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PubMed2006

Model-based automated extraction of microtubules from electron tomography volume.

We propose a model-based automated approach to extracting microtubules from noisy electron tomography volume. Our approach consists of volume enhancement, microtubule localization, and boundary segmentation to exploit the unique geometric and photometric properties of microtubules. The enhancement starts with an anisotropic invariant wavelet transform to enhance the microtubules globally, followed by a three-dimensional (3-D) tube-enhancing filter based on Weingarten matrix to further accentuate the tubular structures locally. The enhancement ends with a modified coherence-enhancing diffusion to complete the interruptions along the microtubules. The microtubules are then localized with a centerline extraction algorithm adapted for tubular objects. To perform segmentation, we novelly modify and extend active shape model method. We first use 3-D local surface enhancement to characterize the microtubule boundary and improve shape searching by relating the boundary strength with the weight matrix of the searching error. We then integrate the active shape model with Kalman filtering to utilize the longitudinal smoothness along the microtubules. The segmentation improved in this way is robust against missing boundaries and outliers that are often present in the tomography volume. Experimental results demonstrate that our automated method produces results close to those by manual process and uses only a fraction of the time of the latter.

Algorithms↗
PubMed2003

Segmentation of prostate boundaries from ultrasound images using statistical shape model.

This paper presents a statistical shape model for the automatic prostate segmentation in transrectal ultrasound images. A Gabor filter bank is first used to characterize the prostate boundaries in ultrasound images in both multiple scales and multiple orientations. The Gabor features are further reconstructed to be invariant to the rotation of the ultrasound probe and incorporated in the prostate model as image attributes for guiding the deformable segmentation. A hierarchical deformation strategy is then employed, in which the model adaptively focuses on the similarity of different Gabor features at different deformation stages using a multiresolution technique, i.e., coarse features first and fine features later. A number of successful experiments validate the algorithm.

Algorithms↗
PubMed2003

Construction of an abdominal probabilistic atlas and its application in segmentation.

There have been significant efforts to build a probabilistic atlas of the brain and to use it for many common applications, such as segmentation and registration. Though the work related to brain atlases can be applied to nonbrain organs, less attention has been paid to actually building an atlas for organs other than the brain. Motivated by the automatic identification of normal organs for applications in radiation therapy treatment planning, we present a method to construct a probabilistic atlas of an abdomen consisting of four organs (i.e., liver, kidneys, and spinal cord). Using 32 noncontrast abdominal computed tomography (CT) scans, 31 were mapped onto one individual scan using thin plate spline as the warping transform and mutual information (MI) as the similarity measure. Except for an initial coarse placement of four control points by the operators, the MI-based registration was automatic. Additionally, the four organs in each of the 32 CT data sets were manually segmented. The manual segmentations were warped onto the "standard" patient space using the same transform computed from their gray scale CT data set and a probabilistic atlas was calculated. Then, the atlas was used to aid the segmentation of low-contrast organs in an additional 20 CT data sets not included in the atlas. By incorporating the atlas information into the Bayesian framework, segmentation results clearly showed improvements over a standard unsupervised segmentation method.

Algorithms↗
PubMed2004

Sphere-filled organ model for virtual surgery system.

We have been developing a virtual surgery system that is capable of simulating surgical maneuvers on elastic organs. In order to perform such maneuvers, we have created a deformable organ model using a sphere-filled method instead of the finite element method. This model is suited for real-time simulation and quantitative deformation. Furthermore, we have equipped this model with a sense of touch and a sense of force by connecting it to a force feedback device. However, in the initial stage the model became problematic when faced with complicated incisions. Therefore, we modified this model by developing an algorithm for organ deformation that performs various, complicated incisions while taking into account the effect of gravity. As a result, the sphere-filled model allowed our system to respond to various incisions that deform the organ. Thus, various physical manipulations that involve pressing, pinching, or incising an organ's surface can be performed. Furthermore, the deformation of the internal organ structures and changes in organ vasculature can be observed via the internal spheres' behavior.

Animals↗
PubMed2004

A quantitative analysis of 3-D coronary modeling from two or more projection images.

A method is introduced to examine the geometrical accuracy of the three-dimensional (3-D) representation of coronary arteries from multiple (two and more) calibrated two-dimensional (2-D) angiographic projections. When involving more then two projections, (multiprojection modeling) a novel procedure is presented that consists of fully automated centerline and width determination in all available projections based on the information provided by the semi-automated centerline detection in two initial calibrated projections. The accuracy of the 3-D coronary modeling approach is determined by a quantitative examination of the 3-D centerline point position and the 3-D cross sectional area of the reconstructed objects. The measurements are based on the analysis of calibrated phantom and calibrated coronary 2-D projection data. From this analysis a confidence region (alpha degrees approximately equal to [35 degrees - 145 degrees]) for the angular distance of two initial projection images is determined for which the modeling procedure is sufficiently accurate for the applied system. Within this angular border range the centerline position error is less then 0.8 mm, in terms of the Euclidean distance to a predefined ground truth. When involving more projections using our new procedure, experiments show that when the initial pair of projection images has an angular distance in the range alpha degrees approximately equal to [35 degrees - 145 degrees], the centerlines in all other projections (gamma = 0 degrees - 180 degrees) were indicated very precisely without any additional centering procedure. When involving additional projection images in the modeling procedure a more realistic shape of the structure can be provided. In case of the concave segment, however, the involvement of multiple projections does not necessarily provide a more realistic shape of the reconstructed structure.

Algorithms↗
PubMed2005

An augmented reality system for patient-specific guidance of cardiac catheter ablation procedures.

We present a system to assist in the treatment of cardiac arrhythmias by catheter ablation. A patient-specific three-dimensional (3-D) anatomical model, constructed from magnetic resonance images, is merged with fluoroscopic images in an augmented reality environment that enables the transfer of electrocardiography (ECG) measurements and cardiac activation times onto the model. Accurate mapping is realized through the combination of: a new calibration technique, adapted to catheter guided treatments; a visual matching registration technique, allowing the electrophysiologist to align the model with contrast-enhanced images; and the use of virtual catheters, which enable the annotation of multiple ECG measurements on the model. These annotations can be visualized by color coding on the patient model. We provide an accuracy analysis of each of these components independently. Based on simulation and experiments, we determined a segmentation error of 0.6 mm, a calibration error in the order of 1 mm and a target registration error of 1.04 +/- 0.45 mm. The system provides a 3-D visualization of the cardiac activation pattern which may facilitate and improve diagnosis and treatment of the arrhytmia. Because of its low cost and similar advantages we believe our approach can compete with existing commercial solutions, which rely on dedicated hardware and costly catheters. We provide qualitative results of the first clinical use of the system in 11 ablation procedures.

Algorithms↗
PubMed2006

An electromechanical model of the heart for image analysis and simulation.

This paper presents a new three-dimensional electromechanical model of the two cardiac ventricles designed both for the simulation of their electrical and mechanical activity, and for the segmentation of time series of medical images. First, we present the volumetric biomechanical models built. Then the transmembrane potential propagation is simulated, based on FitzHugh-Nagumo reaction-diffusion equations. The myocardium contraction is modeled through a constitutive law including an electromechanical coupling. Simulation of a cardiac cycle, with boundary conditions representing blood pressure and volume constraints, leads to the correct estimation of global and local parameters of the cardiac function. This model enables the introduction of pathologies and the simulation of electrophysiology interventions. Moreover, it can be used for cardiac image analysis. A new proactive deformable model of the heart is introduced to segment the two ventricles in time series of cardiac images. Preliminary results indicate that this proactive model, which integrates a priori knowledge on the cardiac anatomy and on its dynamical behavior, can improve the accuracy and robustness of the extraction of functional parameters from cardiac images even in the presence of noisy or sparse data. Such a model also allows the simulation of cardiovascular pathologies in order to test therapy strategies and to plan interventions.

Body Surface Potential Mapping↗
PubMed2006

Phenomenological model of diffuse global and regional atrophy using finite-element methods.

The main goal of this work is the generation of ground-truth data for the validation of atrophy measurement techniques, commonly used in the study of neurodegenerative diseases such as dementia. Several techniques have been used to measure atrophy in cross-sectional and longitudinal studies, but it is extremely difficult to compare their performance since they have been applied to different patient populations. Furthermore, assessment of performance based on phantom measurements or simple scaled images overestimates these techniques' ability to capture the complexity of neurodegeneration of the human brain. We propose a method for atrophy simulation in structural magnetic resonance (MR) images based on finite-element methods. The method produces cohorts of brain images with known change that is physically and clinically plausible, providing data for objective evaluation of atrophy measurement techniques. Atrophy is simulated in different tissue compartments or in different neuroanatomical structures with a phenomenological model. This model of diffuse global and regional atrophy is based on volumetric measurements such as the brain or the hippocampus, from patients with known disease and guided by clinical knowledge of the relative pathological involvement of regions and tissues. The consequent biomechanical readjustment of structures is modelled using conventional physics-based techniques based on biomechanical tissue properties and simulating plausible tissue deformations with finite-element methods. A thermoelastic model of tissue deformation is employed, controlling the rate of progression of atrophy by means of a set of thermal coefficients, each one corresponding to a different type of tissue. Tissue characterization is performed by means of the meshing of a labelled brain atlas, creating a reference volumetric mesh that will be introduced to a finite-element solver to create the simulated deformations. Preliminary work on the simulation of acquisition artefacts is also presented. Cross-sectional and longitudinal sets of simulated data are shown and a visual classification protocol has been used by experts to rate real and simulated scans according to their degree of atrophy. Results confirm the potential of the proposed methodology.

Alzheimer Disease↗
PubMed2006

Evaluation of four probability distribution models for speckle in clinical cardiac ultrasound images.

Segmenting cardiac ultrasound images requires a model for the statistics of speckle in the images. Although the statistics of speckle are well understood for the raw transducer signal, the statistics of speckle in the image are not. This paper evaluates simple empirical models for first-order statistics for the distribution of gray levels in speckle. The models are created by analyzing over 100 images obtained from commercial ultrasound machines in clinical settings. The data in the images suggests a unimodal scalable family of distributions as a plausible model. Four families of distributions (Gamma, Weibull, Normal, and Log-normal) are compared with the data using goodness-of-fit and misclassification tests. Attention is devoted to the analysis of artifacts in images and to the choice of goodness-of-fit and misclassification tests. The distribution of parameters of one of the models is investigated and priors for the distribution are suggested.

Algorithms↗
PubMed2006

Nonrigid 2-D/3-D registration for patient specific bronchoscopy simulation with statistical shape modeling: phantom validation.

This paper presents a nonrigid registration two-dimensional/three-dimensional (2-D/3-D) framework and its phantom validation for subject-specific bronchoscope simulation. The method exploits the recent development of five degrees-of-freedom miniaturized catheter tip electromagnetic trackers such that the position and orientation of the bronchoscope can be accurately determined. This allows the effective recovery of unknown camera rotation and airway deformation, which is modelled by an active shape model (ASM). ASM captures the intrinsic variability of the tracheo-bronchial tree during breathing and it is specific to the class of motion it represents. The method reduces the number of parameters that control the deformation, and thus greatly simplifies the optimisation procedure. Subsequently, pq-based registration is performed to recover both the camera pose and parameters of the ASM. Detailed assessment of the algorithm is performed on a deformable airway phantom, with the ground truth data being provided by an additional six degrees-of-freedom electromagnetic (EM) tracker to monitor the level of simulated respiratory motion.

Algorithms↗
PubMed2006

Normal and pathological NCAT image and phantom data based on physiologically realistic left ventricle finite-element models.

The four-dimensional (4-D) NURBS-based cardiac-torso (NCAT) phantom, which provides a realistic model of the normal human anatomy and cardiac and respiratory motions, is used in medical imaging research to evaluate and improve imaging devices and techniques, especially dynamic cardiac applications. One limitation of the phantom is that it lacks the ability to accurately simulate altered functions of the heart that result from cardiac pathologies such as coronary artery disease (CAD). The goal of this work was to enhance the 4-D NCAT phantom by incorporating a physiologically based, finite-element (FE) mechanical model of the left ventricle (LV) to simulate both normal and abnormal cardiac motions. The geometry of the FE mechanical model was based on gated high-resolution X-ray multislice computed tomography (MSCT) data of a healthy male subject. The myocardial wall was represented as a transversely isotropic hyperelastic material, with the fiber angle varying from -90 degrees at the epicardial surface, through 0 degrees at the midwall, to 90 degrees at the endocardial surface. A time-varying elastance model was used to simulate fiber contraction, and physiological intraventricular systolic pressure-time curves were applied to simulate the cardiac motion over the entire cardiac cycle. To demonstrate the ability of the FE mechanical model to accurately simulate the normal cardiac motion as well as the abnormal motions indicative of CAD, a normal case and two pathologic cases were simulated and analyzed. In the first pathologic model, a subendocardial anterior ischemic region was defined. A second model was created with a transmural ischemic region defined in the same location. The FE-based deformations were incorporated into the 4-D NCAT cardiac model through the control points that define the cardiac structures in the phantom which were set to move according to the predictions of the mechanical model. A simulation study was performed using the FE-NCAT combination to investigate how the differences in contractile function between the subendocardial and transmural infarcts manifest themselves in myocardial Single photon emission computed tomography (SPECT) images. The normal FE model produced strain distributions that were consistent with those reported in the literature and a motion consistent with that defined in the normal 4-D NCAT beating heart model based on tagged magnetic resonance imaging (MRI) data. The addition of a subendocardial ischemic region changed the average transmural circumferential strain from a contractile value of -0.09 to a tensile value of 0.02. The addition of a transmural ischemic region changed average circumferential strain to a value of 0.13, which is consistent with data reported in the literature. Model results demonstrated differences in contractile function between subendocardial and transmural infarcts and how these differences in function are documented in simulated myocardial SPECT images produced using the 4-D NCAT phantom. Compared with the original NCAT beating heart model, the FE mechanical model produced a more accurate simulation for the cardiac motion abnormalities. Such a model, when incorporated into the 4-D NCAT phantom, has great potential for use in cardiac imaging research. With its enhanced physiologically based cardiac model, the 4-D NCAT phantom can be used to simulate realistic, predictive imaging data of a patient population with varying whole-body anatomy and with varying healthy and diseased states of the heart that will provide a known truth from which to evaluate and improve existing and emerging 4-D imaging techniques used in the diagnosis of cardiac disease.

Algorithms↗
PubMed2006

Building models of animals from video.

This paper argues that tracking, object detection, and model building are all similar activities. We describe a fully automatic system that builds 2D articulated models known as pictorial structures from videos of animals. The learned model can be used to detect the animal in the original video--in this sense, the system can be viewed as a generalized tracker (one that is capable of modeling objects while tracking them). The learned model can be matched to a visual library; here, the system can be viewed as a video recognition algorithm. The learned model can also be used to detect the animal in novel images--in this case, the system can be seen as a method for learning models for object recognition. We find that we can significantly improve the pictorial structures by augmenting them with a discriminative texture model learned from a texture library. We develop a novel texture descriptor that outperforms the state-of-the-art for animal textures. We demonstrate the entire system on real video sequences of three different animals. We show that we can automatically track and identify the given animal. We use the learned models to recognize animals from two data sets; images taken by professional photographers from the Corel collection, and assorted images from the Web returned by Google. We demonstrate quite good performance on both data sets. Comparing our results with simple baselines, we show that, for the Google set, we can detect, localize, and recover part articulations from a collection demonstrably hard for object recognition.

Algorithms↗
PubMed2006

A field model for human detection and tracking.

The large shape variability and partial occlusions challenge most object detection and tracking methods for nonrigid targets such as pedestrians. This paper presents a new approach based on a two-layer statistical field model that characterizes the prior of the complex shape variations as a Boltzmann distribution and embeds this prior and the complex image likelihood into a Markov field. A probabilistic variational analysis of this model reveals a set of fixed-point equations characterizing the equilibrium of the field. It leads to computationally efficient methods for calculating the image likelihood and for training the model. Based on that, effective algorithms for detecting nonrigid objects are developed. This new approach has several advantages. First, it is intrinsically suitable for capturing local nonrigidity. In addition, due to the distributed likelihood, this approach is robust to partial occlusions. Moreover, the two-layer structure provides large flexibility of modeling the image observations, which makes the new method robust to clutters. Extensive experiments demonstrate its effectiveness.

Algorithms↗
PubMed2006

Meticulously detailed eye region model and its application to analysis of facial images.

We propose a system that is capable of detailed analysis of eye region images in terms of the position of the iris, degree of eyelid opening, and the shape, complexity, and texture of the eyelids. The system uses a generative eye region model that parameterizes the fine structure and motion of an eye. The structure parameters represent structural individuality of the eye, including the size and color of the iris, the width, boldness, and complexity of the eyelids, the width of the bulge below the eye, and the width of the illumination reflection on the bulge. The motion parameters represent movement of the eye, including the up-down position of the upper and lower eyelids and the 2D position of the iris. The system first registers the eye model to the input in a particular frame and individualizes it by adjusting the structure parameters. The system then tracks motion of the eye by estimating the motion parameters across the entire image sequence. Combined with image stabilization to compensate for appearance changes due to head motion, the system achieves accurate registration and motion recovery of eyes.

Algorithms↗
PubMed2002

Element size effect on phase aberration correction.

The distortion effect of tissue on ultrasonic beamforming is simplified as a 2-D time-shifting screen placed against the array surface. The ideal correction of such distortion requires a 2-D array with infinitesimally small elements. However, elements of finite sizes must be utilized in practice, causing the so-called residual phase error (RPE). As element size is reduced, the magnitude of the RPE is reduced, and its spatial feature becomes finer. Analyses have been performed to reveal that the magnitude of the RPE is proportional to the imaging frequency, the rms magnitude of the original time-delay error, and the diagonal size of individual rectangular elements, and is inversely proportional to the correlation length of the original time-delay error. Simulations have been performed to study the peak sidelobe level caused by the RPE as the element sizes are reduced. The sidelobe is defined here as the difference between the ideal beam (with no phase error) and the beam obtained in the presence of the RPE. For a multi-row array in which a conventional 1-D array is divided into N rows of independent elements in the elevation direction, the peak sidelobe level is found to vary approximately as N(-1) instead of the anticipated N(-2). The reduction is caused by the reduced magnitude of the RPE, and the finer spatial feature of the RPE, although apparent in the reduced spatial correlation length, does not result in additional reduction of the sidelobe level. The reason for this has been analyzed. The results of this study provide guidance for designing multi-row arrays suitable for phase aberration correction.

Fourier Analysis↗
PubMedDate not supplied

Interactive volume rendering of thin thread structures within multivalued scientific data sets.

We present a threads and halos representation for interactive volume rendering of vector-field structure and describe a number of additional components that combine to create effective visualizations of multivalued 3D scientific data. After filtering linear structures, such as flow lines, into a volume representation, we use a multilayer volume rendering approach to simultaneously display this derived volume along with other data values. We demonstrate the utility of threads and halos in clarifying depth relationships within dense renderings and we present results from two scientific applications: visualization of second-order tensor valued magnetic resonance imaging (MRI) data and simulated 3D fluid flow data. In both application areas, the interactivity of the visualizations proved to be important to the domain scientists. Finally, we describe a PC-based implementation of our framework along with domain specific transfer functions, including an exploratory data culling tool, that enable fast data exploration.

Algorithms↗
PubMedDate not supplied

Creating speech-synchronized animation.

We present a facial model designed primarily to support animated speech. Our facial model takes facial geometry as input and transforms it into a parametric deformable model. The facial model uses a muscle-based parameterization, allowing for easier integration between speech synchrony and facial expressions. Our facial model has a highly deformable lip model that is grafted onto the input facial geometry to provide the necessary geometric complexity needed for creating lip shapes and high-quality renderings. Our facial model also includes a highly deformable tongue model that can represent the shapes the tongue undergoes during speech. We add teeth, gums, and upper palate geometry to complete the inner mouth. To decrease the processing time, we hierarchically deform the facial surface. We also present a method to animate the facial model over time to create animated speech using a model of coarticulation that blends visemes together using dominance functions. We treat visemes as a dynamic shaping of the vocal tract by describing visemes as curves instead of keyframes. We show the utility of the techniques described in this paper by implementing them in a text-to-audiovisual-speech system that creates animation of speech from unrestricted text. The facial and coarticulation models must first be interactively initialized. The system then automatically creates accurate real-time animated speech from the input text. It is capable of cheaply producing tremendous amounts of animated speech with very low resource requirements.

Algorithms↗
PubMedDate not supplied

Real-time illustration of vascular structures.

We present real-time vascular visualization methods, which extend on illustrative rendering techniques to particularly accentuate spatial depth and to improve the perceptive separation of important vascular properties such as branching level and supply area. The resulting visualization can and has already been used for direct projection on a patient's organ in the operation theater where the varying absorption and reflection characteristics of the surface limit the use of color. The important contributions of our work are a GPU-based hatching algorithm for complex tubular structures that emphasizes shape and depth as well as GPU-accelerated shadow-like depth indicators, which enable reliable comparisons of depth distances in a static monoscopic 3D visualization. In addition, we verify the expressiveness of our illustration methods in a large, quantitative study with 160 subjects.

Adolescent↗