Center for Integrative Biomedical Computing

SCI Publications


T.J. Badger, M. Daccarett, N.W. Akoum, Y.A. Adjei-Poku, N.S. Burgon, T.S. Haslam, S. Kalvaitis, S. Kuppahally, G. Vergara, L. McMullen, P.A. Anderson, E. Kholmovski, R.S. Macleod, N.F. Marrouche. “Evaluation of left atrial lesions after initial and repeat atrial fibrillation ablation: lessons learned from delayed-enhancement MRI in repeat ablation procedures,” In Circulation. Arrhythmia and Electrophysiology, Vol. 3, No. 3, pp. 249--259. 2010.
PubMed ID: 20335558

J.J.E. Blauer, J. Cates, C.J. McGann, E.G. Kholmovski, A. Alexander, M.W. Prastawa, S. Joshi, N.F. Marrouche, R.S. MacLeod. “MRI Based Injury Characterization Immediately Following Ablation of Atrial Fibrillation,” In Computing in Cardiology, Vol. 37, pp. 165--168. 2010.
ISSN: 0276−6574

J.R. Bronson, J.A. Levine, R.T. Whitaker. “Particle Systems for Adaptive, Isotropic Meshing of CAD Models,” In Proceedings of the 19th International Meshing Roundtable, Note: Awarded Best Paper, Springer, pp. 279-296. 2010.
DOI: 10.1007/978-3-642-15414-0_17


We present a particle-based approach for generating adaptive triangular surface and tetrahedral volume meshes from CAD models. Input shapes are treated as a collection of smooth, parametric surface patches that can meet non-smoothly on boundaries. Our approach uses a hierarchical sampling scheme that places particles on features in order of increasing dimensionality. These particles reach a good distribution by minimizing an energy computed in 3D world space, with movements occurring in the parametric space of each surface patch.

Rather than using a pre-computed measure of feature size, our system automatically adapts to both curvature as well as a notion of topological separation. It also enforces a measure of smoothness on these constraints to construct a sizing field that acts as a proxy to piecewise-smooth feature size. We evaluate our technique with comparisons against other popular triangular meshing techniques for this domain.

K. Bürger, J. Krüger, R. Westermann. “Sample-based surface coloring,” In IEEE Transactions on Visualization and Computer Graphics (TVCG), Vol. 16, No. 5, pp. 763--776. Sept-Oct, 2010.
DOI: 10.1109/TVCG.2009.107
PubMed ID: 20616392
PubMed Central ID: PMC3170521


In this paper, we present a sample-based approach for surface coloring, which is independent of the original surface resolution and representation. To achieve this, we introduce the Orthogonal Fragment Buffer (OFB)-an extension of the Layered Depth Cube-as a high-resolution view-independent surface representation. The OFB is a data structure that stores surface samples at a nearly uniform distribution over the surface, and it is specifically designed to support efficient random read/write access to these samples. The data access operations have a complexity that is logarithmic in the depth complexity of the surface. Thus, compared to data access operations in tree data structures like octrees, data-dependent memory access patterns are greatly reduced. Due to the particular sampling strategy that is employed to generate an OFB, it also maintains sample coherence, and thus, exhibits very good spatial access locality. Therefore, OFB-based surface coloring performs significantly faster than sample-based approaches using tree structures. In addition, since in an OFB, the surface samples are internally stored in uniform 2D grids, OFB-based surface coloring can efficiently be realized on the GPU to enable interactive coloring of high-resolution surfaces. On the OFB, we introduce novel algorithms for color painting using volumetric and surface-aligned brushes, and we present new approaches for particle-based color advection along surfaces in real time. Due to the intermediate surface representation we choose, our method can be used to color polygonal surfaces as well as any other type of surface that can be sampled.

A.N.M. Imroz Choudhury, M.D. Steffen, J.E. Guilkey, S.G. Parker. “Enhanced Understanding of Particle Simulations Through Deformation-Based Visualization,” In Computer Modeling in Engineering & Sciences, Vol. 63, No. 2, pp. 117--136. 2010.

T. Fogal, J. Krüger. “Tuvok, an Architecture for Large Scale Volume Rendering,” In Proceedings of the 15th International Workshop on Vision, Modeling, and Visualization, pp. 139--146. November, 2010.
DOI: 10.2312/PE/VMV/VMV10/139-146

T. Fogal, H. Childs, S. Shankar, J. Krüger, R.D. Bergeron, P. Hatcher. “Large Data Visualization on Distributed Memory Multi-GPU Clusters,” In Proceedings of High Performance Graphics 2010, pp. 57--66. 2010.

S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R.T. Whitaker, the Alzheimers Disease Neuroimaging Initiative (ADNI). “Manifold modeling for brain population analysis,” In Medical Image Analysis, Special Issue on the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2009, Vol. 14, No. 5, Note: Awarded MICCAI 2010, Best of the Journal Issue Award, pp. 643--653. 2010.
ISSN: 1361-8415
DOI: 10.1016/
PubMed ID: 20579930

S. Gerber, P.-T. Bremer, V. Pascucci, R.T. Whitaker. “Visual Exploration of High Dimensional Scalar Functions,” In IEEE Transactions on Visualization and Computer Graphics, IEEE Transactions on Visualization and Computer Graphics, Vol. 16, No. 6, IEEE, pp. 1271--1280. Nov, 2010.
DOI: 10.1109/TVCG.2010.213
PubMed ID: 20975167
PubMed Central ID: PMC3099238

B.M. Isaacson, J.G. Stinstra, R.S. MacLeod, P.F. Pasquina, R.D. Bloebaum. “Developing a Quantitative Measurement System for Assessing Heterotopic Ossification and Monitoring the Bioelectric Metrics from Electrically Induced Osseointegration in the Residual Limb of Service Members,” In Annals of Biomedical Engineering, Vol. 38, No. 9, pp. 2968-–2978. 2010.
PubMed ID: 20458630

S.K. Iyer, E. DiBella, T. Tasdizen. “Edge enhanced spatio-temporal constrained reconstruction of undersampled dynamic contrast enhanced radial MRI,” In IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro, pp. 704--707. 2010.
DOI: 10.1109/ISBI.2010.5490077

F. Jiao, J.M. Phillips, J.G. Stinstra, J. Kueger, R. Varma, E. Hsu, J. Korenberg, C.R. Johnson. “Metrics for Uncertainty Analysis and Visualization of Diffusion Tensor Images,” In Proceedings of the 5th international conference on Medical imaging and augmented reality (MIAR), Beijing, China, Springer-Verlag, Berlin, Heidelberg pp. 179--190. September, 2010.

M. Jolley, J. Stinstra, J. Tate, S. Pieper, R.S. Macleod, L. Chu, P. Wang, J.K. Triedman. “Finite element modeling of subcutaneous implantable defibrillator electrodes in an adult torso,” In Heart Rhythm, Vol. 7, No. 5, pp. 692--698. May, 2010.
DOI: 10.1016/j.hrthm.2010.01.030
PubMed ID: 20230927
PubMed Central ID: PMC3103844


Total subcutaneous implantable subcutaneous defibrillators are in development, but optimal electrode configurations are not known.

We used image-based finite element models (FEM) to predict the myocardial electric field generated during defibrillation shocks (pseudo-DFT) in a wide variety of reported and innovative subcutaneous electrode positions to determine factors affecting optimal lead positions for subcutaneous implantable cardioverter-defibrillators (S-ICD).

An image-based FEM of an adult man was used to predict pseudo-DFTs across a wide range of technically feasible S-ICD electrode placements. Generator location, lead location, length, geometry and orientation, and spatial relation of electrodes to ventricular mass were systematically varied. Best electrode configurations were determined, and spatial factors contributing to low pseudo-DFTs were identified using regression and general linear models.

A total of 122 single-electrode/array configurations and 28 dual-electrode configurations were simulated. Pseudo-DFTs for single-electrode orientations ranged from 0.60 to 16.0 (mean 2.65 +/- 2.48) times that predicted for the base case, an anterior-posterior configuration recently tested clinically. A total of 32 of 150 tested configurations (21%) had pseudo-DFT ratios /=1, indicating the possibility of multiple novel, efficient, and clinically relevant orientations. Favorable alignment of lead-generator vector with ventricular myocardium and increased lead length were the most important factors correlated with pseudo-DFT, accounting for 70% of the predicted variation (R(2) = 0.70, each factor P < .05) in a combined general linear modl in which parameter estimates were calculated for each factor.

Further exploration of novel and efficient electrode configurations may be of value in the development of the S-ICD technologies and implant procedure. FEM modeling suggests that the choice of configurations that maximize shock vector alignment with the center of myocardial mass and use of longer leads is more likely to result in lower DFT.

J. Krüger. “A New Sampling Scheme for Slice Based Volume RenderingA new sampling scheme for slice based volume rendering,” In Proceedings of IEEE/EG International Symposium on Volume Graphics (2010), pp. 1--4. 2010.
DOI: 10.2312/VG/VG10/001-004


In this paper we present a novel approach to generate proxy geometry for slice based volume rendering. The basic idea is derived from the behavior of a ray-caster and is a simple extension of the well known 2D object-aligned texture stack based technique. From this our novel scheme inherits the advantage that it enables hardware-based volume rendering for devices that do not support 3D textures. On these devices previous object-aligned 2D texture based approaches suffered from disturbing view angle dependent stack-switching artifacts which are avoided by our novel method. Our approach also shows benefits compared to the widely used view aligned slicing algorithm as it avoids jagged boundary artifacts and increases performance.

S.S. Kuppahally, N. Akoum, N.S. Burgon, T.J. Badger, E.G. Kholmovski, S. Vijayakumar, S.N. Rao, J. Blauer, E.N. Fish, E.V. Dibella, R.S. Macleod, C. McGann, S.E. Litwin, N.F. Marrouche. “Left atrial strain and strain rate in patients with paroxysmal and persistent atrial fibrillation: relationship to left atrial structural remodeling detected by delayed-enhancement MRI,” In Circ Cardiovasc Imaging, Vol. 3, No. 3, pp. 231--239. 2010.
PubMed ID: 20133512

S.S. Kuppahally, N. Akoum, T.J. Badger, N.S. Burgon, T. Haslam, E. Kholmovski, R.S. Macleod, C. McGann, N.F. Marrouche. “Echocardiographic left atrial reverse remodeling after catheter ablation of atrial fibrillation is predicted by preablation delayed enhancement of left atrium by magnetic resonance imaging,” In American Heart Journal, Vol. 160, No. 5, pp. 877--884. 2010.
DOI: 10.1016/j.ahj.2010.07.003
PubMed ID: 21095275
PubMed Central ID: PMC2995281


Atrial fibrosis is a hallmark of atrial structural remodeling (SRM) and leads to structural and functional impairment of left atrial (LA) and persistence of atrial fibrillation (AF). This study was conducted to assess LA reverse remodeling after catheter ablation of AF in mild and moderate-severe LA SRM.

Catheter ablation was performed in 68 patients (age 62 ± 14 years, 68% males) with paroxysmal (n = 26) and persistent (n = 42) AF. The patients were divided into group 1 with mild LA SRM (10%, n = 37) by delayed enhancement magnetic resonance imaging (DEMRI). Two-dimensional echocardiography, LA strain, and strain rate during left ventricular systole by velocity vector imaging were performed pre and at 6 ± 3 months postablation. The long-term outcome was monitored for 12 months.

Patients in group 1 were younger (57 ± 15 vs 66 ± 13 years, P = .009) with a male predominance (80% vs 57%, P < .05) as compared to group 2. Postablation, group 1 had significant increase in average LA strain (??: 14% vs 4%, P < .05) and strain rate (??: 0.5 vs 0.1 cm/s, P < .05) as compared to group 2. There was a trend toward more patients with persistent AF in group 2 (68% vs 55%, P = .2), but it was not statistically significant. Group 2 had more AF recurrences (41% vs 16%, P = .02) at 12 months after ablation.

Mild preablation LA SRM by DEMRI predicts favorable LA structural and functional reverse remodeling and long-term success after catheter ablation of AF, irrespective of the paroxysmal or persistent nature of AF.

S. Kurugol, N. Ozay, J.G. Dy, G.C. Sharp, D.H. Brooks. “Locally Deformable Shape Model to Improve 3D Level Set based Esophagus Segmentation,” In Proceedings of the IAPR International Conference on Pattern Recognition, pp. 3955--3958. August, 2010.
PubMed ID: 21731883
PubMed Central ID: PMC3127393


In this paper we propose a supervised 3D segmentation algorithm to locate the esophagus in thoracic CT scans using a variational framework. To address challenges due to low contrast, several priors are learned from a training set of segmented images. Our algorithm first estimates the centerline based on a spatial model learned at a few manually marked anatomical reference points. Then an implicit shape model is learned by subtracting the centerline and applying PCA to these shapes. To allow local variations in the shapes, we propose to use nonlinear smooth local deformations. Finally, the esophageal wall is located within a 3D level set framework by optimizing a cost function including terms for appearance, the shape model, smoothness constraints and an air/contrast model.

J.A. Levine, D.J. Swenson, Z. Fu, R.S. MacLeod, R.T. Whitaker. “A Comparison of Delaunay Based Meshing Algorithms for Electrophysiological Cardiac Simulations,” In Virtual Physiological Human, pp. 181--183. 2010.

C. Mahnkopf, T.J. Badger, N.S. Burgon, M. Daccarett, T.S. Haslam, C.T. Badger, C.J. McGann, N. Akoum, E. Kholmovski, R.S. Macleod, N.F. Marrouche. “Evaluation of the left atrial substrate in patients with lone atrial fibrillation using delayed-enhanced MRI: implications for disease progression and response to catheter ablation,” In Heart Rhythm, Vol. 7, No. 10, pp. 1475--1481. 2010.
PubMed ID: 20601148

T.A. Pilcher, J.D. Tate, J.G. Stinstra, E.V. Saarel, M.D. Puchalski, and R.S. MacLeod. “Partially extracted defibrillator coils and pacing leads alter defibrillation thresholds,” In Proceedings of the 15th International Academy of Cardiology World Congress of Cardiology, 2010.