Model-based morphological segmentation and labeling of coronary angiograms

Automated anatomical labeling of a topologically variant abdominal arterial system via probabilistic hypergraph matching

Automated anatomical vessel labeling of the abdominal arterial system is a crucial topic in medical image processing. One reason for this is the importance of the abdominal arterial system in the human body, and another is that such labeling is necessary for the related disease diagnoses, treatments and epidemiological population analyses. We define a hypergraph representation of the abdominal arterial system as a family tree model with a probabilistic hypergraph matching framework for automated vessel labeling. Then we treat the labelling problem as the convex optimization problem and solve it with the maximum a posteriori(MAP) combined the likelihood obtained by geometric labelling with the family tree topology-based knowledge. Geometrically, we utilize XGBoost ensemble learning with an intrinsic geometric feature importance analysis for branch-level labeling. In topology, the defined family tree model of the abdominal arterial system is transferred as a Markov chain model using a constrained traversal order method and further the Markov chain model is optimized by a hidden Markov model (HMM). The probability distribution of the target branches for each candidate anatomical name is predicted and effectively embedded in the HMM model. This approach is evaluated with the leave-one-out method on 37 clinical patients' abdominal arteries, and the average accuracy is 91.94%. The obtained results are better than those of the state-of-art method with an F1 score of 93.00% and a recall of 93.00%, as the proposed method simultaneously handles the anatomical structural variability and discriminates between the symmetric branches. It is demonstrated to be suitable for labelling branches of the abdominal arterial system and can also be extended to similar tubular organ networks, such as arterial or airway networks.

Graph matching survey for medical imaging: On the way to deep learning

The interest on graph matching has not stopped growing since the late seventies. The basic idea of graph matching consists of generating graph representations of different data or structures and compare those representations by searching correspondences between them. There are manifold techniques that have been developed to find those correspondences and the choice of one or another depends on the characteristics of the application of interest. These applications range from pattern recognition (e.g. biometric identification) to signal processing or artificial intelligence. One of the aspects that make graph matching so attractive is its ability to facilitate data analysis, and medical imaging is one of the fields that can benefit from this in a greater extent. The potential of graph matching to find similarities and differences between data acquired at different points in time shows its potential to improve diagnosis, follow-up of human diseases or any other of the clinical scenarios that require comparison between different datasets. In spite of the large amount of papers that were published in this field to the date there is no survey paper of graph matching for clinical applications. This survey aims to fill this gap.

A joint graph inference case study: the C. elegans chemical and electrical connectomes

We investigate joint graph inference for the chemical and electrical connectomes of the Caenorhabditis elegans roundworm. The C. elegans connectomes consist of [Formula: see text] non-isolated neurons with known functional attributes, and there are two types of synaptic connectomes, resulting in a pair of graphs. We formulate our joint graph inference from the perspectives of seeded graph matching and joint vertex classification. Our results suggest that connectomic inference should proceed in the joint space of the two connectomes, which has significant neuroscientific implications.

Computer Vision Techniques for Transcatheter Intervention

Minimally invasive transcatheter technologies have demonstrated substantial promise for the diagnosis and the treatment of cardiovascular diseases. For example, transcatheter aortic valve implantation is an alternative to aortic valve replacement for the treatment of severe aortic stenosis, and transcatheter atrial fibrillation ablation is widely used for the treatment and the cure of atrial fibrillation. In addition, catheter-based intravascular ultrasound and optical coherence tomography imaging of coronary arteries provides important information about the coronary lumen, wall, and plaque characteristics. Qualitative and quantitative analysis of these cross-sectional image data will be beneficial to the evaluation and the treatment of coronary artery diseases such as atherosclerosis. In all the phases (preoperative, intraoperative, and postoperative) during the transcatheter intervention procedure, computer vision techniques (e.g., image segmentation and motion tracking) have been largely applied in the field to accomplish tasks like annulus measurement, valve selection, catheter placement control, and vessel centerline extraction. This provides beneficial guidance for the clinicians in surgical planning, disease diagnosis, and treatment assessment. In this paper, we present a systematical review on these state-of-the-art methods. We aim to give a comprehensive overview for researchers in the area of computer vision on the subject of transcatheter intervention. Research in medical computing is multi-disciplinary due to its nature, and hence, it is important to understand the application domain, clinical background, and imaging modality, so that methods and quantitative measurements derived from analyzing the imaging data are appropriate and meaningful. We thus provide an overview on the background information of the transcatheter intervention procedures, as well as a review of the computer vision techniques and methodologies applied in this area.

CTA coronary labeling through efficient geodesics between trees using anatomy priors

We present an efficient realization of recent work on unique geodesic paths between tree shapes for the application of matching coronary arteries to a standard model of coronary anatomy in order to label the coronary arteries. Automatically labeled coronary arteries would speed reporting for physicians. The efficiency of the approach and the quality of the results are enhanced using the relative position of detected cardiac structures. We explain how to efficiently compute the geodesic paths between tree shapes using Dijkstra's algorithm and we present a methodology to account for missing side branches during matching. For nearly all labels our approach shows promise compared with recent work and we results for 8 additional labels.

Topology preserving thinning of cell complexes

A topology preserving skeleton is a synthetic representation of an object that retains its topology and many of its significant morphological properties. The process of obtaining the skeleton, referred to as skeletonization or thinning, is a very active research area. It plays a central role in reducing the amount of information to be processed during image analysis and visualization, computer-aided diagnosis, or by pattern recognition algorithms. This paper introduces a novel topology preserving thinning algorithm, which removes simple cells-a generalization of simple points-of a given cell complex. The test for simple cells is based on acyclicity tables automatically produced in advance with homology computations. Using acyclicity tables render the implementation of thinning algorithms straightforward. Moreover, the fact that tables are automatically filled for all possible configurations allows to rigorously prove the generality of the algorithm and to obtain fool-proof implementations. The novel approach enables, for the first time, according to our knowledge, to thin a general unstructured simplicial complex. Acyclicity tables for cubical and simplicial complexes and an open source implementation of the thinning algorithm are provided as an additional material to allow their immediate use in the vast number of applications arising in medical imaging and beyond.

Automatic vasculature identification in coronary angiograms by adaptive geometrical tracking

As the uneven distribution of contrast agents and the perspective projection principle of X-ray, the vasculatures in angiographic image are with low contrast and are generally superposed with other organic tissues; therefore, it is very difficult to identify the vasculature and quantitatively estimate the blood flow directly from angiographic images. In this paper, we propose a fully automatic algorithm named adaptive geometrical vessel tracking (AGVT) for coronary artery identification in X-ray angiograms. Initially, the ridge enhancement (RE) image is obtained utilizing multiscale Hessian information. Then, automatic initialization procedures including seed points detection, and initial directions determination are performed on the RE image. The extracted ridge points can be adjusted to the geometrical centerline points adaptively through diameter estimation. Bifurcations are identified by discriminating connecting relationship of the tracked ridge points. Finally, all the tracked centerlines are merged and smoothed by classifying the connecting components on the vascular structures. Synthetic angiographic images and clinical angiograms are used to evaluate the performance of the proposed algorithm. The proposed algorithm is compared with other two vascular tracking techniques in terms of the efficiency and accuracy, which demonstrate successful applications of the proposed segmentation and extraction scheme in vasculature identification.

Computer aided alignment and quantitative 4D structural plasticity analysis of neurons

The rapid development of microscopic imaging techniques has greatly facilitated time-lapse imaging of neuronal morphology. However, analysis of structural dynamics in the vast amount of 4-Dimensional data generated by in vivo or ex vivo time-lapse imaging still relies heavily on manual comparison, which is not only laborious, but also introduces errors and discrepancies between individual researchers and greatly limits the research pace. Here we present a supervised 4D Structural Plasticity Analysis (4D SPA) computer method to align and match 3-Dimensional neuronal structures across different time points on a semi-automated basis. We demonstrate 2 applications of the method to analyze time-lapse data showing gross morphological changes in dendritic arbor morphology and to identify the distribution and types of branch dynamics seen in a series of time-lapse images. Analysis of the dynamic changes of neuronal structure can be done much faster and with greatly improved consistency and reliability with the 4D SPA supervised computer program. Users can format the neuronal reconstruction data to be used for this analysis. We provide file converters for Neurolucida and Imaris users. The program and user manual are publically accessible and operate through a graphical user interface on Windows and Mac OSX.

Anatomical labeling of the Circle of Willis using maximum a posteriori probability estimation

Anatomical labeling of the cerebral arteries forming the Circle of Willis (CoW) enables inter-subject comparison, which is required for geometric characterization and discovering risk factors associated with cerebrovascular pathologies. We present a method for automated anatomical labeling of the CoW by detecting its main bifurcations. The CoW is modeled as rooted attributed relational graph, with bifurcations as its vertices, whose attributes are characterized as points on a Riemannian manifold. The method is first trained on a set of pre-labeled examples, where it learns the variability of local bifurcation features as well as the variability in the topology. Then, the labeling of the target vasculature is obtained as maximum a posteriori probability (MAP) estimate where the likelihood of labeling individual bifurcations is regularized by the prior structural knowledge of the graph they span. The method was evaluated by cross-validation on 50 subjects, imaged with magnetic resonance angiography, and showed a mean detection accuracy of 95%. In addition, besides providing the MAP, the method can rank the labelings. The proposed method naturally handles anatomical structural variability and is demonstrated to be suitable for labeling arterial segments of the CoW.

Coronary artery center-line extraction using second order local features

Of interest is the accurate and robust delineation of vessel center-lines for complete arterial tree structure in coronary angiograms which is an imperative step towards 3D reconstruction of coronary tree and feature-based registration of multiple view angiograms. Most existing center-line tracking methods encounter limitations in coping with abrupt variations in local artery direction and sudden changes of lumen diameter that occur in the vicinity of arterial lesions. This paper presents an improved center-line tracing algorithm for automatic extraction of coronary arterial tree based on robust local features. The algorithm employs an improved scanning schema based on eigenvalues of Hessian matrix for reliable identification of true vessel points as well as an adaptive look-ahead distance schema for calculating the magnitude of scanning profile. In addition to a huge variety of clinical examples, a well-established vessel simulation tool was used to create several synthetic angiograms for objective comparison and performance evaluation. The experimental results on the accuracy and robustness of the proposed algorithm and its counterparts under difficult situations such as poor image quality and complicated vessel geometry are presented.

EXTRACTION OF CORONARY ARTERIAL TREE USING CINE X-RAY ANGIOGRAMS

An efficient and robust method for identification of coronary arteries and evaluation of the severity of the stenosis on the routine X-ray angiograms is proposed. It is a challenging process to accurately identify coronary artery due to poor signal-to-noise ratio, vessel overlap, and superimposition with various anatomical structures such as ribs, spine, or heart chambers. The proposed method consists of two major stages: (a) signal-based image segmentation and (b) vessel feature extraction. The 3D Fourier and 3D Wavelet transforms are first employed to reduce the background and noisy structures in the images. Afterwards, a set of matched filters was applied to enhance the coronary arteries in the images. At the end, clustering analysis, histogram technique, and size filtering were utilized to obtain a binary image that consists of the final segmented coronary arterial tree. To extract vessel features in terms of vessel centerline and diameter, a gradient vector-flow based snake algorithm is applied to determine the medial axis of a vessel followed by the calculations of vessel boundaries and width associated with the detected medial axis.

THIRTY YEARS OF GRAPH MATCHING IN PATTERN RECOGNITION

A recent paper posed the question: "Graph Matching: What are we really talking about?". Far from providing a definite answer to that question, in this paper we will try to characterize the role that graphs play within the Pattern Recognition field. To this aim two taxonomies are presented and discussed. The first includes almost all the graph matching algorithms proposed from the late seventies, and describes the different classes of algorithms. The second taxonomy considers the types of common applications of graph-based techniques in the Pattern Recognition and Machine Vision field.

Automatic segmentation of coronary angiograms based on fuzzy inferring and probabilistic tracking

BACKGROUND

Segmentation of the coronary angiogram is important in computer-assisted artery motion analysis or reconstruction of 3D vascular structures from a single-plan or biplane angiographic system. Developing fully automated and accurate vessel segmentation algorithms is highly challenging, especially when extracting vascular structures with large variations in image intensities and noise, as well as with variable cross-sections or vascular lesions.

METHODS

This paper presents a novel tracking method for automatic segmentation of the coronary artery tree in X-ray angiographic images, based on probabilistic vessel tracking and fuzzy structure pattern inferring. The method is composed of two main steps: preprocessing and tracking. In preprocessing, multiscale Gabor filtering and Hessian matrix analysis were used to enhance and extract vessel features from the original angiographic image, leading to a vessel feature map as well as a vessel direction map. In tracking, a seed point was first automatically detected by analyzing the vessel feature map. Subsequently, two operators [e.g., a probabilistic tracking operator (PTO) and a vessel structure pattern detector (SPD)] worked together based on the detected seed point to extract vessel segments or branches one at a time. The local structure pattern was inferred by a multi-feature based fuzzy inferring function employed in the SPD. The identified structure pattern, such as crossing or bifurcation, was used to control the tracking process, for example, to keep tracking the current segment or start tracking a new one, depending on the detected pattern.

RESULTS

By appropriate integration of these advanced preprocessing and tracking steps, our tracking algorithm is able to extract both vessel axis lines and edge points, as well as measure the arterial diameters in various complicated cases. For example, it can walk across gaps along the longitudinal vessel direction, manage varying vessel curvatures, and adapt to varying vessel widths in situations with arterial stenoses and aneurysms.

CONCLUSIONS

Our algorithm performs well in terms of robustness, automation, adaptability, and applicability. In particular, the successful development of two novel operators, namely, PTO and SPD, ensures the performance of our algorithm in vessel tracking.

Morphological multiscale enhancement, fuzzy filter and watershed for vascular tree extraction in angiogram

This paper presented an automatic morphological method to extract a vascular tree using an angiogram. Under the assumption that vessels are connected in a local linear pattern in a noisy environment, the algorithm decomposes the vessel extraction problem into several consecutive morphological operators, aiming to characterize and distinguish different patterns on the angiogram: background, approximate vessel region and the boundary. It started with a contrast enhancement and background suppression process implemented by subtracting the background from the original angiogram. The background was estimated using multiscale morphology opening operators by varying the size of structuring element on each pixel. Subsequently, the algorithm simplified the enhanced angiogram with a combined fuzzy morphological opening operation, with linear rotating structuring element, in order to fit the vessel pattern. This filtering process was then followed by simply setting a threshold to produce approximate vessel region. Finally, the vessel boundaries were detected using watershed techniques with the obtained approximate vessel centerline, thinned result of the obtained vessel region, as prior marker for vessel structure. Experimental results using clinical digitized vascular angiogram and some comparative performance of the proposed algorithm were reported.

Training models of anatomic shape variability

Learning probability distributions of the shape of anatomic structures requires fitting shape representations to human expert segmentations from training sets of medical images. The quality of statistical segmentation and registration methods is directly related to the quality of this initial shape fitting, yet the subject is largely overlooked or described in an ad hoc way. This article presents a set of general principles to guide such training. Our novel method is to jointly estimate both the best geometric model for any given image and the shape distribution for the entire population of training images by iteratively relaxing purely geometric constraints in favor of the converging shape probabilities as the fitted objects converge to their target segmentations. The geometric constraints are carefully crafted both to obtain legal, nonself-interpenetrating shapes and to impose the model-to-model correspondences required for useful statistical analysis. The paper closes with example applications of the method to synthetic and real patient CT image sets, including same patient male pelvis and head and neck images, and cross patient kidney and brain images. Finally, we outline how this shape training serves as the basis for our approach to IGRT/ART.

A multichannel watershed-based segmentation method for multispectral chromosome classification

Multiplex fluorescent in situ hybridization (M-FISH) is a recently developed chromosome imaging technique where each chromosome class appears to have a distinct color. This technique not only facilitates the detection of subtle chromosomal aberrations but also makes the analysis of chromosome images easier; both for human inspection and computerized analysis. In this paper, a novel method for segmentation and classification of M-FISH chromosome images is presented. The segmentation is based on the multichannel watershed transform in order to define regions of similar spatial and spectral characteristics. Then, a Bayes classifier, task-specific on region classification, is applied. Our method consists of four basic steps: 1) computation of the gradient magnitude of the image, 2) application of the watershed transform to decompose the image into a set of homogenous regions, 3) classification of each region, and 4) merging of similar adjacent regions. The method is evaluated using a publicly available chromosome image database and the obtained overall accuracy is 82.4%. By introducing the classification of each watershed region, the proposed method achieves substantially better results compared to other methods at a lower computational cost. The combination of the multichannel segmentation and the region-based classification is found to improve the overall classification accuracy compared to pixel-by-pixel approaches.

Experimental hip fracture load can be predicted from plain radiography by combined analysis of trabecular bone structure and bone geometry

Computerized analysis of the trabecular structure was used to test whether femur failure load can be estimated from radiographs. The study showed that combined analysis of trabecular bone structure and geometry predicts in vitro failure load with similar accuracy as DXA.

INTRODUCTION

Since conventional radiography is widely available with low imaging cost, it is of considerable interest to discover how well bone mechanical competence can be determined using this technology. We tested the hypothesis that the mechanical strength of the femur can be estimated by the combined analysis of the bone trabecular structure and geometry.

METHODS

The sample consisted of 62 cadaver femurs (34 females, 28 males). After radiography and DXA, femora were mechanically tested in side impact configuration. Fracture patterns were classified as being cervical or trochanteric. Computerized image analysis was applied to obtain structure-related trabecular parameters (trabecular bone area, Euler number, homogeneity index, and trabecular main orientation), and set of geometrical variables (neck-shaft angle, medial calcar and femoral shaft cortex thicknesses, and femoral neck axis length). Multiple linear regression analysis was performed to identify the variables that best explain variation in BMD and failure load between subjects.

RESULTS

In cervical fracture cases, trabecular bone area and femoral neck axis length explained 64% of the variability in failure loads, while femoral neck BMD also explained 64%. In trochanteric fracture cases, Euler number and femoral cortex thickness explained 66% of the variability in failure load, while trochanteric BMD explained 72%.

CONCLUSIONS

Structural parameters of trabecular bone and bone geometry predict in vitro failure loads of the proximal femur with similar accuracy as DXA, when using appropriate image analysis technology.

An improved algorithm for vessel centerline tracking in coronary angiograms

For automated visualization and quantification of artery diseases, the accurate determination of the arterial centerline is a prerequisite. Existing tracking-based approaches usually suffer from the inaccuracy, inflexion and discontinuity in the extracted centerlines, and they may even fail in complicated situations. In this paper, an improved algorithm for coronary arterial centerline extraction is proposed, which incorporates a new tracking direction updating scheme, a self-adaptive magnitude of linear extrapolation and a dynamic-size search window for matched filtering. A simulation study is conducted for the determination of the optimal weighting factor which is used to combine the geometrical topology information and intensity distribution information to obtain the proposed tracking direction. Synthetic and clinical examples, representing some difficult situations that may occur in coronary angiograms, are presented. Results show that the proposed algorithm outperforms the conventional methods. By adopting the proposed algorithm, centerlines are successfully extracted under these complicated situations, and with satisfactory accuracy.

Flow parameters in normal left coronary artery tree. Implication to atherogenesis

The dominant haemodynamic flow parameters of wall pressure (WP), wall shear stress (WSS), molecular viscosity and the spatial gradients: wall pressure gradient (WPG) and wall shear stress gradient (WSSG) along the normal human left coronary artery (LCA) tree are numerically analyzed in relation to atheronegenesis. The LCA tree includes the left main coronary artery, the left anterior descending branch, the left circumflex branch and their major branches. Spatial differentiation indicates that low values of WP (locally), WPG, WSS, WSSG and high molecular viscosity appear opposite flow dividers and this probably correlates to atherosclerosis localization.

Evaluation of an improved technique for automated center lumen line definition in cardiovascular image data

The aim of the study was to evaluate a new method for automated definition of a center lumen line in vessels in cardiovascular image data. This method, called VAMPIRE, is based on improved detection of vessel-like structures. A multiobserver evaluation study was conducted involving 40 tracings in clinical CTA data of carotid arteries to compare VAMPIRE with an established technique. This comparison showed that VAMPIRE yields considerably more successful tracings and improved handling of stenosis, calcifications, multiple vessels, and nearby bone structures. We conclude that VAMPIRE is highly suitable for automated definition of center lumen lines in vessels in cardiovascular image data.

Automatic axis generation for virtual bronchoscopic assessment of major airway obstructions

Virtual bronchoscopy (VB) has emerged as a paradigm for more effective 3D CT image evaluation. Systematic evaluation of a 3D CT chest image using VB techniques, however, requires precomputed guidance data. This guidance data takes the form of central axes, or centerlines, through the major airways. We propose an axes-generation algorithm for VB assessment of 3D CT chest images. For a typical high-resolution 3D CT chest image, the algorithm produces a series of airway-tree axes, corresponding airway cross-sectional area measurements, and a segmented airway tree in a few minutes on a standard PC. Results for phantom and human airway-obstruction cases demonstrate the efficacy of the algorithm. Also, the algorithm is demonstrated in the context of VB-based 3D CT assessment.

Modeling the 3D coronary tree for labeling purposes

Coronary artery diseases are usually revealed using X-ray angiographies. Such images are complex to analyze because they provide a 2D projection of a 3D object. Medical diagnosis suffers from inter- and intra-clinician variability. Therefore, reliable software for the 3D reconstruction and labeling of the coronary tree is strongly desired. It requires the matching of the vessels in the different available angiograms, and an approach which identifies the arteries by their anatomical names is a way to solve this difficult problem. This paper focuses on the automatic labeling of the left coronary tree in X-ray angiography. Our approach is based on a 3D topological model, built from the 3D anthropomorphic phantom, Coronix. The phantom is projected under different angles of view to provide a data base of 2D topological models. On the other hand, the vessel skeleton is extracted from the patient's angiogram. The algorithm compares the skeleton with the 2D topological model which has the most similar vascular net shape. The method performs in a hierarchical manner, first labeling the main artery, then the sub-branches. It handles inter-individual anatomical variations, segmentation errors and image ambiguities. We tested the method on standard angiograms of Coronix and on clinical examinations of nine patients. We demonstrated successful scores of 90% correct labeling for the main arteries and 60% for the sub-branches. The method appears to be particularly efficient for the arteries in focus. It is therefore a very promising tool for the automatic 3D reconstruction of the coronary tree from monoplane temporal angiographic clinical sequences.

Evaluation of center-line extraction algorithms in quantitative coronary angiography

Objective testing of centerline extraction accuracy in quantitative coronary angiography (QCA) algorithms is a very difficult task. Standard tools for this task are not yet available. We present a simulation tool that generates synthetic angiographic images of a single coronary artery with predetermined centerline and diameter function. This simulation tool was used creating a library of images for the objective comparison and evaluation of QCA algorithms. This technique also provides the means for understanding the relationship between the algorithms' performance and limitations and the vessel's geometrical parameters. In this paper, two algorithms are evaluated and the results are presented.