[And2018a] D. N. Anderson, B. Osting, J. Vorwerk, A. D Dorval, C. R Butson.
**“Optimized programming algorithm for cylindrical and directional deep brain stimulation electrodes,”** In *Journal of Neural Engineering*, Vol. 15, No. 2, pp. 026005. 2018.

[Cat2017a] J. Cates, L. Nevell, S. I. Prajapati, L. D. Nelon, J. Y. Chang, M. E. Randolph, B. Wood, C. Keller, R. T. Whitaker.
**“Shape analysis of the basioccipital bone in Pax7-deficient mice,”** In *Scientific Reports*, Vol. 7, No. 1, Springer Nature, Dec, 2017.

DOI: 10.1038/s41598-017-18199-9

[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.

[Ghi2017a] S. Ghimire, J. Dhamala, J. Coll-Font, J. D. Tate, M. S. Guillem, D. H. Brooks, R. S. MacLeod, L. Wang.
**“Overcoming Barriers to Quantification and Comparison of Electrocardiographic Imaging Methods: A Community-Based Approach,”** In *Computing in Cardiology*, Vol. 44, 2017.

[Goo2017a] W. W. Good, B. Erem, J. Coll-Font, D. H. Brooks, R. S. MacLeod.
**“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.

DOI: 10.1101/123844

[Tat2017a] J. Tate, K. Gillette, B. Burton, W. Good, J. Coll-Font, D. Brooks, R. MacLeod.
**“Analyzing Source Sampling to Reduce Error in ECG Forward Simulations,”** In *Computing in Cardiology*, Vol. 44, 2017.

[Wan2017d] Y. Wan, C. Hansen.
**“Uncertainty Footprint: Visualization of Nonuniform Behavior of Iterative Algorithms Applied to 4D Cell Tracking,”** In *Computer Graphics Forum*, Wiley, 2017.

[Wan2017e] Y. Wan, H. Otsuna, H. A. Holman, B. Bagley, M. Ito, A. K. Lewis, M. Colasanto, G. Kardon, K. Ito, C. Hansen.
**“FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis,”** In *BMC Bioinformatics*, Vol. 18, No. 1, Springer Nature, May, 2017.

DOI: 10.1186/s12859-017-1694-9

[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.

[Atk2016a] P.R. Atkins, S.Y. Elhabian, P. Agrawal, M.D. Harris, R.T. Whitaker, J.A. Weiss, C.L. Peters, A.E. Anderson.
**“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.

DOI: 10.1002/jor.23468

[Bak2016a] J.L. Baker, J. Ryou, X.F. Wei, C.R. Butson, N.D. Schiff, K.P. Purpura.
**“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.

DOI: 10.1152/jn.01129.2015

[Elh2016b] S. Elhabian, P. Agrawal, R. Whitaker.
**“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.

DOI: 10.1109/isbi.2016.7493353

[Ere2016a] B. Erem, R.M. Orellana, D.E. Hyde, J.M. Peters, F.H. Duffy, P. Stovicek, S.K. Warfield, R.S. MacLeod, G. Tadmor, D.H. Brooks.
**“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.

DOI: 10.1103/physreve.93.042218

[Fie2016a] L.D.J. Fiederer, J. Vorwerk, F. Lucka, M. Dannhauer, S. Yang, M. Dümpelmann, A. Schulze-Bonhage, A. Aertsen, O. Speck, C.H. Wolters, T. Ball.
**“The role of blood vessels in high-resolution volume conductor head modeling of EEG,”** In *NeuroImage*, Vol. 128, Elsevier, pp. 193--208. March, 2016.

DOI: 10.1016/j.neuroimage.2015.12.041

[Gal2016a] C. Gall, S. Schmidt, M.P. Schittkowski, A. Antal, G. Ambrus, W. Paulus, M. Dannhauer, R. Michalik, A. Mante, M. Bola, A. Lux, S. Kropf, S.A. Brandt, B.A. Sabel.
**“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.

DOI: 10.1371/journal.pone.0156134

[Gul2016a] S. Guler, M. Dannhauer, B. Erem, R.S. Macleod, D. Tucker, S. Turovets, P. Luu, D. Erdogmus, D. Brooks.
**“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.

DOI: 10.1088/1741-2560/13/3/036020

[Hol2016a] B. Hollister, G. Duffley, C. Butson,, C.R. Johnson.
**“Visualization for Understanding Uncertainty in Activation Volumes for Deep Brain Stimulation,”** In *Eurographics Conference on Visualization*, Edited by K.L. Ma G. Santucci, and J. van Wijk, 2016.

[Pat2016a] Y. Pathak, O. Salami, S. Baillet, Z. Li, C.R. Butson.
**“Longitudinal Changes in Depressive Circuitry in Response to Neuromodulation Therapy,”** In *Frontiers in Neural Circuits*, Vol. 10, rontiers Media SA, July, 2016.

DOI: 10.3389/fncir.2016.00050

[Pol2016a] I.A. Polejaeva, R. Ranjan, C.J. Davies, M. Regouski, J. Hall, A.L. Olsen, Q. Meng, H.M. Rutigliano, D.J. Dosdall, N.A. Angel, F.B. Sachse, T. Seidel, A.J. Thomas, R. Stott, K.E. Panter, P.M. Lee, A.J. Van Wettere, J.R. Stevens, Z. Wang, R.S. Macleod, N.F. Marrouche, K.L. White.
**“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.

DOI: 10.1111/jce.13049

[Raj2016a] M. Raj, M. Mirzargar, R. Kirby, R. Whitaker, J. Preston.
**“Evaluating Shape Alignment via Ensemble Visualization,”** In *IEEE Computer Graphics and Applications*, Vol. 36, No. 3, IEEE, pp. 60--71. May, 2016.

DOI: 10.1109/mcg.2015.70

[Ros2016a] P. Rosen, B. Burton, K. Potter, C.R. Johnson.
**“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.

DOI: 10.1007/978-3-319-24523-2_3

[Ton2016a] X. Tong, J. Edwards, C. Chen, H. Shen, C. R. Johnson, P. Wong.
**“View-Dependent Streamline Deformation and Exploration,”** In *Transactions on Visualization and Computer Graphics*, Vol. 22, No. 7, IEEE, pp. 1788--1801. July, 2016.

ISSN: 1077-2626

DOI: 10.1109/tvcg.2015.2502583

[Ara2015a] K.K. Aras, W. Good, J. Tate, B.M. Burton, D.H. Brooks, J. Coll-Font, O. Doessel, W. Schulze, D. Patyogaylo, L. Wang, P. Van Dam,, R.S. MacLeod.
**“Experimental Data and Geometric Analysis Repository: EDGAR,”** In *Journal of Electrocardiology*, 2015.

[CIBCData] CIBC.
Note: *Data Sets: NCRR Center for Integrative Biomedical Computing (CIBC) data set archive. Download from: http://www.sci.utah.edu/cibc/software.html*, 2015.

[Cleaver] CIBC.
Note: *Cleaver: A MultiMaterial Tetrahedral Meshing Library and Application. Scientific Computing and Imaging Institute (SCI), Download from: http://www.sci.utah.edu/cibc/software.html*, 2015.

[Gao2015a] Y. Gao, L. Zhu, J. Cates, R. S. MacLeod, S. Bouix,, A. Tannenbaum.
**“A Kalman Filtering Perspective for Multiatlas Segmentation,”** In *SIAM J. Imaging Sciences*, Vol. 8, No. 2, pp. 1007-1029. 2015.

DOI: 10.1137/130933423

[Gil2015a] K. Gillette, J.D. Tate, B. Kindall, P. Van Dam, E. Kholmovski, R.S. MacLeod.
**“Generation of Combined-Modality Tetrahedral Meshes,”** In *Computing in Cardiology*, 2015.

[ImageVis3D] CIBC.
Note: *ImageVis3D: An interactive visualization software system for large-scale volume data. Scientific Computing and Imaging Institute (SCI), Download from: http://www.imagevis3d.org*, 2015.

[Joh2015c] C.R. Johnson.
**“Computational Methods and Software for Bioelectric Field Problems,”** In *Biomedical Engineering Handbook*, 4, Vol. 1, Ch. 43, Edited by J.D. Bronzino and D.R. Peterson, CRC Press, pp. 1--28. 2015.

[Joh2015d] C.R. Johnson.
**“Visualization,”** In *Encyclopedia of Applied and Computational Mathematics*, Edited by Björn Engquist, Springer, pp. 1537-1546. 2015.

ISBN: 978-3-540-70528-4

DOI: 10.1007/978-3-540-70529-1_368

[Map3d] CIBC.
Note: *map3d: Interactive scientific visualization tool for bioengineering data. Scientific Computing and Imaging Institute (SCI), Download from: http://www.sci.utah.edu/cibc/software.html*, 2015.

[Mcd2015a] K.S. McDowell, S. Zahid, F. Vadakkumpadan, J.J. Blauer, R.S. MacLeod, N.A. Trayanova.
**“Virtual Electrophysiological Study of Atrial Fibrillation in Fibrotic Remodeling,”** In *PLoS ONE*, Vol. 10, No. 2, pp. e0117110. February, 2015.

DOI: 10.1371/journal.pone.0117110

[Ogu2015a] I. OguzI, J. Cates, M. Datar, B. Paniagua, T. Fletcher, C. Vachet, M. Styner, R. Whitaker.
**“Entropy-based particle correspondence for shape populations,”** In *International Journal of Computer Assisted Radiology and Surgery*, Springer, pp. 1-12. December, 2015.

[Par2015a] B.R. Parmar, T.R. Jarrett, E.G. Kholmovski, N. Hu, D. Parker, R.S. MacLeod, N.F. Marrouche, R. Ranjan.
**“Poor scar formation after ablation is associated with atrial fibrillation recurrence,”** In *Journal of Interventional Cardiac Electrophysiology*, Vol. 44, No. 3, pp. 247-256. December, 2015.

[SCIRun] SCI Institute.
Note: *SCIRun: A Scientific Computing Problem Solving Environment, Scientific Computing and Imaging Institute (SCI), Download from: http://www.scirun.org*, 2015.

[Seg3D] CIBC.
Note: *Seg3D: Volumetric Image Segmentation and Visualization. Scientific Computing and Imaging Institute (SCI), Download from: http://www.seg3d.org*, 2015.

[Bla2014a] J.J.E. Blauer, D. Swenson, K. Higuchi, G. Plank, R. Ranjan, N. Marrouche,, R.S. MacLeod.
**“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.

[Bro2014a] J. Bronson, J.A. Levine, R.T. Whitaker.
**“Lattice cleaving: a multimaterial tetrahedral meshing algorithm with guarantees,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, pp. 223--237. 2014.

DOI: 10.1109/TVCG.2013.115

PubMed ID: 24356365

[Eic2014a] S. Eichelbaum, M. Dannhauer, M. Hlawitschka , D.H. Brooks, T.R. Knosche, G. Scheuermanna.
**“Visualizing Simulated Electrical Fields from Electroencephalography and Transcranial Electric Brain Stimulation: A Comparative Evaluation,”** In *Neuroimage*, 2014.

DOI: 10.1016/j.neuroimage.2014.04.085

[Ere2014a] B. Erem P.M. van Dam, D.H. Brooks.
**“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.

DOI: 10.1109/TMI.2014.2297952

PubMed ID: 24710159

PubMed Central ID: PMC3982205

[Ere2014b] B. Erem, J. Coll-Font, R.M. Orellana, P. Stovicek, D.H. Brooks.
**“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.

DOI: 10.1109/TMI.2013.2295220

PubMed ID: 24595345

PubMed Central ID: PMC3950945

[Fog2014a] T. Fogal, F. Proch, A. Schiewe, O. Hasemann, A. Kempf, J. Krüger.
**“Freeprocessing: Transparent in situ visualization via data interception,”** In *Proceedings of the 14th Eurographics Conference on Parallel Graphics and Visualization*, EGPGV, Eurographics Association, 2014.

[Gur2014a] Y. Gur, C.R. Johnson.
**“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.

[Han2014a] C.D. Hansen, M. Chen, C.R. Johnson, A.E. Kaufman, H. Hagen (Eds.).
**“Scientific Visualization: Uncertainty, Multifield, Biomedical, and Scalable Visualization,”** Mathematics and Visualization, Springer, 2014.

ISBN: 978-1-4471-6496-8

[Kur2014a] S. Kurugol, K. Kose, B. Park, J.G. Dy, D.H. Brooks, M. Rajadhyaksha.
**“Automated Delineation of Dermal-Epidermal Junction In Reflectance Confocal Microscopy Image Stacks Of Human Skin,”** In *Journal of Investigative Dermatology*, September, 2014.

DOI: 10.1038/jid.2014.379

PubMed ID: 25184959

[Mcg2014a] 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. Dibella, D. Parker, R.S. MacLeod, N.F. Marrouche.
**“Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI,”** In *Circ Arrhythm Electrophysiol*, Vol. 7, No. 1, pp. 23--30. 2014.

DOI: 10.1161/CIRCEP.113.000689

PubMed ID: 24363354

[Mil2014a] M. Milanič, V. Jazbinšek, R.S. MacLeod, D.H. Brooks, R. Hren.
**“Assessment of regularization techniques for electrocardiographic imaging,”** In *Journal of electrocardiology*, Vol. 47, No. 1, pp. 20--28. 2014.

DOI: 10.1016/j.jelectrocard.2013.10.004

[Par2014a] B.R. Parmar, T.R. Jarrett, N.S. Burgon, E.G. Kholmovski, N.W. Akoum, N. Hu, R.S. Macleod, N.F. Marrouche, R. Ranjan.
**“Comparison of Left Atrial Area Marked Ablated in Electroanatomical Maps with Scar in MRI,”** In *Journal of Cardiovascular Electrophysiology*, 2014.

DOI: 10.1111/jce.12357

[Sic2014a] R. Sicat, J. Krüger, T. Möller, M. Hadwiger.
**“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.

ISBN: 1077-2626

DOI: 10.1109/TVCG.2014.2346324

[Sou2014a] J. Sourati, D. Erdogmus, J.G. Dy, D.H. Brooks.
**“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.

DOI: 10.1109/TIP.2014.2325783

PubMed ID: 24860031

PubMed Central ID: PMC4096329

[Bur2013a] B. Burton, B. Erem, K. Potter, P. Rosen, C.R. Johnson, D. Brooks, R.S. Macleod.
**“Uncertainty Visualization in Forward and Inverse Cardiac Models,”** In *Computing in Cardiology CinC*, pp. 57--60. 2013.

ISSN: 2325-8861

[But2013a] 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*, Vol. 19, No. 1, pp. 108--117. January, 2013.

DOI: 10.1109/TVCG.2012.92

PubMed ID: 22450824

[Col2013a] J. Coll-Font, B. Erem, A. Karma, D.H. Brooks.
**“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.

DOI: 10.1007/978-3-642-38899-6_29

[Dad2013a] A. Daducci, E.J. Canales-Rodriguez, M. Descoteaux, E. Garyfallidis, Y. Gur, Y.-C Lin, M. Mani, S. Merlet, M. Paquette, A. Ramirez-Manzanares, M. Reisert, P.R. Rodrigues, F. Sepehrband, E. Caruyer, J. Choupan, R. Deriche, M. Jacob, G. Menegaz, V. Prckovska, M. Rivera, Y. Wiaux, J.-P. Thiran.
**“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.

ISSN: 0278-0062

DOI: 10.1109/TMI.2013.2285500

[Dat2013a] M. Datar, I. Lyu, S. Kim, J. Cates, M.A. Styner, R.T. Whitaker.
**“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.

PubMed ID: 24579119

[Dos2013a] D.J. Dosdall, R. Ranjan, K. Higuchi, E. Kholmovski, N. Angel, L. Li, R.S. Macleod, L. Norlund, A. Olsen, C.J. Davies, N.F. Marrouche.
**“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.

DOI: 10.1152/ajpheart.00440.2013

PubMed ID: 23812387

PubMed Central ID: PMC4116536

[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.

DOI: 10.1016/j.jelectrocard.2013.05.103

[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.

DOI: 10.1109/ISBI.2013.6556453

[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.

DOI: 10.1145/2503713.2503717

[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.

DOI: 10.1109/GlobalSIP.2013.6736904

[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.

DOI: 10.1007/s10439-013-0762-1

[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.

DOI: 10.1002/jor.22389

[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.

DOI: 10.1111/pace.12084

PubMed ID: 23356963

PubMed Central ID: PMC3651513

[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

DOI: 10.1615/Int.J.UncertaintyQuantification.v3.i2

[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

DOI: 10.1615/Int.J.UncertaintyQuantification.v3.i3

[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

PubMed Central ID: PMC3683979

[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.

DOI: 10.1016/j.bpj.2013.05.025

PubMed ID: 23790385

PubMed Central ID: PMC3686346

[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.

DOI: 10.1161/CIRCEP.113.000689

[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

DOI: 10.1109/ICASSP.2013.6637849

[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.

DOI: 10.1117/12.2006489

[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.

DOI: 10.1109/ISBI.2013.6556769

[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

DOI: 10.1016/j.jcp.2013.05.027

[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.

DOI: 10.1111/j.1540-8167.2011.02140.x

[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

PubMed Central ID: PMC3499137

[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

DOI: 10.1109/TVCG.2012.92

[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.

DOI: 10.1109/PacificVis.2012.6183557

[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.

DOI: 10.1109/EMBC.2012.6347236

PubMed ID: 23367171

PubMed Central ID: PMC3651514

[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

DOI: 10.1007/978-3-642-33555-6_7

[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.

DOI: 10.1109/ISBI.2012.6235658

[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.

DOI: 10.1071/RDv25n1Ab30

[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.

DOI: 10.1117/12.911228

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

PubMed ID: 24236224

PubMed Central ID: PMC3824273

[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.

DOI: 10.1615/Int.J.UncertaintyQuantification.2012004074

PubMed ID: 23543120

PubMed Central ID: PMC3609671

[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.

DOI: 10.1007/978-3-642-32677-6_15

[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.

DOI: 10.1109/MMBIA.2012.6164740

PubMed ID: 23568185

PubMed Central ID: PMC3615562

[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.

DOI: 10.1161/CIRCEP.112.973164

PubMed ID: 23071143

PubMed Central ID: PMC3691079

[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.

PubMed ID: 22025753

PubMed Central ID: PMC3411892

[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.

DOI: 10.1109/EMBC.2012.6346648

PubMed ID: 23366609

PubMed Central ID: PMC3652873

[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.

DOI: 10.1111/j.1540-8167.2010.01876.x

PubMed ID: 20807271

[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.

DOI: 10.1007/978-3-642-24031-7_24

[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.

DOI: 10.1109/IEMBS.2011.6090052

PubMed ID: 22254301

PubMed Central ID: PMC3337752

[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.

DOI: 10.1007/978-3-642-23629-7_45

PubMed ID: 21995050

PubMed Central ID: PMC3346950

[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.

DOI: 10.1109/IEMBS.2011.6091455

PubMed ID: 22255678

PubMed Central ID: PMC3345888

[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.

DOI: 10.1109/IEMBS.2011.6090972

PubMed ID: 22255195

PubMed Central ID: PMC3359386

[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.

DOI: 10.1109/ISBI.2011.5872455

PubMed ID: 21712967

PubMed Central ID: PMC3122924

[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.

DOI: 10.1137/100788951

PubMed Central ID: PMC3360588

[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.

DOI: 10.1109/TBME.2011.2160722

PubMed ID: 21712151

PubMed Central ID: PMC3179554

[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.

DOI: 10.1007/978-3-642-22092-0_44

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.

DOI: 10.1109/IEMBS.2011.6090921

PubMed ID: 2225507

PubMed Central ID: PMC3349355

[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.

DOI: 10.1117/12.875392

PubMed ID: 21709746

PubMed Central ID: PMC3120112

[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.

DOI: 10.1117/1.3549740

[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.

DOI: 10.1145/2082156.2082158

[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.

PubMed ID: 21927642

PubMed Central ID: PMC3172964

[Mcg2011a] C.J. McGann, E.G. Kholmovski, J.J. Blauer, S. Vijayakumar, T.S. Haslam, J.E. Cates, E.V. DiBella, N.S. Burgon, B. Wilson, A.J. Alexander, M.W. Prastawa, M. Daccarett, G. Vergara, N.W. Akoum, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“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.

DOI: 10.1016/j.jacc.2011.04.008

PubMed ID: 21718914

[Qui2011a] T.A. Quinn, S. Granite, M.A. Allessie, C. Antzelevitch, C. Bollensdorff, G. Bub, R.A.B. Burton, E. Cerbai, P.S. Chen, M. Delmar, D. DiFrancesco, Y.E. Earm, I.R. Efimov, M. Egger, E. Entcheva, M. Fink, R. Fischmeister, M.R. Franz, A. Garny, W.R. Giles, T. Hannes, S.E. Harding, P.J. Hunter, s, G. Iribe, J. Jalife, C.R. Johnson, R.S. Kass, I. Kodama, G. Koren, P. Lord, V.S. Markhasin, S. Matsuoka, A.D. McCulloch, G.R. Mirams, G.E. Morley, S. Nattel, D. Noble, S.P. Olesen, A.V. Panfilov, N.A. Trayanova, U. Ravens, S. Richard, D.S. Rosenbaum, Y. Rudy, F. Sachs, F.B. Sachse, D.A. Saint, U. Schotten, O. Solovyova, P. Taggart, L. Tung, A. Varrò, P.G. Volders, K. Wang, J.N. Weiss, E. Wettwer, E. White, R. Wilders, R.L. Winslow, P. Kohl.
**“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.

DOI: 10.1016/j.pbiomolbio.2011.07.001

PubMed Central ID: PMC3190048

[Ros2011b] P. Rosen, V. Popescu.
**“An Evaluation of 3-D Scene Exploration Using a Multiperspective Image Framework,”** In *The Visual Computer*, Vol. 27, No. 6-8, Springer-Verlag New York, Inc., pp. 623--632. 2011.

DOI: 10.1007/s00371-011-0599-2

PubMed ID: 22661796

PubMed Central ID: PMC3364594

[Sam2011a] R. Samuel, H.J. Sant, F. Jiao, C.R. Johnson, B.K. Gale.
**“Microfluidic laminate-based phantom for diffusion tensor-magnetic resonance imaging,”** In *Journal of Micromech. Microeng.*, Vol. 21, pp. 095027--095038. 2011.

DOI: 10.1088/0960-1317/21/9/095027

[Swe2011a] D.J. Swenson, S.E. Geneser, J.G. Stinstra, R.M. Kirby, R.S. MacLeod.
**“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.

DOI: 10.1007/s10439-011-0391-5

PubMed ID: 21909818

PubMed Central ID: PMC336204

[Tam2011a] G. Tamm, A. Schiewe, J. Krüger.
**“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.

[Tat2011a] J.D. Tate, J.G. Stinstra, T. Pilcher, A. Poursaid, E. Saarel, R.S. MacLeod.
**“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.

ISSN: 1557-170X

DOI: 10.1109/IEMBS.2011.6090045

PubMed ID: 22254294

[Tat2011g] J.D. Tate, J.G. Stinstra, T.A. Pilcher, R.S. MacLeod.
**“Measurement of Defibrillator Surface Potentials for Simulation Verification,”** In *Computing in Cardiology*, In *2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society*, IEEE, pp. 853--856. Aug, 2011.

DOI: 10.1109/iembs.2011.6090045

[Ver2011a] G.R. Vergara, S. Vijayakumar, E.G. Kholmovski, J.J. Blauer, M.A. Guttman, C. Gloschat, G. Payne, K. Vij, N.W. Akoum, M. Daccarett, C.J. McGann, R.S. Macleod, N.F. Marrouche.
**“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.

PubMed ID: 21034854

[Wan2011b] D. Wang, R.M. Kirby, C.R. Johnson.
**“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.

PubMed ID: 21382763

PubMed Central ID: PMC3109267

[Wan2011e] D. Wang, R.M. Kirby, R.S. Macleod, C.R. Johnson.
**“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.

DOI: 10.1109/IEMBS.2011.6090483

PubMed ID: 22254648

PubMed Central ID: PMC3336368

[And2010c] J.R. Anderson, B.C. Grimm, S. Mohammed, B.W. Jones, T. Tasdizen, J. Spaltenstein, P. Koshevoy, R.T. Whitaker, R.E. Marc.
**“The Viking Viewer: Scalable Multiuser Annotation and Summarization of Large Volume Datasets,”** In *Journal of Microscopy*, Vol. 241, No. 1, pp. 13--28. 2010.

DOI: 10.1111/j.1365-2818.2010.03402.x

[Bad2010a] T.J. Badger, M. Daccarett, N.W. Akoum, Y.A. Adjei-Poku, N.S. Burgon, T.S. Haslam, S. Kalvaitis, S. Kuppahally, G. Vergara, L. McMullen, P.A. Anderson, E. Kholmovski, R.S. Macleod, N.F. Marrouche.
**“Evaluation of left atrial lesions after initial and repeat atrial fibrillation ablation: lessons learned from delayed-enhancement MRI in repeat ablation procedures,”** In *Circulation. Arrhythmia and Electrophysiology*, Vol. 3, No. 3, pp. 249--259. 2010.

PubMed ID: 20335558

[Bla2010a] J.J.E. Blauer, J. Cates, C.J. McGann, E.G. Kholmovski, A. Alexander, M.W. Prastawa, S. Joshi, N.F. Marrouche, R.S. MacLeod.
**“MRI Based Injury Characterization Immediately Following Ablation of Atrial Fibrillation,”** In *Computing in Cardiology*, Vol. 37, pp. 165--168. 2010.

ISSN: 0276−6574

[Bro2010c] J.R. Bronson, J.A. Levine, R.T. Whitaker.
**“Particle Systems for Adaptive, Isotropic Meshing of CAD Models,”** In *Proceedings of the 19th International Meshing Roundtable*, Note: *Awarded Best Paper*, Springer, pp. 279-296. 2010.

DOI: 10.1007/978-3-642-15414-0_17

[Bur2010a] K. Bürger, J. Krüger, R. Westermann.
**“Sample-based surface coloring,”** In *IEEE Transactions on Visualization and Computer Graphics (TVCG)*, Vol. 16, No. 5, pp. 763--776. Sept-Oct, 2010.

DOI: 10.1109/TVCG.2009.107

PubMed ID: 20616392

PubMed Central ID: PMC3170521

[Cho2010a] A.N.M. Imroz Choudhury, M.D. Steffen, J.E. Guilkey, S.G. Parker.
**“Enhanced Understanding of Particle Simulations Through Deformation-Based Visualization,”** In *Computer Modeling in Engineering & Sciences*, Vol. 63, No. 2, pp. 117--136. 2010.

[Fog2010a] T. Fogal, J. Krüger.
**“Tuvok, an Architecture for Large Scale Volume Rendering,”** In *Proceedings of the 15th International Workshop on Vision, Modeling, and Visualization*, pp. 139--146. November, 2010.

DOI: 10.2312/PE/VMV/VMV10/139-146

[Fog2010b] T. Fogal, H. Childs, S. Shankar, J. Krüger, R.D. Bergeron, P. Hatcher.
**“Large Data Visualization on Distributed Memory Multi-GPU Clusters,”** In *Proceedings of High Performance Graphics 2010*, pp. 57--66. 2010.

[Ger2010a] S. Gerber, T. Tasdizen, P.T. Fletcher, S. Joshi, R.T. Whitaker, the Alzheimers Disease Neuroimaging Initiative (ADNI).
**“Manifold modeling for brain population analysis,”** In *Medical Image Analysis*, Special Issue on the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2009, Vol. 14, No. 5, Note: *Awarded MICCAI 2010, Best of the Journal Issue Award*, pp. 643--653. 2010.

ISSN: 1361-8415

DOI: 10.1016/j.media.2010.05.008

PubMed ID: 20579930

[Ger2010b] S. Gerber, P.-T. Bremer, V. Pascucci, R.T. Whitaker.
**“Visual Exploration of High Dimensional Scalar Functions,”** In *IEEE Transactions on Visualization and Computer Graphics*, IEEE Transactions on Visualization and Computer Graphics, Vol. 16, No. 6, IEEE, pp. 1271--1280. Nov, 2010.

DOI: 10.1109/TVCG.2010.213

PubMed ID: 20975167

PubMed Central ID: PMC3099238

[Isa2010a] B.M. Isaacson, J.G. Stinstra, R.S. MacLeod, P.F. Pasquina, R.D. Bloebaum.
**“Developing a Quantitative Measurement System for Assessing Heterotopic Ossification and Monitoring the Bioelectric Metrics from Electrically Induced Osseointegration in the Residual Limb of Service Members,”** In *Annals of Biomedical Engineering*, Vol. 38, No. 9, pp. 2968-–2978. 2010.

PubMed ID: 20458630

[Iye2010b] S.K. Iyer, E. DiBella, T. Tasdizen.
**“Edge enhanced spatio-temporal constrained reconstruction of undersampled dynamic contrast enhanced radial MRI,”** In *IEEE International Symposium on Biomedical Imaging (ISBI): From Nano to Macro*, pp. 704--707. 2010.

DOI: 10.1109/ISBI.2010.5490077

[Jia2010a] F. Jiao, J.M. Phillips, J.G. Stinstra, J. Kueger, R. Varma, E. Hsu, J. Korenberg, C.R. Johnson.
**“Metrics for Uncertainty Analysis and Visualization of Diffusion Tensor Images,”** In *Proceedings of the 5th international conference on Medical imaging and augmented reality (MIAR)*, Beijing, China, Springer-Verlag, Berlin, Heidelberg pp. 179--190. September, 2010.

[Jol2010a] M. Jolley, J. Stinstra, J. Tate, S. Pieper, R.S. Macleod, L. Chu, P. Wang, J.K. Triedman.
**“Finite element modeling of subcutaneous implantable defibrillator electrodes in an adult torso,”** In *Heart Rhythm*, Vol. 7, No. 5, pp. 692--698. May, 2010.

DOI: 10.1016/j.hrthm.2010.01.030

PubMed ID: 20230927

PubMed Central ID: PMC3103844

[Kru2010a] J. Krüger.
**“A New Sampling Scheme for Slice Based Volume RenderingA new sampling scheme for slice based volume rendering,”** In *Proceedings of IEEE/EG International Symposium on Volume Graphics (2010)*, pp. 1--4. 2010.

DOI: 10.2312/VG/VG10/001-004

[Kup2010a] S.S. Kuppahally, N. Akoum, N.S. Burgon, T.J. Badger, E.G. Kholmovski, S. Vijayakumar, S.N. Rao, J. Blauer, E.N. Fish, E.V. Dibella, R.S. Macleod, C. McGann, S.E. Litwin, N.F. Marrouche.
**“Left atrial strain and strain rate in patients with paroxysmal and persistent atrial fibrillation: relationship to left atrial structural remodeling detected by delayed-enhancement MRI,”** In *Circ Cardiovasc Imaging*, Vol. 3, No. 3, pp. 231--239. 2010.

PubMed ID: 20133512

[Kup2010b] S.S. Kuppahally, N. Akoum, T.J. Badger, N.S. Burgon, T. Haslam, E. Kholmovski, R.S. Macleod, C. McGann, N.F. Marrouche.
**“Echocardiographic left atrial reverse remodeling after catheter ablation of atrial fibrillation is predicted by preablation delayed enhancement of left atrium by magnetic resonance imaging,”** In *American Heart Journal*, Vol. 160, No. 5, pp. 877--884. 2010.

DOI: 10.1016/j.ahj.2010.07.003

PubMed ID: 21095275

PubMed Central ID: PMC2995281

[Kur2010a] S. Kurugol, N. Ozay, J.G. Dy, G.C. Sharp, D.H. Brooks.
**“Locally Deformable Shape Model to Improve 3D Level Set based Esophagus Segmentation,”** In *Proceedings of the IAPR International Conference on Pattern Recognition*, pp. 3955--3958. August, 2010.

PubMed ID: 21731883

PubMed Central ID: PMC3127393

[Lev2010a] J.A. Levine, D.J. Swenson, Z. Fu, R.S. MacLeod, R.T. Whitaker.
**“A Comparison of Delaunay Based Meshing Algorithms for Electrophysiological Cardiac Simulations,”** In *Virtual Physiological Human*, pp. 181--183. 2010.

[Mah2010a] C. Mahnkopf, T.J. Badger, N.S. Burgon, M. Daccarett, T.S. Haslam, C.T. Badger, C.J. McGann, N. Akoum, E. Kholmovski, R.S. Macleod, N.F. Marrouche.
**“Evaluation of the left atrial substrate in patients with lone atrial fibrillation using delayed-enhanced MRI: implications for disease progression and response to catheter ablation,”** In *Heart Rhythm*, Vol. 7, No. 10, pp. 1475--1481. 2010.

PubMed ID: 20601148

[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.

[Pot2010a] K. Potter, J.M. Kniss, R. Riesenfeld, C.R. Johnson.
**“Visualizing Summary Statistics and Uncertainty,”** In *Computer Graphics Forum*, Vol. 29, No. 3, Wiley-Blackwell, pp. 823--831. Aug, 2010.

[Seg2010a] N.M. Segerson, M. Daccarett, T.J. Badger, A. Shabaan, N. Akoum, E.N. Fish, S. Rao, N.S. Burgon, Y. Adjei-Poku, E. Kholmovski, S. Vijayakumar, E.V. DiBella, R.S. MacLeod, N.F. Marrouche.
**“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.

PubMed ID: 19804549

[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.

DOI: 10.1007/s10439-009-9883-y

[Swe2010a] D. Swenson, J.A. Levine, Z. Fu, J.D. Tate, R.S. MacLeod.
**“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.

ISSN: 0276-6547

[Tat2010b] J.D. Tate, J.G. Stinstra, T.A. Pilcher, R.S. MacLeod.
**“Implantable Cardioverter Defibrillator Predictive Simulation Validation,”** In *Computing in Cardiology*, pp. 853-–856. September, 2010.

[Wan2010a] D.F. Wang, R.M. Kirby, C.R. Johnson.
**“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.

[Wan2010c] D.F. Wang, R.M. Kirby, R.S. MacLeod, C.R. Johnson.
**“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.

[Wol2010a] C.H. Wolters, S. Lew, R.S. MacLeod, M.S. Hämäläinen.
**“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.

[Bad2009a] T.J. Badger, R.S. Oakes, M. Daccarett, N.S. Burgon, N. Akoum, E.N. Fish, J.J. Blauer, S.N. Rao, Y. Adjei-Poku, E.G. Kholmovski, S. Vijayakumar, E.V. Di Bella, R.S. MacLeod, N.F. Marrouche.
**“Temporal Left Atrial Lesion Formation After Ablation of Atrial Fibrillation,”** In *Heart Rhythm*, Vol. 6, No. 2, pp. 161--168. February, 2009.

[Bad2009b] T.J. Badger, Y.A. Adjei-Poku, N.S. Burgon, S. Kalvaitis, A. Shaaban, D.N. Sommers, J.J.E. Blauer, E.N. Fish N. Akoum, T.S. Haslem, E.G. Kholmovski, R.S. MacLeod, D.G. Adler, N.F. Marrouche.
**“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.

[Cal2009a] M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.
**“A Meshing Pipeline for Biomedical Models,”** In *Engineering with Computers*, Vol. 25, No. 1, SpringerLink, pp. 115-130. 2009.

DOI: 10.1007/s00366-008-0106-1

[Dat2009a] M. Datar, J. Cates, P.T. Fletcher, S. Gouttard, G. Gerig, R.T. Whitaker.
**“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.

DOI: 10.1007/978-3-642-04271-3_21

PubMed ID: 20426109

[Fle2009b] P.T. Fletcher, J. Moeller, J.M. Phillips, S. Venkatasubramanian.
**“Computing Hulls In Positive Definite Space,”** In *In Proceedings of the 19th Fall Workshop on Computational Geometry*, November, 2009.

[Fog2009b] T. Fogal, J. Krüger.
**“Size Matters - Revealing Small Scale Structures in Large Datasets,”** 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. 41--44. 2009.

[Han2009a] C.D. Hansen, C.R. Johnson, V. Pascucci, C.T. Silva.
**“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.

[Isa2009a] B.M. Isaacson, J.G. Stinstra, R.S. MacLeod, J.B. Webster, J.P. Beck, R.D. Bloebaum.
**“Bioelectric Analyses of an Osseointegrated Intelligent Implant Design System for Amputees,”** In *JoVE*, Vol. 29, 2009.

[Kam2009a] M. Kamali, L.J. Day, D.H. Brooks, X. Zhou, D.M. O'Malley.
**“Automated identification of neurons in 3D confocal datasets from zebrafish brainstem,”** In *Journal of Microscopy*, Vol. 233, No. 1, pp. 114--131. January, 2009.

DOI: 10.1111/j.1365-2818.2008.03102.x

PubMed ID: 19196418

PubMed Central ID: PMC2798854

[Kru2009a] J. Krüger, T. Fogal.
**“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.

[Lew2009a] S. Lew, C.H. Wolters, T. Dierkes, C. Röer, R.S. MacLeod.
**“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.

[Lew2009b] 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. 30, pp. 2862--2878. 2009.

[Mac2009a] R.S. MacLeod, J.G. Stinstra, S. Lew, R.T. Whitaker, D.J. Swenson, M.J. Cole, J. Krüger, D.H. Brooks, C.R. Johnson.
**“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.

[Mar2009a] H.G. Martinez, S.I. Prajapati, C.A. Estrada, F. Jimenez, M.P. Quinones, I. Wu, A. Bahadur, A. Sanderson, C.R. Johnson, M. Shim, C. Keller, S.S. Ahuja.
**“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.

[Mar2009b] H. Martinez, S. Prajapati, C. Estrada, F. Jimenez, I. Wu, A. Bahadur, A. Sanderson, C.R. Johnson, M. Shim, C. Keller, S. Ahuja.
**“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.

[Mil2009a] M. Milanic, V. Jazbinsek, D.F. Wang, J. Sinstra, R.S. Macleod, D.H. Brooks, R. Hren.
**“Evaluation of Approaches of Solving Electrocardiographic Imaging Problem,”** In *Proceeding of Computers in Cardiology 2010*, Park City, Utah, September, 2009.

[Oak2009a] R.S. Oakes, T.J. Badger, E.G. Kholmovski, N. Akoum, N.S. Burgon, E.N. Fish, J.J. Blauer, S.N. Rao, E.V. DiBella, N.M. Segerson, M. Daccarett, J. Windfelder, C.J. McGann, D.L. Parker, R.S. MacLeod, N.F. Marrouche.
**“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.

[Ogu2009a] I. Oguz, M. Niethammer, J. Cates, R.T. Whitaker, P.T. Fletcher, C. Vachet, M. Styner.
**“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.

DOI: 10.1007/978-3-642-02498-6_54

[Par2009a] S.G. Parker, K. Damevski, A. Khan, A. Swaminathan, C.R. Johnson.
**“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.

DOI: 10.1002/9780470558027.ch9

[San2009c] A.R. Sanderson, M.D. Meyer, R.M. Kirby, C.R. Johnson.
**“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.

DOI: 10.1007/s00791-008-0086-0

[Seg2009a] N.M. Segerson, M. Daccarett, T.J. Badger, A. Shabaan, N. Akoum, E.N. Fish, S. Rao, N.S. Burgon, Y. Adjei-Poku, E.G. Kholmovski, S. Vijayakumar, E.V.R. Dibella, R.S. Macleod, N.F. Marrouche.
**“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.

[She2009a] J.F. Shepherd, C.R. Johnson.
**“Hexahedral Mesh Generation for Biomedical Models in SCIRun,”** In *Engineering with Computers*, Vol. 25, No. 1, pp. 97--114. 2009.

[Tao2009a] R. Tao, P.T. Fletcher, R.T. Whitaker.
**“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.

DOI: 10.1007/978-3-642-02498-6_55

PubMed ID: 19694302

[Tat2009a] J.D. Tate, J.G. Stinstra, T. Pilcher, and R.S. MacLeod.
**“Measuring Implantable Cardioverter Defibrillators (ICDs) During Implantation Surgery: Verification of a Simulation,”** In *Computers in Cardiology*, pp. 473--476. 2009.

ISSN: 0276-6547

[Wan2009c] D.F. Wang, R.M. Kirby, C.R. Johnson.
**“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

[Sch2006d] T. Schultz, B. Burgeth, J. Weickert.
**“Flexible Segmentation and Smoothing of DT-MRI Fields Through a Customizable Structure Tensor,”** In *Advances in Visual Computing*, Lecture Notes in Computer Science, Vol. 4291, Edited by G. Bebis and R. Boyle and B. Parvin and D. Koracin and P. Remagnino and A. V. Nefian and M. Gopi and V. Pascucci and J. Zara and J. Molineros and H. Theisel and T. Malzbender, Springer, pp. 455--464. 2006.

[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.