with the transmural ischemic boundary, while ST depression is associated with the lateral ischemic boundaries.     

Reconstruction of 3-D horizons from 3-D seismic datasets

We propose a method for extracting automatically and simultaneously the quasi-horizontal surfaces in three-dimensional (3-D) seismic data. The proposed algorithm identifies connected sets of points which form surfaces in 3-D space. To improve reliability, this algorithm takes into consideration the relative positions of all horizons, and uses globally self-consistent connectivity criteria which respect the temporal order of horizon creation. The first stage of the algorithm consists of the preliminary estimation of the local direction of each horizon at each point of the 3-D space. The second stage consists of smoothing the signal along the detected layer structure to reduce noise. The last stage consists of the simultaneous building of all 3-D horizons. The output of the processing is a set of 3-D horizons represented by a series of triangulated surfaces.     

Path planning of 3-D objects using a new workspace model

The paper proposes a collision avoidance algorithm to solve the problem of (local) path planning for a three-dimensional (3D) object moving among polyhedral obstacles. The algorithm is based on a generalized potential model of workspace (J.-H. Chuang, 1998) which assumes that the boundary of every 3D object is uniformly charged. According to the proposed approach, the repulsive force and torque between the moving object and the obstacles due to the above model is used to adjust the position and orientation of the object so as to keep it away from the obstacles while passing through a bottleneck in the free space. Simulation results demonstrate that the path of a 3D object thus obtained is indeed safe and spatially smooth. The adopted potential field is analytically tractable which makes the path planning efficient     

Least-Square NUFFT Methods Applied to 2-D and 3-D Radially Encoded MR Image Reconstruction

Radially encoded MRI has gained increasing attention due to its motion insensitivity and reduced artifacts. However, because its samples are collected nonuniformly in the $k$-space, multidimensional (especially 3-D) radially sampled MRI image reconstruction is challenging. The objective of this paper is to develop a reconstruction technique in high dimensions with on-the-fly kernel calculation. It implements general multidimensional nonuniform fast Fourier transform (NUFFT) algorithms and incorporates them into a $k$-space image reconstruction framework. The method is then applied to reconstruct from the radially encoded $k$-space data, although the method is applicable to any non-Cartesian patterns. Performance comparisons are made against the conventional Kaiser–Bessel (KB) gridding method for 2-D and 3-D radially encoded computer-simulated phantoms and physically scanned phantoms. The results show that the NUFFT reconstruction method has better accuracy–efficiency tradeoff than the KB gridding method when the kernel weights are calculated on the fly. It is found that for a particular conventional kernel function, using its corresponding deapodization function as a scaling factor in the NUFFT framework has the potential to improve accuracy. In particular, when a cosine scaling factor is used, the NUFFT method is faster than KB gridding method since a closed-form solution is available and is less computationally expensive than the KB kernel (KB griding requires computation of Bessel functions). The NUFFT method has been successfully applied to 2-D and 3-D in vivo studies on small animals.      

Labelling 2-D geometric primitives using probabilistic relaxation:reducing the computational requirements

In previous work, an algorithm for matching geometric features was developed. Although the method worked well, it was demanding in computational resources when applied to large problems. The authors now present methods for reducing the computational requirements, without significantly affecting the reliability of the algorithm     

Quantifying 3-D vascular structures in MRA images using hybrid PDE and geometric deformable models

The aim of this paper is to present a hybrid approach to accurate quantification of vascular structures from magnetic resonance angiography (MRA) images using level set methods and deformable geometric models constructed with 3-D Delaunay triangulation. Multiple scale filtering based on the analysis of local intensity structure using the Hessian matrix is used to effectively enhance vessel structures with various diameters. The level set method is then applied to automatically segment vessels enhanced by the filtering with a speed function derived from enhanced MRA images. Since the goal of this paper is to obtain highly accurate vessel borders, suitable for use in fluid flow simulations, in a subsequent step, the vessel surface determined by the level set method is triangulated using 3-D Delaunay triangulation and the resulting surface is used as a parametric deformable model. Energy minimization is then performed within a variational setting with a first-order internal energy; the external energy is derived from 3-D image gradients. Using the proposed method, vessels are accurately segmented from MRA data.     

Model identification of a noncausal 2-D AR process using a causal 2-D AR model on the nonsymmetric half-plane

If a noncausal two-dimensional (2-D) autoregressive (AR) process is bi-causal, there exists a causal 2-D AR process on the nonsymmetric half-plane having the same autocorrelations as the noncausal 2-D AR process. A formula is presented to relate the AR coefficients of the noncausal 2-D AR process with those of the causal 2-D AR process on the nonsymmetric half plane. The 2-D Yule-Walker equations are derived for causal 2-D AR models on the nonsymmetric half plane. A computationally efficient order-recursive algorithm is proposed to solve the 2-D Yule-Walker equations. Using the autocorrelation equivalence relation and the order-recursive algorithm, we can easily identify a noncausal 2-D AR process from its autocorrelations.     

Dielectric profiles reconstruction via the quadratic approach in 2-D geometry from multifrequency and multifrequency/multiview data

Deals with the reconstruction of the contrast function of a dielectric cylinder with rectangular cross section starting from the knowledge of the electric scattered far field produced under the incidence of plane waves. We analyze the set of the reconstructable Fourier harmonics of the unknown permittivity contrast function with linear and quadratic approaches. This set depends on the ranges of the wavenumbers /spl beta/, of the angles of incidence /spl theta//sub i/ of the impinging plane waves, and of the observation angles /spl theta//sub o/. We discuss a simple way to describe such a dependence, which allows us to find out that the set of the retrievable harmonics for the quadratic approach contains that for the linear one. Moreover, our investigation points out how increasing the amount of independent data through a multifrequency/multiview measurement scheme allows us to enlarge the set of the retrievable unknown harmonics with respect to a multifrequency/single-view one. Our analysis is confirmed by numerical results. Memory storage requirements and processing time consumption for the quadratic approach are greatly reduced thanks to the massive use of the fast Fourier transform algorithm.     

无对应点匹配的三维重建

本文首先纠正了基于二次曲线匹配视觉算法中所存在的推导错误，并对于重建曲线解的存在性进行了讨论，给出了一种能保证解存在的修改算法，其次，为了保证解的唯一性，我们给出了采用三眼视觉的唯一性匹配定理，最后采用机械零件进行了实验，证明所提出的方法可以快速、准确、完整地重建空间曲线。     

Segmentation and quantification of human vessels using a 3-D cylindrical intensity model.

We introduce a new approach for 3-D segmentation and quantification of vessels. The approach is based on a 3-D cylindrical parametric intensity model, which is directly fitted to the image intensities through an incremental process based on a Kalman filter. Segmentation results are the vessel centerline and shape, i.e., we estimate the local vessel radius, the 3-D position and 3-D orientation, the contrast, as well as the fitting error. We carried out an extensive validation using 3-D synthetic images and also compared the new approach with an approach based on a Gaussian model. In addition, the new model has been successfully applied to segment vessels from 3-D MRA and computed tomography angiography image data. In particular, we compared our approach with an approach based on the randomized Hough transform. Moreover, a validation of the segmentation results based on ground truth provided by a radiologist confirms the accuracy of the new approach. Our experiments show that the new model yields superior results in estimating the vessel radius compared to previous approaches based on a Gaussian model as well as the Hough transform.     

3-D/2-D registration by integrating 2-D information in 3-D

In image-guided therapy, high-quality preoperative images serve for planning and simulation, and intraoperatively as "background", onto which models of surgical instruments or radiation beams are projected. The link between a preoperative image and intraoperative physical space of the patient is established by image-to-patient registration. In this paper, we present a novel 3-D/2-D registration method. First, a 3-D image is reconstructed from a few 2-D X-ray images and next, the preoperative 3-D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure (SM). Because the quality of the reconstructed image is generally low, we introduce a novel SM, which is able to cope with low image quality as well as with different imaging modalities. The novel 3-D/2-D registration method has been evaluated and compared to the gradient-based method (GBM) using standardized evaluation methodology and publicly available 3-D computed tomography (CT), 3-D rotational X-ray (3DRX), and magnetic resonance (MR) and 2-D X-ray images of two spine phantoms, for which gold standard registrations were known. For each of the 3DRX, CT, or MR images and each set of X-ray images, 1600 registrations were performed from starting positions, defined as the mean target registration error (mTRE), randomly generated and uniformly distributed in the interval of 0-20 mm around the gold standard. The capture range was defined as the distance from gold standard for which the final TRE was less than 2 mm in at least 95% of all cases. In terms of success rate, as the function of initial misalignment and capture range the proposed method outperformed the GBM. TREs of the novel method and the GBM were approximately the same. For the registration of 3DRX and CT images to X-ray images as few as 2-3 X-ray views were sufficient to obtain approximately 0.4 mm TREs, 7-9 mm capture range, and 80%-90% of successful registrations. To obtain similar results for MR to X-ray registrations, an image, reconstructed from at least 11 X-ray images was required. Reconstructions from more than 11 images had no effect on the registration results.