L. Zhu, Y. Gao, A. Yezzi, R.S. MacLeod, J. Cates, A. Tannenbaum. Automatic Segmentation of the Left Atrium from MRI Images using Salient Feature and Contour Evolution, In Proceedings of the 34th Annual International Conference of the IEEE EMBS, pp. 3211--214. 2012.
PubMed ID: 23366609
PubMed Central ID: PMC3652873
N. Akoum, M. Daccarett, C. McGann, N. Segerson, G. Vergara, S. Kuppahally, T. Badger, N. Burgon, T. Haslam, E. Kholmovski, R.S. MacLeod, N.F. Marrouche. Atrial fibrosis helps select the appropriate patient and strategy in catheter ablation of atrial fibrillation: a DE-MRI guided approach, In Journal of Cardiovascular Electrophysiology, Vol. 22, No. 1, pp. 16--22. 2011.
PubMed ID: 20807271
Atrial fibrillation (AF) is the most common sustained arrhythmia encountered in adult cardiology.1,2 Several studies have demonstrated that AF is associated with electrical, contractile, and structural remodeling (SRM) in the left atrium (LA) that contributes to the persistence and sustainability of the arrhythmia.3-7 It has also been shown that the end result of this remodeling process is loss of atrial myocytes and increased collagen content and hence fibrosis of the LA wall.5 Delayed enhancement MRI (DE-MRI) using gadolinium contrast has been demonstrated to localize and quantify the degree of SRM or fibrosis associated with AF in the LA.8
DE-MRI has also been shown to be useful in localizing and quantifying scar formation in the LA following radiofrequency ablation (RFA).9,10 The pulmonary vein (PV) antral region can be visualized to assess circumferential PV scarring that results from RFA lesions/ablation. In addition, the amount of scarring to the LA after catheter ablation can be quantified as a proportion of the total left atrial volume.
Rhythm control of AF using catheter ablation has yielded varying results in different patient populations.11 Identifying the ideal candidate for catheter ablation remains a significant challenge. In addition, a number of different approaches to catheter ablation have been reported and most experts agree that 1 ablation strategy does not fit allAF patients.11-15 Therefore, selecting the proper strategy for a particular patient is also an important determinant of procedure success.
We used DE-MRI to quantify both the degree of SRM/fibrosis pre-ablation and scar formation post ablation. Our aim was to identify predictors of successful ablation in a group of patients stratified according to pre-ablation fibrosis. This would help select the most appropriate ablation strategy for the individual AF ablation candidate.
N. Andrysco, P. Rosen, V. Popescu, B. Benes, K.R. Gurney. Experiences in Disseminating Educational Visualizations, In Lecture Notes in Computer Science (7th International Symposium on Visual Computing), Vol. 2, pp. 239--248. September, 2011.
B.M. Burton, J.D. Tate, B. Erem, D.J. Swenson, D.F. Wang, D.H. Brooks, P.M. van Dam, R.S. MacLeod. A Toolkit for Forward/Inverse Problems in Electrocardiography within the SCIRun Problem Solving Environment, In Proceedings of the 2011 IEEE Int. Conf. Engineering and Biology Society (EMBC), pp. 267--270. 2011.
PubMed ID: 22254301
PubMed Central ID: PMC3337752
A.N.M. Imroz Choudhury, P. Rosen. Abstract Visualization of Runtime Memory Behavior, In 6th IEEE International Workshop on Visualizing Software for Understanding and Analysis (VISSOFT 2011), pp. 22--29. 2011.
M. Daccarett, T.J. Badger, N. Akoum, N.S. Burgon, C. Mahnkopf, G.R. Vergara, E.G. Kholmovski, C.J. McGann, D.L. Parker, J. Brachmann, R.S. Macleod, N.F. Marrouche. Association of left atrial fibrosis detected by delayed-enhancement magnetic resonance imaging and the risk of stroke in patients with atrial fibrillation, In Journal of the American College of Cardiology, Vol. 57, No. 7, pp. 831--838. 2011.
PubMed ID: 21310320
M. Daccarett, C.J. McGann, N.W. Akoum, R.S. MacLeod, N.F. Marrouche. MRI of the left atrium: predicting clinical outcomes in patients with atrial fibrillation, In Expert Review of Cardiovascular Therapy, Vol. 9, No. 1, pp. 105--111. 2011.
PubMed ID: 21166532
M. Datar, Y. Gur, B. Paniagua, M. Styner, R.T. Whitaker. Geometric Correspondence for Ensembles of Nonregular Shapes, In Proceedings of Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011), Lecture Notes in Computer Science (LNCS), Vol. 6892, pp. 368--375. 2011.
PubMed ID: 21995050
PubMed Central ID: PMC3346950
B. Erem, D.H. Brooks, P.M. van Dam, J.G. Stinstra, R.S. MacLeod. Spatiotemporal Estimation of Activation Times of Fractionated ECGs on Complex Heart Surfaces, In Proceedings of the International Coference of the IEEE Engineering in Medicine and Biology Society (EMBS), pp. 5884--5887. 2011.
PubMed ID: 22255678
PubMed Central ID: PMC3345888
B. Erem, P.M. van Dam, D.H. Brooks. Analysis of the Criteria of Activation-Based Inverse Electrocardiography using Convex Optimization, In Conf Proc IEEE Eng Med Biol Soc, pp. 3913–3916. 2011.
PubMed ID: 22255195
PubMed Central ID: PMC3359386
In inverse electrocardiography (ECG), the problem of finding activation times on the heart noninvasively from body surface potentials is typically formulated as a nonlinear least squares optimization problem. Current solutions rely on iterative algorithms which are sensitive to the presence of local minima. As a result, improved initialization approaches for this problem have been of considerable interest. However, in experiments conducted on a subject with Wolff-Parkinson-White syndrome, we have observed that there may be a mismatch between favorable solutions of the optimization problem and solutions with the desired physiological characteristics. In this work, we use a method based on a convex optimization framework to explore the solution space and analyze whether the optimization criteria target their intended objective.
B. Erem, D.H. Brooks. Differential Geometric Approximation of the Gradient and Hessian on a Triangulated Manifold, In Proceeding of the IEEE International Symposium on Biomedical Imaging: from nano to macro, pp. 504--507. 2011.
PubMed ID: 21712967
PubMed Central ID: PMC3122924
In a number of medical imaging modalities, including measurements or estimates of electrical activity on cortical or cardiac surfaces, it is often useful to estimate spatial derivatives of data on curved anatomical surfaces represented by triangulated meshes. Assuming the triangle vertices are points on a smooth manifold, we derive a method for estimating gradients and Hessians on locally 2D surfaces embedded in 3D directly in the global coordinate system. Accuracy of the method is validated through simulations on both smooth and corrugated surfaces.
T. Fogal, J. Krüger. Efficient I/O for Parallel Visualization, In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (2011), Edited by T. Kuhlen and R. Pajarola and K. Zhou, pp. 81--90. 2011.
Z. Fu, W.-K. Jeong, Y. Pan, R.M. Kirby, R.T. Whitaker. A fast iterative method for solving the Eikonal equation on triangulated surfaces, In SIAM Journal of Scientific Computing, Vol. 33, No. 5, pp. 2468--2488. 2011.
PubMed Central ID: PMC3360588
This paper presents an efficient, fine-grained parallel algorithm for solving the Eikonal equation on triangular meshes. The Eikonal equation, and the broader class of Hamilton–Jacobi equations to which it belongs, have a wide range of applications from geometric optics and seismology to biological modeling and analysis of geometry and images. The ability to solve such equations accurately and efficiently provides new capabilities for exploring and visualizing parameter spaces and for solving inverse problems that rely on such equations in the forward model. Efficient solvers on state-of-the-art, parallel architectures require new algorithms that are not, in many cases, optimal, but are better suited to synchronous updates of the solution. In previous work [W. K. Jeong and R. T. Whitaker, SIAM J. Sci. Comput., 30 (2008), pp. 2512–2534], the authors proposed the fast iterative method (FIM) to efficiently solve the Eikonal equation on regular grids. In this paper we extend the fast iterative method to solve Eikonal equations efficiently on triangulated domains on the CPU and on parallel architectures, including graphics processors. We propose a new local update scheme that provides solutions of first-order accuracy for both architectures. We also propose a novel triangle-based update scheme and its corresponding data structure for efficient irregular data mapping to parallel single-instruction multiple-data (SIMD) processors. We provide detailed descriptions of the implementations on a single CPU, a multicore CPU with shared memory, and SIMD architectures with comparative results against state-of-the-art Eikonal solvers.
B.M. Isaacson, J.G. Stinstra, R.D. Bloebaum, COL P.F. Pasquina, R.S. MacLeod. Establishing Multiscale Models for Simulating Whole Limb Estimates of Electric Fields for Osseointegrated Implants, In IEEE Transactions on Biomedical Engineering, Vol. 58, No. 10, pp. 2991--2994. 2011.
PubMed ID: 21712151
PubMed Central ID: PMC3179554
F. Jiao, Y. Gur, C.R. Johnson, S. Joshi. Detection of crossing white matter fibers with high-order tensors and rank-k decompositions, In Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI 2011), Lecture Notes in Computer Science (LNCS), Vol. 6801, pp. 538--549. 2011.
PubMed Central ID: PMC3327305
S. Kurugol, E. Bas, D. Erdogmus, J.G. Dy, G.C. Sharp, D.H. Brooks. Centerline extraction with principal curve tracing to improve 3D level set esophagus segmentation in CT images, In Proceedings of IEEE International Conference of the Engineering in Medicine and Biology Society (EMBS), pp. 3403--3406. 2011.
PubMed ID: 2225507
PubMed Central ID: PMC3349355
S. Kurugol, J.G. Dy, M. Rajadhyaksha, K.W. Gossage, J. Weissman, D.H. Brooks. Semi-automated Algorithm for Localization of Dermal/ Epidermal Junction in Reflectance Confocal Microscopy Images of Human Skin, In Proceedings of SPIE, Vol. 7904, pp. 79041A-79041A-10. 2011.
PubMed ID: 21709746
PubMed Central ID: PMC3120112
The examination of the dermis/epidermis junction (DEJ) is clinically important for skin cancer diagnosis. Reflectance confocal microscopy (RCM) is an emerging tool for detection of skin cancers in vivo. However, visual localization of the DEJ in RCM images, with high accuracy and repeatability, is challenging, especially in fair skin, due to low contrast, heterogeneous structure and high inter- and intra-subject variability. We recently proposed a semi-automated algorithm to localize the DEJ in z-stacks of RCM images of fair skin, based on feature segmentation and classification. Here we extend the algorithm to dark skin. The extended algorithm first decides the skin type and then applies the appropriate DEJ localization method. In dark skin, strong backscatter from the pigment melanin causes the basal cells above the DEJ to appear with high contrast. To locate those high contrast regions, the algorithm operates on small tiles (regions) and finds the peaks of the smoothed average intensity depth profile of each tile. However, for some tiles, due to heterogeneity, multiple peaks in the depth profile exist and the strongest peak might not be the basal layer peak. To select the correct peak, basal cells are represented with a vector of texture features. The peak with most similar features to this feature vector is selected. The results show that the algorithm detected the skin types correctly for all 17 stacks tested (8 fair, 9 dark). The DEJ detection algorithm achieved an average distance from the ground truth DEJ surface of around 4.7μm for dark skin and around 7-14μm for fair skin.
Keywords: confocal reflectance microscopy, image analysis, skin, classification
S. Kurugol, J.G. Dy, D.H. Brooks, M. Rajadhyaksha. Pilot study of semiautomated localization of the dermal/epidermal junction in reflectance confocal microscopy images of skin, In Journal of biomedical optics, Vol. 16, No. 3, International Society for Optics and Photonics, pp. 036005--036005. 2011.
Reflectance confocal microscopy (RCM) continues to be translated toward the detection of skin cancers in vivo. Automated image analysis may help clinicians and accelerate clinical acceptance of RCM. For screening and diagnosis of cancer, the dermal/epidermal junction (DEJ), at which melanomas and basal cell carcinomas originate, is an important feature in skin. In RCM images, the DEJ is marked by optically subtle changes and features and is difficult to detect purely by visual examination. Challenges for automation of DEJ detection include heterogeneity of skin tissue, high inter-, intra-subject variability, and low optical contrast. To cope with these challenges, we propose a semiautomated hybrid sequence segmentation/classification algorithm that partitions z-stacks of tiles into homogeneous segments by fitting a model of skin layer dynamics and then classifies tile segments as epidermis, dermis, or transitional DEJ region using texture features. We evaluate two different training scenarios: 1. training and testing on portions of the same stack; 2. training on one labeled stack and testing on one from a different subject with similar skin type. Initial results demonstrate the detectability of the DEJ in both scenarios with epidermis/dermis misclassification rates smaller than 10% and average distance from the expert labeled boundaries around 8.5 μm.
M. Leeser, D. Yablonski, D.H. Brooks, L.S. King. The Challenges of Writing Portable, Correct and High Performance Libraries for GPUs, In Computer Architecture News, Vol. 39, No. 4, pp. 2--7. 2011.
Graphics Processing Units (GPUs) are widely used to accelerate scientific applications. Many successes have been reported with speedups of two or three orders of magnitude over serial implementations of the same algorithms. These speedups typically pertain to a specific implementation with fixed parameters mapped to a specific hardware implementation. The implementations are not designed to be easily ported to other GPUs, even from the same manufacturer. When target hardware changes, the application must be re-optimized.
In this paper we address a different problem. We aim to deliver working, efficient GPU code in a library that is downloaded and run by many different users. The issue is to deliver efficiency independent of the individual user parameters and without a priori knowledge of the hardware the user will employ. This problem requires a different set of tradeoffs than finding the best runtime for a single solution. Solutions must be adaptable to a range of different parameters both to solve users' problems and to make the best use of the target hardware.
Another issue is the integration of GPUs into a Problem Solving Environment (PSE) where the use of a GPU is almost invisible from the perspective of the user. Ease of use and smooth interactions with the existing user interface are important to our approach. We illustrate our solution with the incorporation of GPU processing into the Scientific Computing Institute (SCI)Run Biomedical PSE developed at the University of Utah. SCIRun allows scientists to interactively construct many different types of biomedical simulations. We use this environment to demonstrate the effectiveness of the GPU by accelerating time consuming algorithms in the scientist's simulations. Specifically we target the linear solver module, including Conjugate Gradient, Jacobi and MinRes solvers for sparse matrices.
R.S. MacLeod, J.J.E. Blauer. Atrial Fibrillation, In Multimodal Cardiovascular Imaging: Principles and Clinical Applications, Ch. 25, Edited by O. Pahlm and G. Wagner, McGraw Hill, 2011.
Atrial fibrillation (AF) is the most common form of cardiac arrhythmia so that a review of the role imaging in AF is a natural topic to include in this book. Further motivation comes from the fact that the treatment of AF probably includes more different forms of imaging, often merged or combined in a variety of ways, than perhaps any other clinical intervention. A typical clinical electrophysiology lab for the treatment of AF usually contains no less than 6 and often more than 8 individual monitors, each rendering some form of image based information about the patient undergoing therapy. There is naturally great motivation to merge different images and different imaging modalities in the setting of AF but also very challenging because of a host of factors related to the small size, extremely thin walls, the large natural variation in atrial shape, and the fact that fibrillation is occurring so that atrial shape is changing rapidly and irregularly. Thus, the use of multimodal imaging has recently become a very active and challenging area of image processing and analysis research and development, driven by an enormous clinical need to understand and treat a disease that affects some 5 million Americans alone, a number that is predicted to increase to almost 16 million by 2050.
In this chapter we attempt to provide an overview of the large variety of imaging modalities and uses in the management and understanding of atrial fibrillation, with special emphasis on the most novel applications of magnetic resonance imaging (MRI) technology. To provide clinical and biomedical motivation, we outline the basics of the disease together with some contemporary hypotheses about its etiology and management. We then describe briefly the imaging modalities in common use in the management and research of AF, then focus on the use or MRI for all phases of the management of patients with AF and indicate some of the major engineering challenges that can motivate further progress.
Keywords: ablation, carma, cvrti, 5P41-RR012553-10