Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2008


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.



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



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

ABSTRACT

With the continual increase in computing power, volumetric datasets with sizes ranging from only a few megabytes to petascale are generated thousands of times per day. Such data may come from an ordinary source such as simple everyday medical imaging procedures, while larger datasets may be generated from cluster-based scientific simulations or measurements of large scale experiments. In computer science an incredible amount of work worldwide is put into the efficient visualization of these datasets. As researchers in the field of scientific visualization, we often have to face the task of handling very large data from various sources. This data usually comes in many different data formats. In medical imaging, the DICOM standard is well established, however, most research labs use their own data formats to store and process data. To simplify the task of reading the many different formats used with all of the different visualization programs, we present a system for the efficient handling of many types of large scientific datasets (see Figure 1 for just a few examples). While primarily targeted at structured volumetric data, UVF can store just about any type of structured and unstructured data. The system is composed of a file format specification with a reference implementation of a reader. It is not only a common, easy to implement format but also allows for efficient rendering of most datasets without the need to convert the data in memory.



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.



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.



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.



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



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.



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



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.



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.


2007


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



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



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



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.



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.



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.



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.



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.



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.