[Ath2019a] T. Athawale, C. R. Johnson.
**“Probabilistic Asymptotic Decider for Topological Ambiguity Resolution in Level-Set Extraction for Uncertain 2D Data,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 25, No. 1, IEEE, pp. 1163-1172. Jan, 2019.

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[Ath2019b] T. M. Athawale, K. A. Johnson, C. R. Butson, C. R. Johnson.
**“A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes,”** In *Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization*, Vol. 7, No. 4, Taylor & Francis, pp. 438-449. 2019.

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[Han2019a] M. Han, I. Wald, W. Usher, Q. Wu, F. Wang, V. Pascicci, C. D. Hansen, C. R. Johnson.
**“Ray Tracing Generalized Tube Primitives: Method and Applications,”** In *Computer Graphics Forum*, Vol. 38, No. 3, John Wiley & Sons Ltd., 2019.

[Joh2019a] K. A. Johnson, P. T. Fletcher, D. Servello, A. Bona, M. Porta, J. L. Ostrem, E. Bardinet, M. Welter, A. M. Lozano, J. C. Baldermann, J. Kuhn, D. Huys, T. Foltynie, M. Hariz, E. M. Joyce, L. Zrinzo, Z. Kefalopoulou, J. Zhang, F. Meng, C. Zhang, Z. Ling, X. Xu, X. Yu, A. YJM Smeets, L. Ackermans, V. Visser-Vandewalle, A. Y. Mogilner, M. H. Pourfar, L. Almeida, A. Gunduz, W. Hu, K. D. Foote, M. S. Okun, C. R. Butson.
**“Image-based analysis and long-term clinical outcomes of deep brain stimulation for Tourette syndrome: a multisite study,”** In *Journal of Neurology, Neurosurgery & Psychiatry*, BMJ Publishing Group, 2019.

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[War2019a] A. Warner, J. Tate, B. Burton,, C.R. Johnson.
**“A High-Resolution Head and Brain Computer Model for Forward and Inverse EEG Simulation,”** In *bioRxiv*, Cold Spring Harbor Laboratory, Feb, 2019.

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**“Optimized programming algorithm for cylindrical and directional deep brain stimulation electrodes,”** In *Journal of Neural Engineering*, Vol. 15, No. 2, pp. 026005. 2018.

[Ath2018a] T. M. Athawale, K. A. Johnson, C. R. Butson, C. R. Johnson.
**“A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes,”** In *Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization*, Taylor & Francis, pp. 1-12. 2018.

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[Bur2018a] B.M. Burton, K.K. Aras, W.W. Good, J.D. Tate, B. Zenger, R.S. MacLeod.
**“A Framework for Image-Based Modeling of Acute Myocardial Ischemia Using Intramurally Recorded Extracellular Potentials,”** In *Annals of Biomedical Engineering*, Springer Nature, May, 2018.

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[Bur2018b] B.M. Burton, K.K. Aras, W.W. Good, J.D. Tate, B. Zenger, R.S. MacLeod.
**“Image-Based Modeling of Acute Myocardial Ischemia Using Experimentally Derived Ischemic Zone Source Representations,”** In *Journal of Electrocardiology*, Vol. 51, No. 4, Elsevier BV, pp. 725--733. July, 2018.

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[Clu2018a] M.J.M. Cluitmans, S. Ghimire, J. Dhamala, J. Coll-Font, J.D. Tate, S. Giffard-Roisin, J. Svehlikova, O. Doessel, M.S. Guillem, D.H. Brooks, R.S. Macleod, L. Wang.
**“P1125 Noninvasive localization of premature ventricular complexes: a research-community-based approach,”** In *EP Europace*, Vol. 20, No. Supplement, Oxford University Press, March, 2018.

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[Clu2018b] M. Cluitmans, D. H. Brooks, R. MacLeod, O. Dössel, M. S. Guillem, P. M. van Dam, J. Svehlikova, B. He, J. Sapp, L. Wang, L. Bear.
**“Validation and Opportunities of Electrocardiographic Imaging: From Technical Achievements to Clinical Applications,”** In *Frontiers in Physiology*, Vol. 9, Frontiers Media SA, pp. 1305. 2018.

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[Jan2018a] A. Janson, C. Butson.
**“Targeting Neuronal Fiber Tracts for Deep Brain Stimulation Therapy Using Interactive, Patient-Specific Models,”** In *Journal of Visualized Experiments*, No. 138, MyJove Corporation, Aug, 2018.

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**“Deep brain stimulation for the treatment of disorders of consciousness and cognition in traumatic brain injury patients: a review,”** In *Neurosurgical Focus*, Vol. 45, No. 2, Journal of Neurosurgery Publishing Group (JNSPG), pp. E14. Aug, 2018.

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[Pra2018a] A. Prakosa, H. J. Arevalo, D. Deng, P. M. Boyle, P. P. Nikolov, H. Ashikaga, J. J. E. Blauer, E. Ghafoori, C. J. Park, R. C. Blake, F. T. Han, R. S. MacLeod, H. R. Halperin, D. J. Callans, R. Ranjan, J. Chrispin, S. Nazarian, N. A. Trayanova.
**“Personalized virtual-heart technology for guiding the ablation of infarct-related ventricular tachycardia,”** In *Nature Biomedical Engineering*, Springer Nature America, Inc, September, 2018.

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[Rod2018a] A. Rodenhauser, W.W. Good, B. Zenger, J. Tate, K. Aras, B. Burton, R.S. Macleod.
**“PFEIFER: Preprocessing Framework for Electrograms Intermittently Fiducialized from Experimental Recordings,”** In *The Journal of Open Source Software*, Vol. 3, No. 21, The Open Journal, pp. 472. Jan, 2018.

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**“Higher contact force during radiofrequency ablation leads to a much larger increase in edema as compared to chronic lesion size,”** In *Journal of Cardiovascular Electrophysiology*, Wiley, June, 2018.

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[Xio2018a] Z. Xiong, V. V. Fedorov, X. Fu, E. Cheng, R. Macleod, J. Zhao.
**“Fully Automatic Left Atrium Segmentation from Late Gadolinium Enhanced Magnetic Resonance Imaging Using a Dual Fully Convolutional Neural Network,”** In *IEEE Transactions on Medical Imaging*, IEEE, pp. 1--1. 2018.

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**“Shape analysis of the basioccipital bone in Pax7-deficient mice,”** In *Scientific Reports*, Vol. 7, No. 1, Springer Nature, Dec, 2017.

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[Col2017a] J. Coll-Font, S. Ariafar, D. H Brooks.
**“ECG-Based Reconstruction of Heart Position and Orientation with Bayesian Optimization,”** In *Computing in Cardiology*, Vol. 44, 2017.

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**“Characterization of Gadolinium Contrast Enhancement of Radiofrequency Ablation Lesions in Predicting Edema and Chronic Lesion Size,”** In *Circulation: Arrhythmia and Electrophysiology*, Vol. 10, No. 11, Ovid Technologies (Wolters Kluwer Health), pp. e005599. Oct, 2017.

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**“Overcoming Barriers to Quantification and Comparison of Electrocardiographic Imaging Methods: A Community-Based Approach,”** In *Computing in Cardiology*, Vol. 44, 2017.

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**“Detecting Ischemic Stress to the Myocardium Using Laplacian Eigenmaps and Changes to Conduction Velocity,”** In *Computing in Cardiology*, Vol. 44, IEEE, 2017.

[Ker2017a] M. Kern, A. Lex, N. Gehlenborg, C. R. Johnson.
**“Interactive Visual Exploration And Refinement Of Cluster Assignments,”** In *BMC Bioinformatics*, Cold Spring Harbor Laboratory, April, 2017.

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[Tat2017a] J. Tate, K. Gillette, B. Burton, W. Good, J. Coll-Font, D. Brooks, R. MacLeod.
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**“Uncertainty Footprint: Visualization of Nonuniform Behavior of Iterative Algorithms Applied to 4D Cell Tracking,”** In *Computer Graphics Forum*, Wiley, 2017.

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**“FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis,”** In *BMC Bioinformatics*, Vol. 18, No. 1, Springer Nature, May, 2017.

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[Ara2016a] K. Aras B. Burton, D. Swenson, R.S. MacLeod.
**“Spatial organization of acute myocardial ischemia,”** In *Journal of Electrocardiology*, Vol. 49, No. 3, Elsevier, pp. 323–336. May, 2016.

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**“Quantitative comparison of cortical bone thickness using correspondence-based shape modeling in patients with cam femoroacetabular impingement,”** In *Journal of Orthopaedic Research*, Wiley-Blackwell, Nov, 2016.

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**“Robust modulation of arousal regulation, performance, and frontostriatal activity through central thalamic deep brain stimulation in healthy nonhuman primates,”** In *Journal of Neurophysiology*, Vol. 116, No. 5, American Physiological Society, pp. 2383--2404. Aug, 2016.

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**“Optimal parameter map estimation for shape representation: A generative approach,”** In *2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)*, IEEE, pp. 660--663. April, 2016.

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**“Extensions to a manifold learning framework for time-series analysis on dynamic manifolds in bioelectric signals,”** In *Physical Review E*, Vol. 93, No. 4, American Physical Society, apr, 2016.

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**“The role of blood vessels in high-resolution volume conductor head modeling of EEG,”** In *NeuroImage*, Vol. 128, Elsevier, pp. 193--208. March, 2016.

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**“Alternating Current Stimulation for Vision Restoration after Optic Nerve Damage: A Randomized Clinical Trial,”** In *PLOS ONE*, Vol. 11, No. 6, Public Library of Science, pp. e0156134. June, 2016.

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**“Optimization of focality and direction in dense electrode array transcranial direct currentstimulation (tDCS),”** In *Journal of Neural Engineering*, Vol. 13, No. 3, IOP Publishing, pp. 036020. May, 2016.

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**“Increased Susceptibility to Atrial Fibrillation Secondary to Atrial Fibrosis in Transgenic Goats Expressing Transforming Growth Factor-β1,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 27, No. 10, Wiley-Blackwell, pp. 1220--1229. Aug, 2016.

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**“Evaluating Shape Alignment via Ensemble Visualization,”** In *IEEE Computer Graphics and Applications*, Vol. 36, No. 3, IEEE, pp. 60--71. May, 2016.

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**“muView: A Visual Analysis System for Exploring Uncertainty in Myocardial Ischemia Simulations,”** In *Visualization in Medicine and Life Sciences III*, Springer Nature, pp. 49--69. 2016.

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**“View-Dependent Streamline Deformation and Exploration,”** In *Transactions on Visualization and Computer Graphics*, Vol. 22, No. 7, IEEE, pp. 1788--1801. July, 2016.

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**“Experimental Data and Geometric Analysis Repository: EDGAR,”** In *Journal of Electrocardiology*, 2015.

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**“A Kalman Filtering Perspective for Multiatlas Segmentation,”** In *SIAM J. Imaging Sciences*, Vol. 8, No. 2, pp. 1007-1029. 2015.

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[Map3d] CIBC.
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**“Virtual Electrophysiological Study of Atrial Fibrillation in Fibrotic Remodeling,”** In *PLoS ONE*, Vol. 10, No. 2, pp. e0117110. February, 2015.

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[SCIRun] SCI Institute.
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**“Sensitivity and Specificity of Substrate Mapping: An In Silico Framework for the Evaluation of Electroanatomical Substrate Mapping Strategies,”** In *Journal of Cardiovascular Electrophysiology*, In *Journal of Cardiovascular Electrophysiology*, Vol. 25, No. 7, Note: *Featured on journal cover.*, pp. 774--780. May, 2014.

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**“Lattice cleaving: a multimaterial tetrahedral meshing algorithm with guarantees,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, pp. 223--237. 2014.

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**“Visualizing Simulated Electrical Fields from Electroencephalography and Transcranial Electric Brain Stimulation: A Comparative Evaluation,”** In *Neuroimage*, 2014.

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**“Identifying model inaccuracies and solution uncertainties in noninvasive activation-based imaging of cardiac excitation using convex relaxation,”** In *IEEE Trans Med Imaging*, Vol. 33, No. 4, pp. 902--912. 2014.

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**“Using transmural regularization and dynamic modeling for noninvasive cardiac potential imaging of endocardial pacing with imprecise thoracic geometry,”** In *IEEE Trans Med Imaging*, Vol. 33, No. 3, pp. 726--738. 2014.

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**“Generalized HARDI Invariants by Method of Tensor Contraction,”** In *Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 718--721. April, 2014.

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**“Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization,”** Mathematics and Visualization, Springer, 2014.

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**“Automated Delineation of Dermal-Epidermal Junction In Reflectance Confocal Microscopy Image Stacks Of Human Skin,”** In *Journal of Investigative Dermatology*, September, 2014.

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**“Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI,”** In *Circ Arrhythm Electrophysiol*, Vol. 7, No. 1, pp. 23--30. 2014.

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**“Assessment of regularization techniques for electrocardiographic imaging,”** In *Journal of electrocardiology*, Vol. 47, No. 1, pp. 20--28. 2014.

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**“Comparison of Left Atrial Area Marked Ablated in Electroanatomical Maps with Scar in MRI,”** In *Journal of Cardiovascular Electrophysiology*, 2014.

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**“Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. PP, No. 99, pp. 1--1. 2014.

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**“Accelerated learning-based interactive image segmentation using pairwise constraints,”** In *IEEE Transactions on Medical Image Processing*, Vol. 23, No. 7, pp. 3057-3070. July, 2014.

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**“Uncertainty Visualization in Forward and Inverse Cardiac Models,”** In *Computing in Cardiology CinC*, pp. 57--60. 2013.

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**“Evaluation of Interactive Visualization on Mobile Computing Platforms for Selection of Deep Brain Stimulation Parameters,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 19, No. 1, pp. 108--117. January, 2013.

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**“An inverse spectral method to localize discordant alternans regions on the heart from body surface measurements,”** In *Functional Imaging and Modeling of the Heart*, pp. 241--248. 2013.

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**“Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI,”** In *IEEE Transactions on Medical Imaging*, Vol. 33, No. 2, pp. 384--399. 2013.

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**“Geodesic distances to landmarks for dense correspondence on ensembles of complex shapes,”** In *Proceedings of Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011)*, Vol. 16(Pt. 2), pp. 19--26. 2013.

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**“Chronic atrial fibrillation causes left ventricular dysfunction in dogs but not goats: experience with dogs, goats, and pigs,”** In *American Journal of Physiology: Heart and Circulatory Physiology*, Vol. 305, No. 5, pp. H725--H731. September, 2013.

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[Ere2013a] B. Erem, J. Coll-Font, R.M. Orellana, P. Stovicek, D.H. Brooks, R.S. MacLeod.
**“Noninvasive reconstruction of potentials on endocardial surface from body surface potentials and CT imaging of partial torso,”** In *Journal of Electrocardiology*, Vol. 46, No. 4, pp. e28. 2013.

DOI: 10.1016/j.jelectrocard.2013.05.104

[Ere2013b] B. Erem, R.M. Orellana, P. Stovicek, D.H. Brooks, R.S. MacLeod.
**“Improved averaging of multi-lead ECGs and electrograms,”** In *Journal of Electrocardiology*, Vol. 46, No. 4, Elsevier, pp. e28. July, 2013.

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[Fog2013a] T. Fogal, A. Schiewe, J. Krüger.
**“An Analysis of Scalable GPU-Based Ray-Guided Volume Rendering,”** In *2013 IEEE Symposium on Large Data Analysis and Visualization (LDAV)*, 2013.

[Gar2013a] G. Gardner, A. Morris, K. Higuchi, R.S. MacLeod, J. Cates.
**“A Point-Correspondence Approach to Describing the Distribution of Image Features on Anatomical Surfaces, with Application to Atrial Fibrillation,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 226--229. 2013.

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[Gru2013a] J. Grüninger, J. Krüger.
**“The impact of display bezels on stereoscopic vision for tiled displays,”** In *Proceedings of the 19th ACM Symposium on Virtual Reality Software and Technology (VRST)*, pp. 241--250. 2013.

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[Ham2013a] D.K. Hammond, Y. Gur, C.R. Johnson.
**“Graph Diffusion Distance: A Difference Measure for Weighted Graphs Based on the Graph Laplacian Exponential Kernel,”** In *Proceedings of the IEEE global conference on information and signal processing (GlobalSIP'13)*, Austin, Texas, pp. 419--422. 2013.

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[Hao2013a] X. Hao, P.T. Fletcher.
**“Joint Fractional Segmentation and Multi-Tensor Estimation in Diffusion MRI,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), pp. (accepted). 2013.

[Har2013a] M.D. Harris, S.P. Reese, C.L. Peters, J.A. Weiss, A.E. Anderson.
**“Three-dimensional Quantification of Femoral Head Shape in Controls and Patients with Cam-type Femoroacetabular Impingement,”** In *Annals of Biomedical Engineering*, Vol. 41, No. 6, pp. 1162--1171. 2013.

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[Har2013b] M.D. Harris, M. Datar, R.T. Whitaker, E.R. Jurrus, C.L. Peters, A.E. Anderson.
**“Statistical Shape Modeling of Cam Femoroacetabular Impingement,”** In *Journal of Orthopaedic Research*, Vol. 31, No. 10, pp. 1620--1626. 2013.

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[Her2013a] H. Hernandez, J. Knezevic, T. Fogal, T. Sherman, T. Jevremovic.
**“Visual numerical steering in 3D AGENT code system for advanced nuclear reactor modeling and design,”** In *Annals of Nuclear Energy*, Vol. 55, pp. 248--257. 2013.

[Hig2013a] K. Higuchi, M. Akkaya, M. Koopmann, J.J. Blauer, N.S. Burgon, K. Damal, R. Ranjan, E. Kholmovski, R.S. Macleod, N.F. Marrouche..
**“The Effect of Fat Pad Modification during Ablation of Atrial Fibrillation: Late Gadolinium Enhancement MRI Analysis,”** In *Pacing and Clinical Electrophysiology (PACE)*, Vol. 36, No. 4, pp. 467--476. April, 2013.

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PubMed ID: 23356963

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[Jia2013a] F. Jiao, J.M. Phillips, Y. Gur, C.R. Johnson.
**“Uncertainty Visualization in HARDI based on Ensembles of ODFs,”** In *Proceedings of 2013 IEEE Pacific Visualization Symposium*, pp. 193--200. 2013.

PubMed ID: 24466504

PubMed Central ID: PMC3898522

[Joh2013a] C.R. Johnson, A. Pang (Eds.).
**“International Journal for Uncertainty Quantification,”** Subtitled **“Special Issue on Working with Uncertainty: Representation, Quantification, Propagation, Visualization, and Communication of Uncertainty,”** In *Int. J. Uncertainty Quantification*, Vol. 3, No. 2, Begell House, Inc., pp. vii--viii. 2013.

ISSN: 2152-5080

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[Joh2013b] C.R. Johnson, A. Pang (Eds.).
**“International Journal for Uncertainty Quantification,”** Subtitled **“Special Issue on Working with Uncertainty: Representation, Quantification, Propagation, Visualization, and Communication of Uncertainty,”** In *Int. J. Uncertainty Quantification*, Vol. 3, No. 3, Begell House, Inc., 2013.

ISSN: 2152-5080

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[Jon2013b] C. Jones, M. Seyedhosseini, M. Ellisman, T. Tasdizen.
**“Neuron Segmentation in Electron Microscopy Images Using Partial Differential Equations,”** In *Proceedings of 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1457--1460. April, 2013.

DOI: 10.1109/ISBI.2013.6556809

[Jon2013c] K.B. Jones, M. Datar, S. Ravichandran, H. Jin, E. Jurrus, R.T. Whitaker, M.R. Capecchi.
**“Toward an Understanding of the Short Bone Phenotype Associated with Multiple Osteochondromas,”** In *Journal of Orthopaedic Research*, Vol. 31, No. 4, pp. 651--657. 2013.

DOI: 10.1002/jor.22280

PubMed ID: 23192691

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[Mcd2013a] K.S. McDowell, F. Vadakkumpadan, R. Blake, J. Blauer, G.t Plank, R.S. MacLeod, N.A. Trayanova.
**“Mechanistic Inquiry into the Role of Tissue Remodeling in Fibrotic Lesions in Human Atrial Fibrillation,”** In *Biophysical Journal*, Vol. 104, pp. 2764--2773. 2013.

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PubMed ID: 23790385

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[Mcg2013a] C. McGann, N. Akoum, A. Patel, E. Kholmovski, P. Revelo, K. Damal, B. Wilson, J. Cates, A. Harrison, R. Ranjan, N.S. Burgon, T. Greene, D. Kim, E.V.R. DiBella, D. Parker, R.S. MacLeod, N.F. Marrouche.
**“Atrial Fibrillation Ablation Outcome is Predicted by Left Atrial Remodeling on MRI,”** In *Circulation: Arrhythmia and Electrophysiology*, Note: *Published online before print.*, December, 2013.

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[Ore2013a] R.M. Orellana, B. Erem, D.H. Brooks.
**“Time invariant multi electrode averaging for biomedical signals,”** In *Proceedings of the 2013 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)*, pp. 1242--1246. 2013.

ISSN: 1520-6149

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[Sou2013a] J. Sourati, D.H. Brooks, J.G. Dy, E. Erdogmus.
**“Constrained Spectral Clustering for Image Segmentation,”** In *IEEE International Workshop on Machine Learning for Signal Processing*, pp. 1--6. 2013.

DOI: 10.1109/MLSP

[Sou2013b] J. Sourati, K. Kose, M. Rajadhyaksha, J.G. Dy, D. Erdogmus, D.H. Brooks.
**“Automated localization of wrinkles and the dermo-epidermal junction in obliquely oriented reflectance confocal microscopic images of human skin,”** In *Proc. SPIE 8565, Photonic Therapeutics and Diagnostics IX*, Vol. 8565, 2013.

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[Ven2013a] G. Veni, Z. Fu, S.P. Awate, R.T. Whitaker.
**“Proper Ordered Meshing of Complex Shapes and Optimal Graph Cuts Applied to Atrial-Wall Segmentation from DE-MRI,”** In *Proceedings of the 2013 IEEE 10th International Symposium on Biomedical Imaging (ISBI)*, pp. 1296--1299. 2013.

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[Ven2013b] G. Veni, S. Awate, Z. Fu, R.T. Whittaker.
**“Bayesian Segmentation of Atrium Wall using Globally-Optimal Graph Cuts on 3D Meshes,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), Vol. 23, pp. 656--677. 2013.

PubMed ID: 24684007

[Wan2013b] D. Wang, R.M. Kirby, R.S. MacLeod, C.R. Johnson.
**“Inverse Electrocardiographic Source Localization of Ischemia: An Optimization Framework and Finite Element Solution,”** In *Journal of Computational Physics*, Vol. 250, Academic Press, pp. 403--424. 2013.

ISSN: 0021-9991

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[Wan2013f] Y. Wan.
**“Fluorender, An Interactive Tool for Confocal Microscopy Data Visualization and Analysis,”** Note: *Ph.D. Thesis*, *School of Computing, University of Utah*, June, 2013.

[Zhu2013a] X. Zhu, Y. Gur, W. Wang, P.T. Fletcher.
**“Model Selection and Estimation of Multi-Compartment Models in Diffusion MRI with a Rician Noise Model,”** In *Proceedings of the International Conference on Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LNCS), Vol. 23, pp. 644--655. 2013.

PubMed ID: 24684006

[Ako2012a] N.W. Akoum, C.J. McGann, G. Vergara, T. Badger, R. Ranjan, C. Mahnkopf, E.G. Kholmovski, R.S. Macleod, N.F. Marrouche.
**“Atrial Fibrosis Quantified Using Late Gadolinium Enhancement MRI is AssociatedWith Sinus Node Dysfunction Requiring Pacemaker Implant,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 23, No. 1, pp. 44--50. 2012.

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[Awa2012a] S.P. Awate, P. Zhu, R.T. Whitaker.
**“How Many Templates Does It Take for a Good Segmentation?: Error Analysis in Multiatlas Segmentation as a Function of Database Size,”** In *Int. Workshop Multimodal Brain Image Analysis (MBIA) at Int. Conf. MICCAI*, Lecture Notes in Computer Science (LNCS), Vol. 2, Note: *Recieved Best Paper Award*, pp. 103--114. 2012.

PubMed ID: 24501720

PubMed Central ID: PMC3910563

[Bro2012c] J.R. Bronson, J.A. Levine, R.T. Whitaker.
**“Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality,”** In *Proceedings of the 21st International Meshing Roundtable*, pp. 191--209. 2012.

[Bro2012d] J.R. Bronson, J.A. Levine, R.T. Whitaker.
**“Particle Systems for Adaptive, Isotropic Meshing of CAD Models,”** In *Engineering with Computers*, Vol. 28, No. 4, pp. 331--344. 2012.

PubMed ID: 23162181

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[But2012a] C. Butson, G. Tamm, S. Jain, T. Fogal, J. Krüger.
**“Evaluation of Interactive Visualization on Mobile Computing Platforms for Selection of Deep Brain Stimulation Parameters,”** In *IEEE Transactions on Visualization and Computer Graphics*, pp. (accepted). 2012.

ISSN: 1077-2626

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[Cho2012a] A.N.M. Imroz Choudhury, Bei Wang, P. Rosen, V. Pascucci.
**“Topological Analysis and Visualization of Cyclical Behavior in Memory Reference Traces,”** In *Proceedings of the IEEE Pacific Visualization Symposium (PacificVis 2012)*, pp. 9--16. 2012.

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[Dan2012a] M. Dannhauer, D.H. Brooks, D. Tucker, R.S. MacLeod.
**“A pipeline for the simulation of transcranial direct current stimulation for realistic human head models using SCIRun/BioMesh3D,”** In *Proceedings of the 2012 IEEE Int. Conf. Engineering and Biology Society (EMBC)*, pp. 5486--5489. 2012.

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PubMed ID: 23367171

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[Dat2012a] M. Datar, P. Muralidharan, A. Kumar, S. Gouttard, J. Piven, G. Gerig, R.T. Whitaker, P.T. Fletcher.
**“Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy,”** In *Spatio-temporal Image Analysis for Longitudinal and Time-Series Image Data*, Lecture Notes in Computer Science, Vol. 7570, Springer Berlin / Heidelberg, pp. 76--87. 2012.

ISBN: 978-3-642-33554-9

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[Ere2012a] B. Erem, P. Stovicek, D.H. Brooks.
**“Manifold learning for analysis of low-order nonlinear dynamics in high-dimensional electrocardiographic signals,”** In *Proceedings of the 9th IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 844--847. 2012.

DOI: 10.1109/ISBI.2012.6235680

[Gol2012a] F.N. Golabchi, D.H. Brooks.
**“Axon segmentation in microscopy images - A graphical model based approach,”** In *Proceedings of the 9th IEEE International Symposium on Biomedical Imaging (ISBI)*, pp. 756-759. 2012.

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[Gur2012a] Y. Gur, F. Jiao, S.X. Zhu, C.R. Johnson.
**“White matter structure assessment from reduced HARDI data using low-rank polynomial approximations,”** In *Proceedings of MICCAI 2012 Workshop on Computational Diffusion MRI (CDMRI12)*, Nice, France, Lecture Notes in Computer Science (LNCS), pp. 186-197. October, 2012.

[Joh2012a] C.R. Johnson.
**“Biomedical Visual Computing: Case Studies and Challenges,”** In *IEEE Computing in Science and Engineering*, Vol. 14, No. 1, pp. 12--21. 2012.

PubMed ID: 22545005

PubMed Central ID: PMC3336198

[Kne2012a] J. Knezevic, R.-P. Mundani, E. Rank, A. Khan, C.R. Johnson.
**“Extending the SCIRun Problem Solving Environment to Large-Scale Applications,”** In *Proceedings of Applied Computing 2012*, *IADIS*, pp. 171--178. October, 2012.

[Kur2012a] S. Kurugol, M. Rajadhyaksha, J.G. Dy, D.H. Brooks.
**“Validation study of automated dermal/epidermal junction localization algorithm in reflectance confocal microscopy images of skin,”** In *Proceedings of SPIE Photonic Therapeutics and Diagnostics VIII*, Vol. 8207, No. 1, pp. 820702-820711. 2012.

DOI: 10.1117/12.909227

PubMed ID: 24376908

PubMed Central ID: PMC3872972

[Mcd2012a] K.S. McDowell, F. Vadakkumpadan, R. Blake, J. Blauer, G. Plank, R.S. MacLeod, N.A. Trayanova.
**“Methodology for patient-specific modeling of atrial fibrosis as a substrate for atrial fibrillation,”** In *Journal of Electrocardiology*, Vol. 45, No. 6, pp. 640--645. 2012.

DOI: 10.1016/j.jelectrocard.2012.08.005

PubMed ID: 22999492

PubMed Central ID: PMC3515859

[Men2012c] Q. Meng, J. Hall, H. Rutigliano, X. Zhou, B.R. Sessions, R. Stott, K. Panter, C.J. Davies, R. Ranjan, D. Dosdall, R.S. MacLeod, N. Marrouche, K.L. White, Z. Wang, I.A. Polejaeva.
**“30 Generation of Cloned Transgenic Goats with Cardiac Specific Overexpression of Transforming Growth Factor β1,”** In *Reproduction, Fertility and Development*, Vol. 25, No. 1, pp. 162--163. 2012.

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[Pan2012a] B. Paniagua, L. Bompard, J. Cates, R.T. Whitaker, M. Datar, C. Vachet, M. Styner.
**“Combined SPHARM-PDM and entropy-based particle systems shape analysis framework,”** In *Medical Imaging 2012: Biomedical Applications in Molecular, Structural, and Functional Imaging*, SPIE Intl Soc Optical Eng, March, 2012.

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PubMed ID: 24027625

PubMed Central ID: PMC3766973

[Per2012a] D. Perry, A. Morris, N. Burgon, C. McGann, R.S. MacLeod, J. Cates.
**“Automatic classification of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation,”** In *SPIE Proceedings*, Vol. 8315, pp. (published online). 2012.

DOI: 10.1117/12.910833

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[Pot2012a] K. Potter, R.M. Kirby, D. Xiu, C.R. Johnson.
**“Interactive visualization of probability and cumulative density functions,”** In *International Journal of Uncertainty Quantification*, Vol. 2, No. 4, pp. 397--412. 2012.

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[Pot2012b] K. Potter, P. Rosen, C.R. Johnson.
**“From Quantification to Visualization: A Taxonomy of Uncertainty Visualization Approaches,”** In *Uncertainty Quantification in Scientific Computing*, IFIP Advances in Information and Communication Technology Series, Vol. 377, Edited by Andrew Dienstfrey and Ronald Boisvert, Springer, pp. 226--249. 2012.

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[Pra2012a] M.W. Prastawa, S.P. Awate, G. Gerig.
**“Building Spatiotemporal Anatomical Models using Joint 4-D Segmentation, Registration, and Subject-Speci fic Atlas Estimation,”** In *Proceedings of the 2012 IEEE Mathematical Methods in Biomedical Image Analysis (MMBIA) Conference*, pp. 49--56. 2012.

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[Ran2012a] R. Ranjan, E.G. Kholmovski, J. Blauer, S. Vijayakumar, N.A. Volland, M.E. Salama, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“Identification and Acute Targeting of Gaps in Atrial Ablation Lesion Sets Using a Real-Time Magnetic Resonance Imaging System,”** In *Circulation: Arrhythmia and Electrophysiology*, Vol. 5, pp. 1130--1135. 2012.

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[Ros2012a] P. Rosen, V. Popescu.
**“Simplification of Node Position Data for Interactive Visualization of Dynamic Datasets,”** In *IEEE Transactions on Visualization and Computer Graphics (IEEE Visweek 2012 TVCG Track)*, pp. 1537--1548. 2012.

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[Ros2012b] P. Rosen.
**“Rectilinear Texture Warping for Fast Adaptive Shadow Mapping,”** In *Proceedings of the ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games (I3D '12)*, pp. 151--158. 2012.

[Zhu2012a] 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.

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[Ako2011a] 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.

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[And2011c] 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.

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[Bur2011a] 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.

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[Cho2011a] 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.

[Dac2011a] 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

[Dac2011b] 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

[Dat2011a] 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.

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[Ere2011a] 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.

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[Ere2011b] 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.

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[Ere2011c] 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.

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[Fog2011a] 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.

[Fu2011a] 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.

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[Isa2011a] 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.

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[Jia2011b] 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.

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PubMed Central ID: PMC3327305

[Kur2011a] 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.

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[Kur2011b] 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.

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[Kur2011c] 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.

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[Lee2011a] 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.

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[Mac2011a] 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.

ISBN: 0071613463

[Mad2011a] M.Q. Madrigal, G. Tadmor, G. C. Cano, D.H. Brooks.
**“Low-Order 4D Dynamical Modeling of Heart Motion Under Respiration,”** In *Proceeding of the IEEE International Symposium on Biomedical Imaging: from nano to macro*, pp. 1326--1329. 2011.

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**“Dark Regions of No-Reflow on Late Gadolinium Enhancement Magnetic Resonance Imaging Result in Scar Formation After Atrial Fibrillation Ablation,”** In *Journal of the American College of Cardiology*, Vol. 58, No. 2, pp. 177--185. 2011.

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**“Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): Standardised reporting for model reproducibility, interoperability, and data sharing,”** In *Progress in Biophysics and Molecular Biology*, Vol. 107, No. 1, Elsevier, pp. 4--10. October, 2011.

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**“Cardiac Position Sensitivity Study in the Electrocardiographic Forward Problem Using Stochastic Collocation and Boundary Element Methods,”** In *Annals of Biomedical Engineering*, Vol. 39, No. 12, pp. 2900--2910. 2011.

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**“ZAPP – A management framework for distributed visualization systems,”** In *Proceedings of CGVCVIP 2011 : IADIS International Conference on Computer Graphics, Visualization, Computer Vision And Image Processing*, pp. (accepted). 2011.

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**“Measuring Defibrillator Surface Potentials for Simulation Verification,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society EMBS 33rd Annual International Conference*, pp. 239 - 242. 2011.

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**“Real-time magnetic resonance imaging-guided radiofrequency atrial ablation and visualization of lesion formation at 3 Tesla,”** In *Heart Rhythm*, Vol. 8, No. 2, pp. 295--303. 2011.

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**“Finite Element Based Discretization and Regularization Strategies for 3D Inverse Electrocardiography,”** In *IEEE Transactions for Biomedical Engineering*, Vol. 58, No. 6, pp. 1827--1838. 2011.

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**“An optimization framework for inversely estimating myocardial transmembrane potentials and localizing ischemia,”** In *Proceedings of the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS)*, pp. 1680--1683. 2011.

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**“The Viking Viewer: Scalable Multiuser Annotation and Summarization of Large Volume Datasets,”** In *Journal of Microscopy*, Vol. 241, No. 1, pp. 13--28. 2010.

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**“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.

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**“MRI Based Injury Characterization Immediately Following Ablation of Atrial Fibrillation,”** In *Computing in Cardiology*, Vol. 37, pp. 165--168. 2010.

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**“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.

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**“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.

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**“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.

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**“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.

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**“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.

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**“Finite element modeling of subcutaneous implantable defibrillator electrodes in an adult torso,”** In *Heart Rhythm*, Vol. 7, No. 5, pp. 692--698. May, 2010.

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**“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.

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**“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.

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**“A Comparison of Delaunay Based Meshing Algorithms for Electrophysiological Cardiac Simulations,”** In *Virtual Physiological Human*, pp. 181--183. 2010.

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**“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.

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[Pil2010a] 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.

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**“Visualizing Summary Statistics and Uncertainty,”** In *Computer Graphics Forum*, Vol. 29, No. 3, Wiley-Blackwell, pp. 823--831. Aug, 2010.

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**“Magnetic resonance imaging-confirmed ablative debulking of the left atrial posterior wall and septum for treatment of persistent atrial fibrillation: rationale and initial experience,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 21, No. 2, pp. 126--132. 2010.

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[Sti2010a] J.G. Stinstra, R.S. MacLeod, C.S. Henriquez.
**“Incorporating Histology into a 3D Microscopic Computer Model of Myocardium to Study Propagation at a Cellular Level,”** In *Annals of Biomedical Engineering (ABME)*, Vol. 38, No. 4, pp. 3399--1414. 2010.

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**“The Effect of Non-Conformal Finite Element Boundaries on Electrical Monodomain and Bidomain Simulations,”** In *Computing in Cardiology*, Vol. 37, IEEE, pp. 97--100. 2010.

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**“Implantable Cardioverter Defibrillator Predictive Simulation Validation,”** In *Computing in Cardiology*, pp. 853-–856. September, 2010.

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**“Resolution Strategies for the Finite-Element-Based Solution of the ECG Inverse Problem,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 57, No. 2, pp. 220--237. February, 2010.

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**“A New Family of Variational-Form-Based Regularizers for Reconstructing Epicardial Potentials from Body-Surface Mapping,”** In *Computing in Cardiology, 2010*, pp. 93--96. 2010.

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**“Combined EEG/MEG source analysis using calibrated finite element head models,”** In *Proc. of the 44th Annual Meeting, DGBMT*, Note: *to appear, http://conference.vde.com/bmt-2010*, Rostock-Warnemünde, Germany, Oct.5-8, 2010 2010.

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**“Temporal Left Atrial Lesion Formation After Ablation of Atrial Fibrillation,”** In *Heart Rhythm*, Vol. 6, No. 2, pp. 161--168. February, 2009.

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**“Initial Experience of Assessing Esophageal Tissue Injury and Recovery Using Delayed-Enhancement MRI After Atrial Fibrillation Ablation,”** In *Circulation: Arrhythmia and Electrophysiology*, Vol. 2, pp. 620--625. 2009.

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**“A Meshing Pipeline for Biomedical Models,”** In *Engineering with Computers*, Vol. 25, No. 1, SpringerLink, pp. 115-130. 2009.

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**“Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging,”** In *Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009*, Lecture Notes in Computer Science LNCS, Vol. 5762, pp. 167--174. 2009.

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**“Computing Hulls In Positive Definite Space,”** In *In Proceedings of the 19th Fall Workshop on Computational Geometry*, November, 2009.

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**“Visualization for Data-Intensive Science,”** In *The Fourth Paradigm: Data-Intensive Science*, Edited by S. Tansley and T. Hey and K. Tolle, Microsoft Research, pp. 153--164. 2009.

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**“Bioelectric Analyses of an Osseointegrated Intelligent Implant Design System for Amputees,”** In *JoVE*, Vol. 29, 2009.

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**“Automated identification of neurons in 3D confocal datasets from zebrafish brainstem,”** In *Journal of Microscopy*, Vol. 233, No. 1, pp. 114--131. January, 2009.

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**“Focus and Context - Visualization without the Complexity,”** In *Proceedings of the World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany*, IFMBE Proceedings, Vol. 25/13, Springer Berlin Heidelberg, pp. 44--48. 2009.

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**“Accuracy and run-time comparison for different potential approaches and iterative solvers in finite element method based EEG source analysis,”** In *Applied Numerical Mathematics*, Vol. 59, pp. 1970--1988. 2009.

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**“Improved EEG Source Analysis Using Low-Resolution Conductivity Estimation in a Four-Compartment Finite Element Head Model,”** In *Human Brain Mapping*, Vol. 30, pp. 2862--2878. 2009.

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**“Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples,”** In *Philosophical Transactions of The Royal Society A, Mathematical, Physical & Engineering Sciences*, Vol. 367, No. 1896, pp. 2293--2310. 2009.

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**“Microscopic Computed Tomography Based Virtual Histology for Visualization and Morphometry of Atherosclerosis in Diabetic Apolipoprotein E Mutant Mice,”** In *Circulation: Journal of the American Heart Association*, Vol. 120, No. 9, pp. 821--822. 2009.

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**“Microscopic Computed Tomography–Based Virtual Histology for Visualization and Morphometry of Atherosclerosis in Diabetic Apolipoprotein E Mutant Mice,”** In *Circulation*, Vol. 120, No. 821--822, 2009.

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**“Detection and quantification of left atrial structural remodeling with delayed-enhancement magnetic resonance imaging in patients with atrial fibrillation,”** In *Circulation*, Vol. 119, No. 13, pp. 1758--1767. 2009.

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**“Cortical Correspondence with Probabilistic Fiber Connectivity,”** In *Information Processing in Medical Imaging (IPMI)*, Lecture Notes in Computer Science (LCNS), Vol. 5636, pp. 651--663. 2009.

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**“The SCIJump Framework for Parallel and Distributed Scientific Computing,”** In *Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications*, Edited by Manish Parashar and Xiaolin Li and Sumir Chandra, Wiley-Blackwell, pp. 149--170. 2009.

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**“A Framework for Exploring Numerical Solutions of Advection Reaction Diffusion Equations using a GPU Based Approach,”** In *Journal of Computing and Visualization in Science*, Vol. 12, pp. 155--170. 2009.

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**“Magnetic Resonance Imaging-Confirmed Ablative Debulking of the Left Atrial Posterior Wall and Septum for Treatment of Persistent Atrial Fibrillation: Rationale and Initial Experience,”** In *Journal of Cardiovascular Electrophysiology*, Vol. 21, No. 2, pp. 126--132. 2009.

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**“Hexahedral Mesh Generation for Biomedical Models in SCIRun,”** In *Engineering with Computers*, Vol. 25, No. 1, pp. 97--114. 2009.

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**“A Variational Image-Based Approach to the Correction of Susceptibility Artifacts in the Alignment of Diffusion Weighted and Structural MRI,”** In *Lecture Notes in Computer Science*, Springer, pp. 664--675. 2009.

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**“Measuring Implantable Cardioverter Defibrillators (ICDs) During Implantation Surgery: Verification of a Simulation,”** In *Computers in Cardiology*, pp. 473--476. 2009.

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**“Finite Element Discretization Strategies for the Inverse Electrocardiographic (ECG) Problem,”** In *Proceedings of the 11th World Congress on Medical Physics and Biomedical Engineering*, Munich, Germany, Vol. 25/2, pp. 729-732. September, 2009.

[Wan2009d] D.F. Wang, R.M. Kirby, C.R. Johnson.
**“Finite Element Refinements for Inverse Electrocardiography: Hybrid-Shaped Elements, High-Order Element Truncation and Variational Gradient Operator,”** In *Proceeding of Computers in Cardiology 2009*, Park City, September, 2009.

[Cat2008a] J. Cates, P.T. Fletcher, Z. Warnock, R.T. Whitaker.
**“A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11,”** In *Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08)*, pp. 512--516. 2008.

DOI: 10.1109/ISBI.2008.4541045

[Cat2008b] J. Cates, P.T. Fletcher, M. Styner, H. Hazlett, R.T. Whitaker.
**“Particle-Based Shape Analysis of Multi-Object Complexes,”** In *Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08)*, Lecture Notes In Computer Science (LCNS), pp. 477--485. 2008.

ISBN: 978-3-540-85987-1

[Gen2008a] S.E. Geneser, R.M. Kirby, R.S. MacLeod.
**“Application of Stochastic Finite Element Methods to Study the Sensitivity of ECG Forward Modeling to Organ Conductivity,”** In *IEEE Transations on Biomedical Engineering*, Vol. 55, No. 1, pp. 31--40. January, 2008.

[Joh2008a] C.R. Johnson, X. Tricoche.
**“Biomedical Visualization,”** In *Advances in Biomedical Engineering*, Ch. 6, Edited by Pascal Verdonck, Elsvier Science, pp. 209--272. 2008.

[Jol2008a] M. Jolley, J.G. Stinstra, S. Pieper, R.S. MacLeod, D.H. Brooks, F. Cecchin, J.K. Triedman.
**“A Computer Modeling Tool for Comparing Novel ICD Electrode Orientations in Children and Adults,”** In *Heart Rhythm*, Vol. 5, No. 4, pp. 565--572. April, 2008.

PubMed ID: 18362024

[Kru2008b] J. Krüger, K. Potter, R.S. MacLeod, C.R. Johnson.
**“Unified Volume Format: A General System For Efficient Handling Of Large Volumetric Datasets,”** In *Proceedings of IADIS Computer Graphics and Visualization 2008 (CGV 2008)*, pp. 19--26. 2008.

PubMed ID: 20953270

[Led2008a] C. Ledergerber, G. Guennebaud, M.D. Meyer, M. Bacher, H. Pfister.
**“Volume MLS Ray Casting,”** In *IEEE Transactions on Visualization and Computer Graphics (Proceedings of Visualization 2008)*, Vol. 14, No. 6, pp. 1539--1546. 2008.

[Lew2008a] S. Lew, C.H. Wolters, A. Anwander, S. Makeig, R.S. Macleod.
**“Improved EEG Source Analysis Using Low-Resolution Conductivity Estimation in a Four-Compartment Finite Element Head Model,”** In *Human Brain Mapping*, Vol. 31, December, 2008.

[Li2008a] G.-S. Li, X. Tricoche, D. Weiskopf, C.D. Hansen.
**“Flow Charts: Visualization of Vector Fields on Arbitrary Surfaces,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 14, No. 5, pp. 1--14. September/October, 2008.

[Liv2008a] Y. Livnat, S.G. Parker, C.R. Johnson.
**“Fast Isosurface Extraction Methods for Large Image Data Sets,”** In *Handbook of Medical Image Processing and Analysis*, 2nd edition, Ch. 47, Note: *(to appear)*, Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.

[Mcg2008a] C.J. McGann, E.G. Kholmovski, R.S. Oakes, J.J. Blauer, M. Daccarett, N. Segerson, K.J. Airey, N. Akoum, E. Fish, T.J. Badger, E.V. DiBella, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“New Magnetic Resonance Imaging-Based Method for Defining the Extent of Left Atrial Wall Injury After the Ablation of Atrial Fibrillation,”** In *Journal of the American College of Cardiology*, Vol. 52, No. 15, pp. 1263--1271. Oct 7, 2008.

[Mey2008a] M.D. Meyer, R.T. Whitaker, R.M. Kirby, C. Ledergerber, H. Pﬁster.
**“Particle-based Sampling and Meshing of Surfaces in Multimaterial Volumes,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 14, No. 6, pp. 1539--1546. 2008.

[Ogu2008a] I. Oguz, J. Cates, P.T. Fletcher, R.T. Whitaker, D. Cool, S. Aylward, M. Styner.
**“Cortical Correspondence using Entropy-Based Particle Systems and Local Features,”** In *5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008. (ISBI 2008)*, pp. 1637--1640. 2008.

[Piz2008g] S. Pizer, M. Styner, T. Terriberry, R. Broadhurst, S. Joshi, E. Chaney, P.T. Fletcher.
**“Statistical Applications with Deformable M-Reps,”** In *Computational Imaging and Vision*, Springer, pp. 269--308. 2008.

DOI: 10.1007/978-1-4020-8658-8_9

[Pot2008a] K. Potter, J. Krüger, C.R. Johnson.
**“Towards the Visualization of Multi-Dimentional Stochastic Distribution Data,”** In *Proceedings of The International Conference on Computer Graphics and Visualization (IADIS) 2008*, pp. 191--196. 2008.

[She2008a] J.F. Shepherd, C.R. Johnson.
**“Hexahedral Mesh Generation Constraints,”** In *Journal of Engineering with Computers*, Vol. 24, No. 3, pp. 195--213. 2008.

[Shv2008a] A.G. Shvedko, M.D. Warren, S. Shome, J.G. Stinstra, A.V. Zaitsev.
**“Influence of the Skeletal Muscle Activity on Time and Frequency Domain Properties of the Body Surface ECG During Evolving Ventricular Fibrillation in the Pig,”** In *Resuscitation*, Vol. 78, No. 2, pp. 215--223. May 24, 2008.

DOI: 10.1016/j.resuscitation.2008.03.010

[Sti2008a] J.G. Stinstra, M.A. Jolley, J.D. Tate, D.H. Brooks, J.K. Triedman, R.S. MacLeod.
**“The Role of Volume Conductivities in Simulation of Implantable Defibrillators,”** In *Computers in Cardiology*, Bologna, Italy, 2008.

[Sti2008b] J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod.
**“Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,”** In *Proceedings of the 29th Annual International Conference of the IEEE EMBS*, pp. 1422-1425. 2008.

ISBN: 978-1-4244-0787-3

[Sut2008a] D.R. Sutherland, Q. Ni, R.S. MacLeod, R.L. Lux, B.B. Punske.
**“Experimental Measures of Ventricular Activation and Synchrony,”** In *Pacing and Clinical Electrophysiology*, Vol. 31, No. 12, pp. 1560--1570. December, 2008.

[Tac2008a] B. Taccardi, B.B. Punske, E. Macchi, R.S. MacLeod, P.R. Ershler.
**“Epicardial and Intramural Excitation During Ventricular Pacing: Effect of Myocardial Structure,”** In *The American Journal of Physiology - Heart and Circulatory Physiology*, Vol. 294, No. 4, pp. H1753--1766. April, 2008.

DOI: 10.1152/ajpheart.01400.2007

[Tri2008a] X. Tricoche, R.S. MacLeod, C.R. Johnson.
**“Visual Analysis of Bioelectric Fields,”** In *Visualization in Medicine and Life Sciences*, Mathematics and Visualization, Springer-Verlag, pp. 205--220. 2008.

[Tri2008b] J.K. Triedman, M. Jolley, J. Stinstra, D.H. Brooks, R.S. MacLeod.
**“Predictive Modeling of Defibrillation Using Hexahedral and Tetrahedral Finite Element Models: Recent Advances,”** In *Journal of Electrocardiology*, Vol. 41, pp. 483--486. 2008.

[Vas2008a] S.X. Vasquez, M.S. Hansen, A.N. Bahadur, M.F. Hockin, G.L. Kindlmann, L. Nevell, I.Q. Wu, D.J. Grunwald, D.M. Weinstein, G.M. Jones, C.R. Johnson, J.L. Vandeberg, M.R. Capecchi, C. Keller.
**“Optimization of Volumetric Computed Tomography for Skeletal Analysis of Model Genetic Organisms,”** In *The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology*, Vol. 291, pp. 475--487. 2008.

PubMed ID: 18286615

[Adl2007a] G. Adluru, S.P. Awate, T. Tasdizen, R.T. Whitaker, E.V.R. DiBella.
**“Temporally Constrained Reconstruction of Dynamic Cardiac Perfusion MRI,”** In *Magnetic Resonance in Medicine*, Vol. 57, pp. 1027--1036. 2007.

[Adl2007b] G. Adluru, R.T. Whitaker, E.V.R. DiBella.
**“Spatio-Temporal Constrained Reconstruction of Sparse Dynamic Contrast Enhanced Radial MRI Data,”** In *Proceedings of the IEEE International Symposium on Biomedical Imaging*, pp. 109--112. 2007.

[Adl2007c] G. Adluru, E. Hsu, E.V.R. DiBella.
**“Constrained Reconstruction of Sparse Cardiac MR DTI Data,”** In *Proceedings of FIMH 2007*, LNCS, No. 4466, pp. 91--99. 2007.

[Bro2007a] D.H. Brooks, A. Keely, A. Ghodrati, G. Tadmor, R.S. MacLeod.
**“Some Spatio-Temporal Approaches to Inverse Electrocardiography,”** In *Proc. Asilomar Conf. on Signals, Systems, and Computers*, Pacific Grove, CA, November, 2007.

DOI: 10.1109/ACSSC.2007.4487316

[Cal2007a] M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.
**“BioMesh3D: A Meshing Pipeline for Biomedical Models,”** SCI Institute Technical Report, No. UUSCI-2007-009, *University of Utah*, 2007.

[Cal2007b] M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.
**“A Meshing Pipeline for Biomedical Computing,”** In *Engineering with Computers*, Special Issue on Computational Bioengineering, pp. (in press). 2007.

[Cat2007a] J. Cates, P.T. Fletcher, M. Styner, M. Shenton, R.T. Whitaker.
**“Shape Modeling and Analysis with Entropy-Based Particle Systems,”** In *Proceedings of Information Processing in Medical Imaging (IPMI) 2007*, LNCS 4584, pp. 333--345. 2007.

[Gen2007a] S.E. Geneser, R.M. Kirby, D. Xiu, F.B. Sachse.
**“Stochastic Markovian Modeling of Electrophysiology of Ion Channels: Reconstruction of Standard Deviations in Macroscopic Currents,”** In *Journal of Theoretical Biology*, Vol. 245, No. 4, pp. 627--637. 2007.

DOI: 10.1016/j.jtbi.2006.10.016

[Gho2007a] A. Ghodrati, D.H. Brooks, R.S. MacLeod.
**“Methods of Solving Reduced Lead Systems for Inverse Electrocardiography,”** In *IEEE Trans Biomed Eng*, Vol. 54, No. 2, pp. 339--343. February, 2007.

PubMed ID: 17278592

[Jeo2007a] W.-K. Jeong, P.T. Fletcher, R. Tao, R.T. Whitaker.
**“Interactive Visualization of Volumetric White Matter Connectivity in DT-MRI Using a Parallel-Hardware Hamilton-Jacobi Solver,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 6, pp. 1480--1487. 2007.

PubMed ID: 17968100

[Jol2007a] M. Jolley, J.G. Stinstra, D.M. Weinstein, S. Pieper, R.S.J. Estepar, G. Kindlmann, R.S. MacLeod, D.H. Brooks, J.K. Triedman.
**“Open-Source Environment for Interactive Finite Element Modeling of Optimal ICD Electrode Placement,”** In *Functional Imaging and Modeling of the Heart*, Lecture Notes in Computer Science (LCNS), Vol. 4466/2007, pp. 373--382. 2007.

ISBN: 978-3-540-72906-8

[Kin2007a] G. Kindlmann, D.B. Ennis, R.T. Whitaker, C.-F. Westin.
**“Diffusion Tensor Analysis With Invariant Gradients and Rotation Tangents,”** In *IEEE Transactions on Medical Imaging*, Vol. 26, No. 11, pp. 1483--1499. 2007.

[Lew2007a] S. Lew, C. Wolters, A. Anwander, S. Makeig, R.S. MacLeod.
**“Low Resolution Conductivity Estimation to Improve Source Localization,”** In *New Frontiers in Biomagnetism. Proceedings of the 15th International Conference on Biomagnetism, Vancouver, BC, Canada, August 21-25, 2006.*, International Congress Series, Vol. 1300, pp. 149--152. June, 2007.

[Mal2007a] M. Malik, Y. Birnbaum, R.S. MacLeod, V. Shusterman.
**“Markers of impaired repolarization,”** In *Journal of Electrocardiology*, Vol. 40, No. 1, pp. S54--S57. January, 2007.

[Mey2007b] M.D. Meyer, R.M. Kirby, R.T. Whitaker.
**“Topology, Accuracy, and Quality of Isosurface Meshes Using Dynamic Particles,”** In *IEEE Transactions on Visualization and Computer Graphics*, Vol. 13, No. 6, IEEE, pp. 1704--1711. Nov, 2007.

[She2007c] J.F. Shepherd, C.R. Johnson.
**“Hexahedral Mesh Generation for Biomedical Models in SCIRun,”** SCI Institute Technical Report, No. UUSCI-2007-008, *University of Utah*, 2007.

[Sho2007a] S. Shome, R.L. Lux, B.B. Punske, R.S. MacLeod.
**“Ischemic Preconditioning Protects Against Arrhythmogenesis Through Maintenance of Both Active as well as Passive Electrical Properties in Ischemic Canine Hearts,”** In *Journal of Electrocardiology*, Vol. 40, No. 6 supp, pp. S150--S159. Nov-Dec, 2007.

[Sho2007b] S. Shome, J.G. Stinstra, C Henriquez, R.S. Macleod.
**“Influence of Extracellular Potassium and Reduced Extracellular Space on Conduction Velocity During Acute Ischemia: A Simulation Study,”** In *Journal of Electrocardiology*, Vol. 40, No. 4, pp. S5--S6. 2007.

[Sti2007a] J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod.
**“Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,”** In *Proceedings of the 29th Annual International Conference of the IEEE EMBS*, pp. 1422--1425. 2007.

[Tri2007a] J.K. Triedman, M. Jolley, R.S. MacLeod, J.G. Stinstra, D.H. Brooks, S. Pieper.
**“A System for Image Based Finite Element Modeling of Novel Defibrillation Strategies,”** In *Life Science Systems and Applications Workshop, 2007. LISA 2007*, pp. 63--66. 2007.

[Tri2007c] J.K. Triedman, M. Jolley, R.S. MacLeod, J. Stinstra, D.H. Brooks, S. Pieper.
**“Finite Element Modeling of Novel Defibrillation Approaches in Children and Adults,”** In *Proc. LISSA Conf.*, Bethesda, MD, November, 2007.

[Vas2007a] S.X. Vasquez, A.N. Bahadur, J.T. Johnson III, D.R. Rodriguez, C. Keller.
**“Severe Runting of a Laboratory Mouse (Mus musculus),”** In *Lab Animal*, Vol. 36, No. 1, pp. 19, 22--23. January, 2007.

[Wol2007b] C.H. Wolters, H. Köstler, C. Möller, J. Härtlein, L. Grasedyck, W. Hackbusch.
**“Numerical Mathematics of the Subtraction Method for the Modeling of a Current Dipole in EEG Source Reconstruction Using Finite Element Head Models,”** In *SIAM J. on Scientific Computing*, Vol. 30, No. 1, pp. 24--45. 2007.

[Wol2007c] C.H. Wolters, H. Köstler, C. Möller, J. Härdtlein, A. Anwander.
**“Numerical Approaches for Dipole Modeling in Finite Element Method Based Source Analysis,”** In *New Frontiers in Biomagnetism. Proceedings of the 15th International Conference on Biomagnetism, Vancouver, BC, Canada, August 21-25, 2006.*, International Congress Series, Vol. 1300, pp. 189--192. June, 2007.

[Yih2007a] B. Yihnaz, R.S. MacLeod, B.B. Punske, B. Taccardi, and D.H. Brooks.
**“Generalized training subset selection for statistical estimation of epicardial activation maps from intravenous catheter measurements,”** In *Compo in BioI. and Med.*, In *Compo in BioI. and Med.*, Vol. 37, No. 3, pp. 328--336. 2007.

[Yil2007a] B. Yilmaz, R.S. MacLeod.
**“Generalized Training Subset Selection for Statistical Estimation of Epicardial Activation Maps from Intravenous Catheter Measurements,”** In *Computers in Biology and Medicine*, Vol. 37, No. 9, pp. 328--336. March, 2007.

[Adl2006a] G. Adluru, E.V.R. DiBella, R.T. Whitaker.
**“Automatic Segmentation of Cardiac Short Axis Slices in Perfusion MRI,”** In *Proceedings of The 2006 IEEE International Symposium on Biomedical Imaging*, pp. 133--136. 2006.

[Adl2006b] G. Adluru, E.V.R. DiBella.
**“Segmentation Based Registration of Myocardium in Cardiac Perfusion Images,”** In *Proceedings of The 14th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM)*, Vol. 14, pp. 1223. 2006.

[Arm2006a] R. Armstrong, G. Kumfert, L.C. McInnes, S.G. Parker, B. Allan, M. Sottile, T. Epperly, T. Dahlgren.
**“The CCA Component Model for High-Performance Scientific Computing,”** In *Concurrency and Computation: Practice & Experience*, Vol. 18, No. 2, John Wiley and Sons Ltd., Chichester, UK pp. 215--229. 2006.

ISSN: 1532-0626

[Awa2006c] S.P. Awate, T. Tasdizen, R.T. Whitaker.
**“Unsupervised Texture Segmentation with Nonparametric Neighborhood Statistics,”** SCI Institute Technical Report, No. UUSCI-2006-011, *University of Utah*, 2006.

[Awa2006d] S.P. Awate, R.T. Whitaker.
**“Unsupervised, Information-Theoretic, Adaptive Image Filtering for Image Restoration,”** In *IEEE Trans. Pattern Anal. & Mach. Intel.*, Vol. 28, No. 3, pp. 364--376. March, 2006.

PubMed ID: 16526423

[Bab2006a] S. Babaeizadeh, D.H. Brooks.
**“Imaging Error from Mislocation of Surface Sensors: Sensitivity, Detection, and Estimate Correction, with Application to EIT,”** In *Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing*, Toulouse, France May, 2006.

[Bro2006a] S. Browd, L.J. Healy, G. Dobie, J.T. Johnson III, G.M. Jones, L.F. Rodriguez, D.L. Brockmeyer.
**“Morphometric and Qualitative Analysis of Congenital Occipitocervical Instability in Children: Implications for Down Syndrome Patients,”** In *Journal of Neurosurgery: Pediatrics*, Vol. 105, No. 1 , Journal of Neurosurgery Publishing Group, pp. 50--54. July, 2006.

DOI: 10.3171/ped.2006.105.1.50

[Cat2006b] J. Cates, D. Weinsten, M. Davis.
**“The Center for Integrative Biomedical Computing: Advancing Biomedical Science with Open Source,”** In *Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI) 2006*, 2006.

[Gho2006a] A. Ghodrati, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“Wavefront-based Models for Inverse Electrocardiography,”** In *IEEE Trans Biomed. Eng.*, Vol. 53, No. 9, pp. 1821--1831. 2006.

DOI: 10.1109/TBME.2006.878117

[Gho2006b] A. Ghodrati, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“Lead Selection for Inverse Electrocardiography,”** In *IEEE Trans Biomed. Eng.*, pp. in press. 2006.

[Gho2006c] A. Ghodrati, A. Keely, G. Tadmor, R.S. MacLeod, D.H. Brooks.
**“A Wavefront-Based Constraint for Potential Surface Solutions in Inverse Electrocardiography,”** In *2006 International Conference of the IEEE Engineering in Medicine and Biology Society*, IEEE, New York, NY, USA August, 2006.

DOI: 10.1109/IEMBS.2006.260373

[Gho2006d] A. Ghodrati, D.H Brooks, G. Tadmor, R.S. MacLeod.
**“A Threshold-Based Method for Inverse Solutions to Reconstruct Complex Obstacles, with Application to the Inverse Problem of Electrocardiography,”** In *SIAM Conference on Imaging Science*, Minneapolis, MN, USA May, 2006.

[Joh2006a] C.R. Johnson, D.M. Weinstein.
**“Biomedical Computing and Visualization,”** In *Proceedings of the Twenty-Ninth Australasian Computer Science Conference (ACSC2006): Conferences in Research and Practice in Information Technology (CRPIT)*, Hobart, Australia, Vol. 48, Edited by Vladimir Estivill-Castro and Gill Dobbie, pp. 3-10. 2006.

[Joh2006c] J.T. Johnson III, M.S. Hansen, I. Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C. Keller.
**“Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping,”** In *PLoS Genetics*, Vol. 2, No. 1, pp. 471--477. April, 2006.

[Joh2006d] C.R. Johnson.
**“Computational Methods and Software for Bioelectric Field Problems,”** In *Biomedical Engineering Handbook, 2nd Edition*, Vol. 1, Ch. 23, Edited by J.D. Bronzino, CRC Press, Boca Raton, pp. 1--23. 2006.

[Joh2006f] J.T. Johnson III, M.S. Hansen, I.Q Wu, L.J. Healy, C.R. Johnson, G.M. Jones, M.R. Capecchi, C.Keller.
**“Virtual Histology of Transgenic Mouse Embryos for High-Throughput Phenotyping,”** In *Proceedings of the Teratology 46th Annual Meeting*, Tucson, AZ, 2006.

[Jol2006a] M. Jolley, J. Triedman, C.-F. Westin, D.M. Weinstein, R.S. MacLeod, D.H. Brooks.
**“Image Based Modeling of Defibrillation in Children,”** In *Proceedings of the 26th Annual International Conference of the IEEE EMBS*, New York, NY, USA August, 2006.

[Jur2006a] E. Jurrus, T. Tasdizen, P. Koshevoy, P.T. Fletcher, M. Hardy, C-B. Chien, W. Denk, R.T. Whitaker.
**“Axon Tracking in Serial Block-Face Scanning Electron Microscopy,”** In *Workshop on Microscopic Image Analysis with Applications in Biology, MICCAI*, October, 2006.

[Kin2006a] G. Kindlmann, X. Tricoche, C.-F. Westin.
**“Anisotropy Creases Delineate White Matter Structure in Diffusion Tensor MRI,”** In *Proceedings of the Ninth International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'06)*, Copenhagen, Denmark, Springer Lecture Notes in Computer Science 4190, pp. 126--133. October, 2006.

[Kum2006a] G. Kumfert, D.E. Bernholdt, T.G.W. Epperly, J.A. Kohl, L.C. McInnes, S.G. Parker, J. Ray.
**“How the Common Component Architecture Advances Computational Science,”** In *J. Phys.: Conf. Ser.*, Vol. 46, pp. 479--493. 2006.

[Li2006a] G. Li, X. Tricoche, C.D. Hansen.
**“GPUFLIC: Interactive and Accurate Dense Visualization of Unsteady Flows,”** In *Proceedings of Euro Vis 2006*, pp. 29--34. 2006.

[Lor2006a] L. Lorenzo, R.S. MacLeod, R.T. Whitaker, G. Adluru, E.V.R. DiBella.
**“Level Sets and Shape Models for Segmentation of Cardiac Perfusion MRI,”** In *Proceedings of International Society for Optical Engineering (SPIE) Conference on Medical Imaging 2006*, Vol. 6144, pp. 1320--1331. 2006.

[Moo2006a] C.R. Johnson, R. Moorhead, T. Munzner, H. Pfister, P. Rheingans, T. Yoo.
**“NIH/NSF Visualization Research Challenges Report Summary,”** Note: *NIH/NSF*, pp. 66-73. 2006.

[Nag2006a] S. Nagarajan, O. Portniaguine, D. Hwang, C.R. Johnson, K. Sekihara.
**“Controlled Support MEG Imaging,”** In *NeuroImage*, Vol. 15;33, No. 3, pp. 878--885. 2006.

[Par2006b] S.G. Parker, K. Zhang, K. Damevski, C.R. Johnson.
**“Integrating Component-Based Scientific Computing Software,”** In *Parallel Processing for Scientific Computing*, Edited by M.A. Heroux and P. Raghavan and H.D. Simon, SIAM Press, pp. 271--288. 2006.

ISBN: 0-89871-619-5

[Ser2006a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Improved Performance of Bayesian Solutions for Inverse Electrocardiography Using Multiple Information Sources,”** In *IEEE Trans Biomed. Eng.*, Vol. 53, No. 10, pp. 2024--2034. October, 2006.

[She2006a] J.F. Shepherd.
**“Hexahedral Mesh Generation Constraints,”** SCI Institute Technical Report, No. UUSCI-2006-010, *University of Utah*, 2006.

[Sti2006a] J.G. Stinstra, S.F. Roberts, J.B. Pormann, R.S. MacLeod, C.S. Henriquez.
**“A Model of 3D Propagation in Discrete Cardiac Tissue,”** In *Proceedings of Computers in Cardiology 2006*, Vol. 33, pp. 41. 2006.

[Tri2006a] X. Tricoche, X. Zheng, A. Pang.
**“Visualizing the Topology of Symmetric, Second-Order, Time-varying Two-Dimensional Tensor Fields,”** In *Visualization and Processing of Tensor Fields*, Springer, pp. 225--240. 2006.

[Wol2006a] C.H. Wolters, A. Anwander, X. Tricoche, D.M. Weinstein, M.A. Koch, R.S. MacLeod.
**“Influence of Tissue Conductivity Anisotropy on EEG/MEG Field and Return Current Computation in a Realistic Head Model: A Simulation and Visualization Study Using High-Resolution Finite Element Modeling,”** In *Neuroimage*, Vol. 30, No. 3, pp. 813--826. April, 2006.

[Wol2006b] C.H. Wolters, A. Anwander, G. Berti, U. Hartmann.
**“Geometry-Adapted Hexahedral Meshes Improve Accuracy of Finite Element Method Based EEG Source Analysis,”** In *IEEE Transactions on Biomedical Engineering*, Vol. 54, No. 8, pp. 1446--1453. August, 2006.

[Wol2006c] D. Güllmar, J. Haueisen, M. Eiselt, F. Giessler, L. Flemming, A. Anwander, T. Knösche, C.H. Wolters, M. Dümpelmann, D.S. Tuch, J.R. Reichenbach.
**“Influence of Anisotropic Conductivity on EEG Source Reconstruction: Investigations in a Rabbit Model,”** In *IEEE Trans. Biomed. Eng.*, Vol. 53, No. 9, pp. 1841--1850. 2006.

[Yil2006a] B. Yilmaz, R.S. Macleod.
**“Instance Selection for Estimation of Epicardial Activation Sequence from Venous Catheter Measurements,”** In *Proceedings of the 28th IEEE EMBS Annual International Conference*, pp. 3982--3985. 2006.

[Awa2005b] S.P. Awate, R.T. Whitaker.
**“Higher-Order Image Statistics for Unsupervised, Information-Theoretic, Adaptive, Image Filtering,”** SCI Institute Technical Report, No. UUSCI-2005-004, *University of Utah*, 2005.

[Awa2005c] S.P. Awate, R.T. Whitaker.
**“Nonparametric Neighborhood Statistics for MRI Denoising,”** SCI Institute Technical Report, No. UUSCI-2005-005, *University of Utah*, 2005.

[Awa2005e] S.P. Awate, R.T. Whitaker.
**“Nonparametric Neighborhood Statistics for MRI Denoising,”** In *In Proc. Int. Conf. Information Processing in Medical Imaging (IPMI), 2005. Lecture Notes in Computer Science*, Vol. 3565, pp. 677--688. July, 2005.

[Awa2005f] S.P. Awate, R.T. Whitaker.
**“Higher-Order Image Statistics for Unsupervised, Information-Theoretic, Adaptive, Image Filtering,”** In *Proceedings of the IEEE Int. Conf. Computer Vision and Pattern Recognition (CVPR)*, pp. 44--51. 2005.

[Awa2005g] S.P. Awate, R.T. Whitaker.
**“Unsupervised, Information-Theoretic, Adaptive Image Filtering for Image Restoration,”** In *IEEE Trans. Pattern Anal. & Mach. Intel.*, Vol. 28, No. 3, pp. 364--376. 2005.

[Cal2005b] F. Calderero, A. Ghodrati, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“A Method to Reconstruct Activation Wavefronts Without Isotropy Assumptions Using a Level Sets Approach,”** In *Functional Imaging and Modeling of the Heart: Third International Workshop (FIMH 2005)*, Barcelona, June 2-4, pp. 195. 2005.

[Gen2005a] S.E. Geneser, S. Choe, R.M. Kirby, R.S. MacLeod.
**“Influence of Stochastic Organ Conductivity in 2D ECG Forward Modeling: A Stochastic Finite Element Study,”** In *Proceedings of The Joint Meeting of The 5th International Conference on Bioelectromagnetism and The 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart*, pp. 5528--5531. 2005.

[Gho2005a] A. Ghodrati, D.H. Brooks, G. Tadmor, B.B. Punske, R.S. MacLeod.
**“Wavefront-based Inverse Electrocardiography using an Evolving Curve State Vector and Phenomenological Propagation and Potential Models,”** In *IJBEM*, Vol. 7, No. 2, pp. 210--213. 2005.

[Gul2005a] D. Gullmar, J.R. Reichenbach, A. Anwander, T. Knosche, C.H. Wolters, M. Eiselt, J. Haueisen.
**“Influence of Anisotropic Conductivity of the White Matter Tissue on EEG Source Reconstruction - An FEM Simulation Study,”** In *Int. J. Bioelectromag.*, Vol. 7, No. 1, pp. 108--110. 2005.

[Haw2005a] P. Hawkes, G. Kindlmann, D. Weinstein, G.M. Jones, C. Keller.
**“Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors,”** In *Proceedings of 2005 SMI Conference, 4th Annual Meeting of the Society for Molecular Imaging*, Cologne, Germany, 2005.

[Hop2005a] B. Hopenfeld, J.G. Stinstra, R.S. MacLeod.
**“The Effect of Conductivity on ST-Segment Epicardial Potentials Arising from Subendocardial Ischemia,”** In *Annal. Biomed. Eng.*, Vol. 33, No. 6, pp. 751--763. 2005.

[Kho2005a] E.G. Khölmovski, E.V.R. DiBella, A.A. Samsonov.
**“Accurate Assessment of the Arterial Input Function using MRI with Radial Sampling,”** In *Proceedings of the Society for Cardiovascular Magnetic Resonance (SCMR) 8th Annual Scientific Sessions*, Vol. 7, pp. 292--294. 2005.

[Kin2005a] G.L. Kindlmann, D.M. Weinstein, G.M. Jones, C.R. Johnson, M.R. Capecchi, C. Keller.
**“Practical Vessel Imaging by Computed Tomography in Live Transgenic Mouse Models for Human Tumors,”** In *Journal of Molecular Imaging*, Vol. 4, No. 4, pp. 417--424. 2005.

[Kni2005a] J.M. Kniss, G. Kindlmann, C.D. Hansen.
**“Multidimentional Transfer Functions for Volume Rendering,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 189--210. 2005.

ISBN: 0-12-387582-X

[Lew2005a] S. Lew, C. Wolters, K. Lee, S. Makeig, G. Worrell, R.S. MacLeod.
**“Epileptogenic Source Localization For Open Skull Head Model of Epilepsy By Independent Component Analysis And Inverse Dipole Fit Method,”** In *1st Annual Mountain West Biomedical Engineering Conference*, 2005.

[Liv2005d] Y. Livnat, X. Tricoche.
**“Shadows for Incomplete Point-based Isosurfaces,”** SCI Institute Technical Report, No. UUSCI-2005-001, *University of Utah*, 2005.

[Mac2005a] R.S. MacLeod, B. Yilmaz, B.B. Punske, B. Taccardi, D.H. Brooks.
**“Epicardial Activation Mapping from Multielectrode Venous Catheters,”** In *J. Electrocardiol.*, pp. (in press). 2005.

[Mac2005b] R.S. MacLeod, S. Shome, J.G. Stinstra, B.P. Punske, B. Hopenfeld.
**“Mechanisms of Ischemia-Induced ST-Segment Changes,”** In *J. Electrocardiol.*, Vol. 38(4 Suppl), pp. 8--13. November, 2005.

[Mac2005c] R.S. MacLeod.
**“Mechanisms of ischemia-induced ST-segment changes,”** In *Journal of Electrocardiology*, Vol. 38, No. 4 , Elsevier, pp. 8--13. Oct, 2005.

DOI: 10.1016/j.jelectrocard.2005.06.095

[Mac2005e] R.S. MacLeod, F. Kornreich, A. van Oosterom, P. Rautaharju, R. Selvester, G. Wagner, C. Zywietz.
**“Report of the First Virtual Visualization of the Reconstructed Electrocardiographic Display Symposium,”** In *Journal of Electrocardiology*, Vol. 38, pp. 385--399. 2005.

[Sam2005a] A.A. Samsonov, E.V.R. DiBella, P. Kellman, E.G. Kholmovski, C.R. Johnson.
**“Adaptive k-t BLAST/k-t SENSE for Accelerating Cardiac Perfusion MRI,”** In *Proceedings of the Society for Cardiovascular Magnetic Resonance (SCMR) 8th Annual Scientific Sessions*, pp. 277--278. 2005.

[Sch2005a] G. Scheuermann, X. Tricoche.
**“Topological Methods for Flow Visualization,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 341--356. 2005.

ISBN: 0-12-387582-X

[Ser2005a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Bayesian Solutions and Performance Analysis in Bioelectric Inverse Problems,”** In *IEEE Trans Biomed. Eng.*, Vol. 52, No. 6, pp. 1009--1020. June, 2005.

[Sti2005a] J.G. Stinstra, D.M. Weinstein, B. Hopenfeld, C.S. Henriquez, R.S. MacLeod.
**“Software Challenges in the New Field of Integrated Cardiac Models,”** In *Proceedings of The Joint Meeting of The 5th International Conference on Bioelectromagnetism and The 5th International Symposium on Noninvasive Functional Source Imaging within the Human Brain and Heart*, Vol. 7, pp. 195--198. 2005.

[Sti2005b] J.G. Stinstra, B. Hopenfeld, R.S. MacLeod.
**“On the Passive Cardiac Conductivity,”** In *Annal. Biomed. Eng.*, Vol. 33, No. 12, pp. 1743--1751. 2005.

[Sti2005c] J.G. Stinstra, S. Shome, B. Hopenfeld, R.S. MacLeod.
**“Modelling Passive Cardiac Conductivity During Ischaemia,”** In *Med. Biol. Eng. Comput.*, Vol. 43, No. 6, pp. 776--782. 2005.

[Tac2005a] B. Taccardi, B.B. Punske, F. Sachse, X. Tricoche, P. Colli-Franzone, L.F. Pavarino, C. Zabawa.
**“Intramural Activation and Repolarization Sequences in Canine Ventricles. Experimental and Simulation Studies,”** In *J. Electrocardiol.*, Vol. 38, No. 4, pp. 131-137. 2005.

[Tas2005a] T. Tasdizen, S.P. Awate, R.T. Whitaker, N. Foster.
**“MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach,”** In *Proceedings of The 8th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI)*, pp. 517--525. 2005.

PubMed ID: 16685999

[Whi2005a] R.T. Whitaker.
**“Isosurfaces and Level-Sets,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 97--123. 2005.

ISBN: 0-12-387582-X

[Wol2005b] C. H. Wolters, A. Anwander, X. Tricoche, S. Lew, C.R. Johnson.
**“Influence of Local and Remote White Matter Conductivity Anisotropy for a Thalamic Source on EEG/MEG Field and Return Current Computation,”** In *Int.Journal of Bioelectromagnetism*, Vol. 7, No. 1, pp. 203--206. 2005.

[Yil2005a] B. Yilmaz, R.S. MacLeod, B.B. Punske, B. Taccardi, D.H. Brooks.
**“Training Set Selection for Statistical Estimation of Epicardial Activation Mapping from Intravenous Multielectrode Catheters,”** In *IEEE Trans Biomed. Eng.*, pp. (in press). 2005.

[Yil2005b] B. Yilmaz, R.S. MacLeod, B.B. Punske, B. Taccardi, D.H. Brooks.
**“Venous Catheter Based Mapping of Ectopic Epicardial Activation: Training Data Set Selection for Statistical Estimation,”** In *IEEE Trans Biomed Eng*, Vol. 52, No. 11, pp. 1823--1831. November, 2005.

[Zha2005a] S. Zhang, D.H. Laidlaw, G. Kindlmann.
**“Diffusion Tensor MRI Visualization,”** In *The Visualization Handbook*, Edited by C.D. Hansen and C.R. Johnson, Elsevier, pp. 327--340. 2005.

ISBN: 0-12-387582-X

[Bro2004b] D.H. Brooks, A. Ghodrati, Y. Zhang, G. Tadmor, R.S. MacLeod.
**“Inverse Electrocardiography in the Framework of Dynamic Imaging Problems,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference*, San Francisco, CA, pp. 3565--3568. September, 2004.

[Cat2004b] J. Cates, R.T. Whitaker, G.M. Jones.
**“Case Study: An Evaluation of User-Assisted Hierarchical Watershed Segmentation,”** No. UUCS-04-006, *University of Utah School of Computing*, 2004.

[Cat2004c] J. Cates, A. Lefohn, R.T. Whitaker.
**“GIST: An Interactive, GPU-Based Level Set Segmentation Tool for 3D Medical Images,”** In *Medical Image Analysis*, Vol. 8, No. 3, pp. 217--231. September, 2004.

[Che2004a] A.B. Cheryauka, J.N. Lee, A.A. Samsonov, M. Defrise, G.T. Gullberg.
**“MRI Diffusion Tensor Reconstruction with PROPELLER Data Acquisition,”** In *J. Mag. Res. Imag.*, Vol. 22, No. 2, pp. 139--148. 2004.

[Gar2004a] C. Garth, X. Tricoche, G. Scheuermann.
**“Tracking of Vector Field Singularities in Unstructured 3D Time-Dependent Datasets,”** In *Proceeding of IEEE Visualization 2004*, pp. 329--336. 2004.

[Gar2004b] C. Garth, X. Tricoche, T. Salzbrunn, T. Bobach, G. Scheuermann.
**“Surface Techniques for Vortex Visualization,”** In *Proceedings of Joint Eurographics - IEEE TCVG Symposium on Visualization*, pp. 155--164. May, 2004.

[Gho2004a] A. Ghodrati, D.H. Brooks, R.S. MacLeod.
**“On Selecting and Using Reduced Sets of Leads for Electrocardiographic Imaging Using Reconstruction-Quality Criteria,”** In *Proceedings of The SIAM Conference on Imaging Science 2004*, Salt Lake City, UT, Note: *abstract.*, May, 2004.

[Gho2004b] A. Ghodrati, F. Calderero, D.H. Brooks, G. Tadmor, R.S. MacLeod.
**“A Level Sets Algorithm for the Inverse Problem of Electrocardiography,”** In *Proceedings of the Asilomar Conf. on Sig. and Sys.*, Vol. 2, pp. 1590--1594. November, 2004.

[Hen2004a] C.S. Henriquez, J.V. Tranquillo, D.M. Weinstein, E.W. Hsu, C.R. Johnson.
**“Three-dimensional Propagation in Mathematic Models: Integrative Model of the Mouse Heart,”** In *Cardiac Electrophysiology: From Cell to Bedside*, 4th edition, Ch. 30, Edited by D.P. Zipes and J. Jalife, Saunders, pp. 273--281. 2004.

[Hop2004a] B. Hopenfeld, J.G. Stinstra, R.S. MacLeod.
**“Mechanism for ST Depression Associated with Contiguous Subendocardial Ischemia,”** In *J. Cardiovasc. Electrophysiol.*, Vol. 15, No. 10, pp. 1200--1206. 2004.

[Joh2004a] C.R. Johnson.
**“Top Scientific Visualization Research Problems,”** In *IEEE Computer Graphics and Applications: Visualization Viewpoints*, Vol. 24, No. 4, pp. 13--17. July/August, 2004.

[Kin2004a] G Kindlmann.
**“Superquadric Tensor Glyphs,”** In *Proceeding of The Joint Eurographics - IEEE TCVG Symposium on Visualization 2004*, pp. 147--154. May, 2004.

[Kin2004b] G.L. Kindlmann, D.M. Weinstein, A.D. Lee, A.W. Toga, P.M. Thompson.
**“Visualization of Anatomic Covariance Tensor Fields,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference*, 2004.

[Kni2004a] J.M. Kniss, J.P. Schulze, U. Wössner, P. Winkler, U. Lang, C.D. Hansen.
**“Medical Applications of Multi-field Volume Rendering and VR Techniques,”** In *Proceeding of The Joint Eurographics - IEEE TCVG Symposium on Visualization 2004*, pp. 249--254. 2004.

[Lef2004a] A.E. Lefohn, J.M. Kniss, C.D. Hansen, R.T. Whitaker.
**“A Streaming Narrow-Band Algorithm: Interactive Deformation and Visualization of Level Sets,”** In *IEEE Trans. Vis & Comp. Graph.*, pp. 422--433. 2004.

[Liv2004a] Y. Livnat, X. Tricoche.
**“Interactive Point Based Isosurface Extraction,”** In *Proceeding of IEEE Visualization 2004*, pp. 457--464. 2004.

[Mac2004a] R.S. Macleod, D.M. Weinstein, J.D. de St. Germain, D.H. Brooks, C.R. Johnson, S.G. Parker.
**“SCIRun/BioPSE: Integrated Problem Solving Environment for Bioelectric Field Problems and Visualization,”** In *Proceedings of the Int. Symp. on Biomed. Imag.*, Arlington, Va, pp. 640--643. April, 2004.

[Sam2004e] A.A. Samsonov, E.G. Kholmovski, C.R. Johnson.
**“Phase-Constrained Reconstruction of Sensitivity-Encoded MRI Data with POCSENSE,”** In *Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM)*, Kyoto, Japan, pp. 2647. 2004.

[Sam2004f] A.A. Samsonov, C.R. Johnson.
**“Noise-Adaptive Nonlinear Diffusion Filtering of MR Images with Spatially Varying Noise Levels,”** In *Magn. Reson. Med.*, Vol. 52, pp. 798--806. 2004.

[Sam2004g] A.A. Samsonov, E.G. Kholmovski, D.L. Parker, C.R. Johnson.
**“POCSENSE: POCS-based reconstruction for sensitivity encoded MRI,”** In *Magn. Reson. Med.*, Vol. 52, pp. 1397--1406. 2004.

[Sam2004h] A.A. Samsonov, C.R. Johnson.
**“Multicoil MRI Artifacts Correction Using Parallel Pocs,”** In *Proceedings of The 12th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM)*, 2004.

[San2004a] A.R. Sanderson, C.R. Johnson, R.M. Kirby.
**“Display of Vector Fields Using a Reaction Diffusion Model,”** In *Proceeding of IEEE Visualization 2004*, pp. 115--122. 2004.

[Sch2004a] U. Schmitt, C.H. Wolters, A. Anwander, T. Knoesche.
**“STR: A New Spatio-Temporal Approach for Accurate and Efficient Current Density Reconstruction,”** In *Proceedings of The 14th International Conference on Biomagnetism*, pp. 591--592. 2004.

[Tas2004a] T. Tasdizen, D.M. Weinstein, J.N. Lee.
**“Automatic Tissue Classification for the Human Head from Multispectral MRI,”** SCI Institute Technical Report, No. UUSCI-2004-001, *University of Utah*, March, 2004.

[Tas2004b] T. Tasdizen, R.T. Whitaker.
**“Higher-order nonlinear priors for surface reconstruction,”** In *IEEE Trans. Pattern Anal. & Mach. Intel.*, Vol. 26, No. 7, pp. 878--891. July, 2004.

[Tri2004a] X. Tricoche, C. Garth, G. Kindlmann, E. Deines, G. Scheuermann, Markus Ruetten, Charles D. Hansen.
**“Visualization of Intricate Flow Structures for Vortex Breakdown Analysis,”** In *Proceeding of IEEE Visualization 2004*, pp. 187--194. 2004.

[Wol2004a] C.H. Wolters, L. Grasedyck, A. Anwander, H. Hackbusch.
**“Efficient Computation of Lead Field Bases and Influence Matrix for the FEM-Based EEG and MEG Inverse Problem,”** In *Proceedings of The 14th International Conference on Biomagnetism*, Boston, MA, pp. 104--107. August, 2004.

[Wol2004b] C.H. Wolters, L. Grasedyck, W. Hackbusch.
**“Efficient Computation of Lead Field Bases and Influence Matrix for the FEM-Based EEG and MEG Inverse Problem,”** In *Inverse Problems*, Vol. 20, No. 4, pp. 1099--1116. 2004.

[Wol2004c] C.H. Wolters, A. Anwander, B. Maess, R.S. MacLeod, A.D. Friederici.
**“The Influence of Volume Conduction Effects on the EEG/MEG Reconstruction of the Sources of the Early Left Anterior Negativity,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference*, San Francisco, CA, Vol. 5, pp. 3569--3572. September, 2004.

[Wol2004d] C.H. Wolters, A. Anwander, S. Reitzinger, G. Haase.
**“Algebraic Multigrid with Multiple Right-Hand-Side Treatment for an Efficient Computation of EEG and MEG Lead Field Bases,”** In *Proceedings of The 14th International Conference on Biomagnetism*, Boston, MA, pp. 465--466. August, 2004.

[Wol2004e] C.H. Wolters, A. Anwander, S. Reitzinger, G. Haase.
**“Avoiding the Problem of FE Meshing: A Parallel Algebraic Multigrid with Multiple Right-Hand Side Treatment for an Efficient and Memory-Economical Computation of High Resolution EEG and MEG Lead Field Bases,”** In *poster*, September, 2004.

[Col2003a] M. Cole, S.G. Parker.
**“Dynamic Compilation of C++ Template Code,”** In *Scientific Programming*, Vol. 11, IOS Press, pp. 321--327. 2003.

[Cor2003a] A. Corlan, R.S. MacLeod, L.D. Ambroggi.
**“Low Variability of Autocorrelation Maps with Intrathoracic Heart Position,”** In *Int. J. Bioelectromag.*, Vol. 5, No. 1, pp. 139--140. 2003.

[Ser2003a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Prior Model Selection for Bayesian Inverse Electrocardiography,”** In *Proceedings of the NFSI Conference 2003*, Chieti, Italy, 2003.

[Ser2003b] Y. Serinagaoglu, R.S. MacLeod, D.H. Brooks.
**“A Bayesian Approach to Inclusion and Performance Analysis of Using Extra Information in Bioelectric Inverse Problems,”** In *Proceedings of the IEEE International Conference on Image Processing*, 2003.

[Ser2003c] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Combining Numerical and Physiological Constraints in Inverse Electrocardiography,”** In *Int. J. Bioelectromag.*, Vol. 5, No. 1, pp. 215--217. 2003.

[Sti2003a] J.G. Stinstra, B. Hopenfeld, R.S. MacLeod.
**“A Model for the Passive Cardiac Conductivity,”** In *Int. J. Bioelectromag.*, Vol. 5, No. 1, pp. 185--186. 2003.

[Wei2003b] D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson.
**“BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation,”** In *International Journal of Bioelectromagnetism*, Vol. 5, No. 1, pp. 314--315. 2003.

[Zyp2003a] K. Zyp.
**“The Transfer Operator for Multigrid on Inverse Bioelectric Field Problems,”** SCI Institute Technical Report, No. UUSCI-2003-001, Note: *Masters thesis*, *University of Utah*, May, 2003.

[Joh2002a] C.R. Johnson, S.G. Parker, D. Weinstein, S. Heffernan.
**“Component-Based Problem Solving Environments for Large-Scale Scientific Computing,”** In *J. Conc. & Comp.: Prac. & Exper.*, Vol. 14, pp. 1337--1349. 2002.

[Kho2002a] E.G. Kholmovski, A.A. Samsonov, D.L. Parker.
**“POCSENSE: POCS-based method for reconstruction from sensitivity-encoded data,”** In *Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM)*, Honolulu, pp. 194. 2002.

[Kho2002b] E.G. Kholmovski, A.A. Samsonov, D.L. Parker.
**“Motion Artifact Reduction Technique for Dual Contrast FSE Imaging,”** In *Magnetic Resonance Imaging*, Vol. 20, No. 6, pp. 455--462. 2002.

[Mac2002a] R.S. MacLeod, Q. Ni, B. Taccardi.
**“Modeling Cardiac Bioelectricity in Realistic Volumes: How Real is Real?,”** In *Einthoven 2002*, Leiden, Edited by M.J. Schalij and M.J. Janse and A. van Oosterom and H.J.J. Wellens and E.E. van der Wall, *The Einthoven Foundation*, pp. 45-56. 2002.

[Mac2002b] R.S. MacLeod, E.D. DiBella, B.B. Punske, E.K. Jeong.
**“Multimodal Imaging of Cardiac Activation, Perfusion, and Ischemia,”** In *14th Annual Research Symposium of the Medical Imaging Research Laboratory*, 2002.

[Qua2002a] H.W. Quartero, J.G. Stinstra, E.G. Golbach, E.J. Meijboom, M.J. Peters.
**“Clinical Implications of Fetal Magnetocardiography,”** In *Ultrasound Obstet Gynecol*, Vol. 20, No. 2, pp. 142--153. 2002.

[Sam2002d] A.A. Samsonov, E.G. Kholmovski.
**“Method for Quality Improvement of Images Reconstructed From Sensitivity-Encoded Data,”** In *Proceedings of The 10th Annual Scientific Meeting of The International Society for Magnetic Resonance in Medicine (ISMRM)*, Honolulu, pp. 2408. 2002.

[Ser2002a] Y. Serinagaoglu, D.H. Brooks, R.S. MacLeod.
**“Including Sparse Noisy Epicardial Potential Measurements Into Bayesian Inverse Electrocardiography,”** In *Proceedings of EMBC 2002*, 2002.

[Ser2002b] Y. Serinagaoglu, R.S. MacLeod, B. Yilmaz, D.H. Brooks.
**“Multielectrode Venous Catheter Mapping as a High Quality Constraint for Electrocardiographic Inverse Solution,”** In *J. Electrocardiol.*, Vol. 35 (supplement), 2002.

[Sti2002a] J. Stinstra, M. Peters.
**“The Influence of Fetoabdominal Tissues on Fetal ECGs and MCGs,”** In *Arch Physiol Biochem*, Vol. 110, No. 3, pp. 165--176. 2002.

[Tac2002a] B. Taccardi, B.B. Punske, R.S. MacLeod, Q. Ni.
**“Visualization, Analysis and Physiological Interpretation of Three-dimentional Cardiac Electric Fields,”** In *Proceedings of 24th Annual International Conference of the IEEE Engineering in Medicine and Biology Society*, 2002.

[Uit2002b] R. Van Uitert, C.R. Johnson.
**“Can a Spherical Model Substitute for a Realistic Head Model in Forward and Inverse MEG Simulations?,”** In *Proceedings of The 13th International Conference on Biomagnetism*, Jena, Germany, August, 2002.

[But2001a] C.R. Butson.
**“From Action Potentials to Surface Potentials,”** In *Multilevel Neuronal Modeling Workshop*, Edinburgh, Scotland, May, 2001.

[Gum2001a] S. Gumhold, X. Wang, R.S. MacLeod.
**“Feature Extraction from Point Clouds,”** In *Proceedings, 10th International Meshing Round Table*, Sandia National Laboratories, pp. 293--305. 2001.

[Joh2001a] C.R. Johnson, D. Brederson, C.D. Hansen, M. Ikits, G. Kindlmann, Y. Livnat, S.G. Parker, D.M. Weinstein, R.T. Whitaker.
**“Computational Field Visualization,”** In *Computer Graphics*, Vol. 35, No. 4, pp. 5--9. 2001.

[Joh2001c] C.R. Johnson, M. Mohr, U. Ruede, A. Samsonov, K. Zyp.
**“Multilevel Methods for Inverse Bioelelectric Field Problems,”** In *Lecture Notes in Computational Science and Engineering - Multiscale and Multiresolution Methods: Theory and Applications*, Vol. 20, Edited by T.J. Barth and T.F. Chan and R. Haimes, Springer-Verlag Publishing, Heidelberg pp. 331--346. October, 2001.

[Joh2001d] C.R. Johnson.
**“Adaptive Finite Element and Local Regularization Methods for the Inverse ECG Problem,”** In *Inverse Problems in Electrocardiology*, Advances in Computational Biomedicine, Vol. 5, Edited by Peter Johnston, WIT Press, pp. 51--88. 2001.

[Joh2001e] C.R. Johnson.
**“Computational Bioimaging for Medical Diagnosis and Treatment,”** In *Communications of the ACM*, Vol. 44, No. 3, pp. 74--76. March, 2001.

[Mac2001a] R.S. MacLeod, B. Yilmaz, B. Taccardi, B.B. Punske, Y. Serina, D.H. Brooks.
**“Direct and Inverse Methods for Cardiac Mapping Using Multielectrode Catheter Measurements,”** In *Journal of Biomedizinische Technik*, Vol. 46(supp), pp. 207--209. 2001.

[Mac2001b] R.S. MacLeod, B.B. Punske, B. Yilmaz, S. Shome, B. Taccardi.
**“The Role of Heart Rate in Myocardial Ischemia From Restricted Coronary Perfusion,”** In *J. Electrocardiol.*, Vol. 34 (supp), Note: *ISCE conference paper*, pp. 43--51. 2001.

[Por2001a] O. Portniaguine, D.M. Weinstein, C.R. Johnson.
**“Focusing Inversion of Electroencephalography and Magnetoencephalography Data,”** In *3rd International Symposium On Noninvasive Functional Source Imaging*, Journal of Biomedizinische Technik (special issue), Vol. 46, Innsbruck, Austria pp. 115--117. Sep, 2001.

[Tac2001a] B. Taccardi, B.B. Punske, R.S. MacLeod, Q. Ni.
**“Extracardiac Effects of Myocardial Electrical Anisotropy,”** In *Biomed. Technik*, Vol. 46(suppl 2), pp. 216--218. 2001.

[Uit2001] R. Van Uitert, D. Weinstein, C.R. Johnson, L. Zhukov.
**“Finite Element EEG and MEG Simulations for Realistic Head Models: Quadratic vs. Linear Approximations,”** In *Biomed. Technik*, Vol. 46, pp. 32--34. 2001.

[Wei2001a] D. Weinstein, O. Portniaguine, L. Zhukov.
**“A Comparison of Dipolar and Focused Inversion for EEG Source Localization,”** In *Biomed. Technik*, Vol. 46 (special issue), pp. 121--123. Sep, 2001.

[Zhu2001] L. Zhukov, D.M. Weinstein, C.R. Johnson, R.S. Macleod.
**“Spatio-temporal Multi-dipole Source Localization Using ICA and Lead-Fields in FEM Head Models,”** In *Proceedings of the IEEE Engineering in Medicine and Biology Society 23rd Annual International Conference*, Istanbul, Turkey Oct, 2001.

[Joh2000b] C.R. Johnson, S.G. Parker, D. Weinstein.
**“Large-Scale Computational Science Applications Using the SCIRun Problem Solving Environment,”** In *Proceedings of The International Supercomputer Conference 2000*, 2000.

[Kin2000] G.L. Kindlmann, D.M. Weinstein, D. Hart.
**“Strategies for Direct Volume Rendering of Diffusion Tensor Fields,”** In *IEEE Trans. Vis & Comp. Graph.*, Vol. 6, No. 2, pp. 124--138. April-June, 2000.

[Liv2000] Y. Livnat, S.G. Parker, C.R. Johnson.
**“Fast Isosurface Extraction Methods for Large Image Data Sets,”** In *Handbook of Medical Imaging*, Edited by A.N. Bankman, Academic Press, San Diego, CA pp. 731--745. Nov, 2000.

[Wei2000a] D.M. Weinstein, L. Zhukov, G. Potts.
**“Localization of Multiple Deep Epileptic Sources in a Realistic Head Model via Independent Component Analysis,”** School of Computing Technical Report, No. UUCS-2000-004, *University of Utah*, February, 2000.

[Wei2000b] D.M. Weinstein, L. Zhukov, C.R. Johnson.
**“Lead-Field Bases for EEG Source Imaging,”** In *Annal. Biomed. Eng.*, Vol. 28, No. 9, pp. 1059--1065. Sep, 2000.

[Wei2000c] D. Weinstein.
**“Scanline Surfacing: Building Separating Surfaces from Planar Contours,”** In *Proceeding of IEEE Visualization 2000*, pp. 283--289. 2000.

[Wei2000d] D.M. Weinstein, L. Zhukov, C.R. Johnson.
**“An Inverse EEG Problem Solving Environment and its Applications to EEG Source Localization,”** In *NeuroImage (suppl.)*, pp. 921. 2000.

[Wei2000f] D.M. Weinstein, L. Zhukov, C.R. Johnson, S.G. Parker, R. Van Uitert, R.S. MacLeod, C.D. Hansen.
**“Interactive Source Imaging with BioPSE,”** In *Chicago 2000 World Congress on Medical Physics and Biomedical Engineering*, Chicago, IL., Note: *Refereed abstract.*, July, 2000.

[Wei2000g] D.M. Weinstein, P. Krysl, C.R. Johnson.
**“The BioPSE Inverse EEG Modeling Pipeline,”** In *ISGG 7th International Conference on Numerical Grid Generation in Computation Field Simulations*, The International Society of Grid Generation, Mississippi State University pp. 1091--1100. 2000.

[Zhu2000a] L. Zhukov, D. Weinstein, C.R. Johnson.
**“Statistical Analysis For FEM EEG Source Localization in Realistic Head Models,”** School of Computing Technical Report, No. UUCS-2000-003, *University of Utah*, February, 2000.

[Zhu2000b] L. Zhukov, D.M. Weinstein, C.R. Johnson.
**“Reciprocity Basis for EEG Source Imaging,”** In *NeuroImage (suppl.)*, pp. 598. 2000.

[Zhu2000c] L. Zhukov, D. Weinstein, C.R. Johnson.
**“Independent Component Analysis for EEG Source Localization in Realistic Head Models,”** In *IEEE Engineering in Medicine and Biology*, Vol. 19, No. 3, pp. 87--96. 2000.

[Bro1999a] D.H. Brooks, G.F. Ahmad, R.S. MacLeod, G.M. Maratos.
**“Inverse Electrocardiography by Simultaneous Imposition of Multiple Constraints,”** In *IEEE Trans Biomed. Eng.*, Vol. 46, No. 1, pp. 3--18. 1999.

[Joh99c] C.R. Johnson, S.G. Parker, C.D. Hansen, G.L. Kindlmann, Y. Livnat.
**“Interactive Simulation and Visualization,”** In *IEEE Computer*, Vol. 32, No. 12, pp. 59--65. Dec, 1999.

[Mil1999a] M. Miller, C.D. Hansen, C.R. Johnson.
**“The SCIRun Problem Solving Environment: Implementation within a Distributed Environment,”** In *Ninth SIAM Conference on Parallel Processing for Scientific Computing*, Note: *extended abstract*, 1999.

[Wei1999c] D.M. Weinstein, L. Zhukov, C.R. Johnson.
**“Lead Field Basis for FEM Source Localization,”** School of Computing Technical Report, No. UUCS-99-014, *University of Utah*, Salt Lake City, UT October, 1999.

[Zhu99a] L. Zhukov, D.M. Weinstein, C.R. Johnson.
**“Independent Component Analysis For EEG Source Localization In Realistic Head Models,”** In *Third International Conference on Inverse Problems in Engineering*, 1999.

[Joh1992e] C.R. Johnson, R.S. MacLeod, P.R. Ershler.
**“A Computer Model for the Study of Electrical Current Flow in the Human Thorax,”** In *Computers in Biology and Medicine*, Vol. 22, No. 5, Elsevier BV, pp. 305--323. 1992.