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

2009


H.C. Hazlett, M.D. Poe, A.A. Lightbody, G. Gerig, J.R. MacFall, A.K. Ross, J. Provenzale, A. Martin, A.L. Reiss, J. Piven. “Teasing apart the heterogeneity of autism: Same behavior, different brains in toddlers with fragile X syndrome and autism,” In Journal of Neurodevelopmental Disorders, Vol. 1, No. 1, pp. 81--90. 2009.
PubMed ID: 20700390



H.B. Henninger, S.A. Maas, J.H. Shepherd, S. Joshi, J.A. Weiss. “Transversely Isotropic Distribution of Sulfated Glycosaminoglycans in Human Medial Collateral Ligament: A Quantitative Analysis,” In Journal of Structural Biology, Vol. 165, pp. 176-183. 2009.
PubMed ID: 19126431



T.L. Henriksen, G.J. Nathan, Z.T. Alwahabi, N. Qamar, T.A. Ring, E.G. Eddings. “Planar Measurements of Soot Volume Fraction and OH in a JP-8 Pool Fire,” In Combustion and Flame, Vol. 156, No. 7, pp. 1480--1492. 2009.
DOI: 10.1016/j.combustflame.2009.03.002

ABSTRACT

The simultaneous measurement of soot volume fraction by laser induced incandescence (LII) and qualitative imaging of OH by laser induced fluorescence (LIF) was performed in a JP-8 pool fire contained in a 152 mm diameter pan. Line of sight extinction was used to calibrate the LII system in a laminar flame, and to provide an independent method of measuring average soot volume fraction in the turbulent flame. The presence of soot in the turbulent flame was found to be approximately 50% probable, resulting in high levels of optical extinction, which increased slightly through the flame from approximately 30% near the base, to approximately 50% at the tip. This high soot loading pushes both techniques toward their detection limit. Nevertheless, useful accuracy was obtained, with the LII measurement of apparent extinction in the turbulent flame being approximately 21% lower than a direct measurement, consistent with the influence of signal trapping. The axial and radial distributions of soot volume fraction are presented, along with PDFs of volume fraction, and new insight into the behavior of soot sheets in pool fires are sought from the simultaneous measurements of OH and LII.

Keywords: Incandescence, Fluorescence, Pool fire, JP-8



H.B. Henninger, S.P. Reese, A.E. Anderson, J.A. Weiss. “Validation of computational models in biomechanics,” In Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine, Vol. 224, No. 7, SAGE Publications, pp. 801--812. 2009.



J. Hinkle, P.T. Fletcher, Brian Wang, B. Salter, S. Joshi. “4D MAP image reconstruction incorporating organ motion,” In Information Processing in Medical Imaging, Lecture Notes in Computer Science LNCS, Vol. 5636, pp. 676--687. 2009.
PubMed ID: 19694303



J.B. Hooper, D. Bedrov, G.D. Smith, B. Hanson, O. Borodin, D.M. Dattelbaum, E.M. Kober. “A molecular dynamics simulation study of the pressure-volume-temperature behavior of polymers under high pressure,” In Journal of Chemical Physics, 2009.
DOI: 10.1063/1.3077868

ABSTRACT

Isothermal compression of poly (dimethylsiloxane), 1,4-poly(butadiene), and a model Estane® (in both pure form and a nitroplasticized composition similar to PBX-9501 binder) at pressures up to 100kbars has been studied using atomistic molecular dynamics (MD) simulations. Comparison of predicted compression, bulk modulus, and Us--up behavior with experimental static and dynamic compression data available in the literature reveals good agreement between experiment and simulation, indicating that MD simulations utilizing simple quantum-chemistry-based potentials can be used to accurately predict the behavior of polymers at relatively high pressure. Despite their very different zero-pressure bulk moduli, the compression, modulus, and Us--up behavior (including low-pressure curvature) for the three polymers could be reasonably described by the Tait equation of state(EOS) utilizing the universal C parameter. The Tait EOS was found to provide an excellent description of simulation PVT data when the C parameter was optimized for each polymer. The Tait EOS parameters, namely, the zero-pressure bulk modulus and the C parameter, were found to correlate well with free volume for these polymers as measured in simulations by a simple probe insertion algorithm. Of the polymers studied, PDMS was found to have the most free volume at low pressure, consistent with its lower ambient pressurebulk modulus and greater increase in modulus with increasing pressure (i.e., crush-up behavior).



L.K. Huynh, H.R. Zhang, S. Zhang, E.G. Eddings, A.F. Sarofim, M.E. Law, P.R. Westmoreland, T.N. Truong. “Kinetics of Enol Formation from Reaction of OH with Propene,” In Journal of Physical Chemistry, Vol. 113, No. 13, pp. 3177--3185. 2009.
DOI: 10.1021/jp808050j

ABSTRACT

Kinetics of enol generation from propene has been predicted in an effort to understand the presence of enols in flames. A potential energy surface for reaction of OH with propene was computed by CCSD(T)/cc-pVDZ//B3LYP/cc-pVTZ calculations. Rate constants of different product channels and branching ratios were then calculated using the Master Equation formulation (J. Phys. Chem. A 2006, 110, 10528). Of the two enol products, ethenol is dominant over propenol, and its pathway is also the dominant pathway for the OH + propene addition reactions to form bimolecular products. In the temperature range considered, hydrogen abstraction dominated propene + OH consumption by a branching ratio of more than 90%. Calculated rate constants of enol formation were included in the Utah Surrogate Mechanism to model the enol profile in a cyclohexane premixed flame. The extended model shows consistency with experimental data and gives 5% contribution of ethenol formation from OH + propene reaction, the rest coming from ethene + OH.



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.



W.-K. Jeong, J. Beyer, M. Hadwiger, A. Vazquez, H. Pfister, R.T. Whitaker. “Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets,” In IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2009 IEEE Visualization Conference, Vol. 15, No. 6, pp. 1505--1514. Sept/Oct, 2009.



E. Jurrus, M. Hardy, T. Tasdizen, P.T. Fletcher, P. Koshevoy, C.-B. Chien, W. Denk, R.T. Whitaker. “Axon Tracking in Serial Block-Face Scanning Electron Microscopy,” In Medical Image Analysis (MEDIA), Vol. 13, No. 1, Elsevier, pp. 180--188. February, 2009.
PubMed ID: 18617436



E. Jurrus, A.R.C. Paiva, S. Watanabe, R.T. Whitaker, E.M. Jorgensen, T. Tasdizen. “Serial Neural Network Classifier for Membrane Detection using a Filter Bank.,” SCI Technical Report, No. UUSCI-2009-006, SCI Institute, University of Utah, 2009.



E. Jurrus, A.R.C. Paiva, S. Watanabe, R. Whitaker, E.M. Jorgensen, T. Tasdizen. “Serial Neural Network Classifier for Membrane Detection using a Filter Bank,” In Proc. Workshop on Microscopic Image Analysis with Applications in Biology, Bethesda, MD, USA, 2009.



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

ABSTRACT

Many kinds of neuroscience data are being acquired regarding the dynamic behaviour and phenotypic diversity of nerve cells. But as the size, complexity and numbers of 3D neuroanatomical datasets grow ever larger, the need for automated detection and analysis of individual neurons takes on greater importance. We describe here a method that detects and identifies neurons within confocal image stacks acquired from the zebrafish brainstem. The first step is to create a template that incorporates the location of all known neurons within a population - in this case the population of reticulospinal cells. Once created, the template is used in conjunction with a sequence of algorithms to determine the 3D location and identity of all fluorescent neurons in each confocal dataset. After an image registration step, neurons are segmented within the confocal image stack and subsequently localized to specific locations within the brainstem template - in many instances identifying neurons as specific, individual reticulospinal cells. This image-processing sequence is fully automated except for the initial selection of three registration points on a maximum projection image. In analysing confocal image stacks that ranged considerably in image quality, we found that this method correctly identified on average approximately 80% of the neurons (if we assume that manual detection by experts constitutes 'ground truth'). Because this identification can be generated approximately 100 times faster than manual identification, it offers a considerable time savings for the investigation of zebrafish reticulospinal neurons. In addition to its cell identification function, this protocol might also be integrated with stereological techniques to enhance quantification of neurons in larger databases. Our focus has been on zebrafish brainstem systems, but the methods described should be applicable to diverse neural architectures including retina, hippocampus and cerebral cortex.



A. Knoll, I. Wald, C.D. Hansen. “Coherent Multiresolution Isosurface Ray Tracing,” In The Visual Computer, Vol. 25, No. 3, pp. 209--225. 2009.



A. Knoll, Y. Hijazi, C.D. Hansen, I. Wald, H. Hagen. “Fast Ray Tracing of Arbitrary Implicit Surfaces with Interval and Affine Arithmetic,” In Computer Graphics Forum, Vol. 28, No. 1, pp. 26--40. 2009.



A. Knoll, Y. Hijazi, R. Westerteiger, M. Schott, C.D. Hansen, H. Hagen. “Volume Ray Casting with Peak Finding and Differential Sampling,” In IEEE Transactions on Visualization and Computer Graphics, Proceedings of the 2009 IEEE Visualization Conference, Vol. 15, No. 6, pp. 1571--1578. Sept/Oct, 2009.



A. Knoll, Y. Hijazi, R. Westerteiger, M. Schott, C.D. Hansen, Hans Hagen. “Volume Ray Casting with Peak Finding and Differential Sampling,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 15, No. 6, pp. 1571-1578. 2009.



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.



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.



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.