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


 C.R. Butson, G.A. Clark. “Mechanisms of noise-induced improvement in light-intensity encoding in Hermissenda photoreceptor network,” In Journal of Neurophysiology, Vol. 99, No. 1, pp. 155--165. January, 2008.
ISSN: 0022-3077
DOI: 10.1152/jn.01250.2006
PubMed ID: 18003872

ABSTRACT

In a companion paper we showed that random channel and synaptic noise improve the ability of a biologically realistic, GENESIS-based computational model of the Hermissenda eye to encode light intensity. In this paper we explore mechanisms for noise-induced improvement by examining contextual spike-timing relationships among neurons in the photoreceptor network. In other systems, synaptically connected pairs of spiking cells can develop phase-locked spike-timing relationships at particular, well-defined frequencies. Consequently, domains of stability (DOS) emerge in which an increase in the frequency of inhibitory postsynaptic potentials can paradoxically increase, rather than decrease, the firing rate of the postsynaptic cell. We have extended this analysis to examine DOS as a function of noise amplitude in the exclusively inhibitory Hermissenda photoreceptor network. In noise-free simulations, DOS emerge at particular firing frequencies of type B and type A photoreceptors, thus producing a nonmonotonic relationship between their firing rates and light intensity. By contrast, in the noise-added conditions, an increase in noise amplitude leads to an increase in the variance of the interspike interval distribution for a given cell; in turn, this blocks the emergence of phase locking and DOS. These noise-induced changes enable the eye to better perform one of its basic tasks: encoding light intensity. This effect is independent of stochastic resonance, which is often used to describe perithreshold stimuli. The constructive role of noise in biological signal processing has implications both for understanding the dynamics of the nervous system and for the design of neural interface devices.

Keywords: Action Potentials, Action Potentials: physiology, Animals, Artifacts, Computer Simulation, Eye, Eye: cytology, Hermissenda, Hermissenda: physiology, Invertebrate, Invertebrate: physiology, Nerve Net, Nerve Net: physiology, Neurons, Neurons: physiology, Ocular, Ocular Physiological Phenomena, Ocular: physiology, Photic Stimulation, Photoreceptor Cells, Reaction Time, Reaction Time: physiology, Sensory Thresholds, Sensory Thresholds: physiology, Synaptic Transmission, Synaptic Transmission: physiology, Vision


 C.R. Butson, G.A. Clark. “Random noise paradoxically improves light-intensity encoding in Hermissenda photoreceptor network,” In Journal of Neurophysiology, Vol. 99, No. 1, pp. 146--154. January, 2008.
ISSN: 0022-3077
DOI: 10.1152/jn.01247.2006
PubMed ID: 18003873

ABSTRACT

Neurons are notoriously noisy devices. Although the traditional view posits that noise degrades system performance, recent evidence suggests that noise may instead enhance neural information processing under certain conditions. Here we report that random channel and synaptic noise improve the ability of a biologically realistic computational model of the Hermissenda eye to encode light intensity. The model was created in GENESIS and is based on a previous model used to examine effects of changes in type B photoreceptor excitability, synaptic strength, and network architecture. The network consists of two type A and three type B multicompartmental photoreceptors. Each compartment contains a population of Hodgkin-Huxley-type ion channels and each cell is stimulated via artificial light currents. We found that the addition of random channel and synaptic noise yielded a significant improvement in the accuracy of the network's encoding of light intensity across eight light levels spanning 3.5 log units (P

Keywords: Action Potentials, Action Potentials: physiology, Animals, Artifacts, Computer Simulation, Eye, Eye: cytology, Hermissenda, Hermissenda: physiology, Invertebrate, Invertebrate: physiology, Nerve Net, Nerve Net: physiology, Neurons, Neurons: physiology, Ocular, Ocular Physiological Phenomena, Ocular: physiology, Photic Stimulation, Photoreceptor Cells, Reaction Time, Reaction Time: physiology, Sensory Thresholds, Sensory Thresholds: physiology, Synaptic Transmission, Synaptic Transmission: physiology, Vision


 C.R. Butson, C.C. McIntyre. “Current Steering to Control the Volume of Tissue Activated During Deep Brain Stimulation,” In Brain Stimulation, Vol. 1, No. 1, pp. 7--15. January, 2008.
DOI: 10.1016/j.brs.2007.08.004
PubMed ID: 19142235

ABSTRACT

BACKGROUND: Over the last two decades, deep brain stimulation (DBS) has become a recognized and effective clinical therapy for numerous neurological conditions. Since its inception, clinical DBS technology has progressed at a relatively slow rate; however, advances in neural engineering research have the potential to improve DBS systems. One such advance is the concept of current steering, or the use of multiple stimulation sources to direct current flow through targeted regions of brain tissue.

OBJECTIVE: The goals of this study were to develop a theoretical understanding of the effects of current steering in the context of DBS, and use that information to evaluate the potential utility of current steering during stimulation of the subthalamic nucleus.

METHODS: We used finite element electric field models, coupled to multi-compartment cable axon models, to predict the volume of tissue activated (VTA) by DBS as a function of the stimulation parameter settings.

RESULTS: Balancing current flow through adjacent cathodes increased the VTA magnitude, relative to monopolar stimulation, and current steering enabled us to sculpt the shape of the VTA to fit a given anatomical target.

CONCLUSIONS: These results provide motivation for the integration of current steering technology into clinical DBS systems, thereby expanding opportunities to customize DBS to individual patients, and potentially enhancing therapeutic efficacy.


 S.P. Callahan, J.H. Callahan, C.E. Scheidegger, C.T. Silva. “Direct Volume Rendering: A 3D Plotting Technique for Scientific Data,” In Computing in Science and Engineering, Vol. 10, No. 1, pp. 88--92. 2008.


S.P. Callahan. “Adaptive Visualization of Dynamic Unstructured Meshes,” SCI Technical Report, No. UUSCI-2008-003, Note: Ph.D. Thesis, University of Utah School of Computing, 2008.


S.P. Callahan, C.T. Silva. “Image-Space Acceleration for Direct Volume Rendering of Unstructured Grids using Joint Bilateral Upsampling,” SCI Technical Report, No. UUSCI-2008-002, University of Utah, 2008.


S.P. Callahan, J. Freire, C.E. Scheidegger, C.T. Silva, and H.T. Vo. “Towards a Provenance-Enabling ParaView,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 120--127. 2008.


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


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


A.N.M. Imroz Choudhury, K. Potter, S.G. Parker. “Interactive Visualization for Memory Reference Traces,” In Computer Graphics Forum, In Proceedings of EuroVis 2008, Vol. 27, No. 3, pp. 815--822. May, 2008.


J.D. Daniels, T. Ochotta, L. Ha, C.T. Silva. “Spline-Based Feature Curves from Point-Sampled Geometry,” In The Visual Computer, Vol. 24, No. 6, pp. 449--462. 2008.


J.D. Daniels, C.T. Silva, J. Shepherd, E. Cohen. “Quadrilateral Mesh Simplification,” In ACM Transactions on Graphics - Proceedings of ACM SIGGRAPH Asia 2008, Vol. 27, No. 5, 2008.
DOI: 10.1145/1409060.1409101


H. Davande, D. Bedrov, G.D. Smith. “Thermodynamic, Transport and Viscoelastic Properties of PBX-9501 Binder: A Molecular Dynamics Simulation Study,” In Journal of Energetic Materials, Vol. 26, No. 2, pp. 115--138. 2008.
DOI: 10.1080/07370650701801937

ABSTRACT

Atomistic molecular dynamics simulations were performed on a low-molecular-weight nitroplasticized Estane® mixture representative of the binder used in PBX-9501. Pressure-volume-temperature (PVT) behavior over a wide range of pressures and temperatures above the order-disorder temperature (ODT) of Estane was determined and represented with the empirical Tait and Sun equations of state. The effect of temperature, pressure, and plasticization on transport properties of the mixture was also examined. A combination of molecular dynamics simulations and theoretical reptation models was used to predict the shear stress relaxation modulus G(t) of PBX-9501 binder at 473 K and 1 atm pressure. Data obtained from simulations of the model PBX-9501 binder presented here can be utilized to predict the temperature and pressure dependence of the shear stress relaxation modulus for temperatures above the ODT.


 S.B. Davidson, J. Freire. “Provenance and Scientific Workflows: Challenges and Opportunities,” In Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, pp. 1345--1350. 2008.
ISBN: 978-1-60558-102-6


C. Dietrich, J. Comba, L. Nedel, C.E. Scheidegger, C.T. Silva. “Edge Groups: A New Approach to Understanding the Mesh Quality of Marching Methods,” In IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008), Vol. 14, No. 6, pp. 1651 - 1666. 2008.
DOI: 10.1109/TVCG.2008.122


G. Draper, R. Riesenfeld. “Who Votes For What? A Visual Query Language for Opinion Data,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 6, IEEE, pp. 1197--1204. Nov, 2008.
DOI: 10.1109/tvcg.2008.187


G. Draper, Y. Livnat, R. Riesenfeld. “A Visual Query Language for Correlation Discovery and Management,” In Proceedings of Visual and Iconic Language Conference (VaIL 2008), pp. 14--23. 2008.


T. Ellkvist, D. Koop, E.W. Anderson, J. Freire, C.T. Silva. “Using Provenance to Support Real-Time Collaborative Design of Workflows,” In Proceedings of the Second International Provenance and Annotation Workshop (IPAW 2008), pp. 266--279. 2008.


T. Ellkvist, D. Koop, J. Freire, C.T. Silva, L. Stromback. “Using Mediation to Achieve Provenance Interoperability,” In Proceedings of the 2008 Fourth IEEE International Conference on eScience, pp. 398--399. 2008.


A. Fedorov, E. Billet, M.W. Prastawa, G. Gerig, A. Radmanesh, S.K. Warfield, R. Kikinis, N. Chrisochoides. “Evaluation of Brain MRI Alignment with the Robust Hausdorff Distance Measures,” In Lecture Notes in Computer Science, Vol. 5358, Springer, pp. 594--603. 2008.
DOI: 10.1007/978-3-540-89639-5_57