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Staff information

James Carson

Systems Toxicology
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352
509/371-6894

Research Interests

  • Spatial organization of biological information

Education and Credentials

  • B.S. & M.E.E. from Rice University's Department of Electrical Engineering
  • Ph.D. from Baylor College of Medicine's Program in Structural and Computational Biology & Molecular Biophysics

Affiliations and Professional Service

  • IEEE
  • Society of Neuroscience

PNNL Publications

2013

  • Einstein DR, AP Kuprat, X Jiao, JP Carson, DM Einstein, RA Corley, and RE Jacob. 2013. "An Efficient Algorithm for Mapping Imaging Data to 3D Unstructured Grids in Computational Biomechanics." International Journal for Numerical Methods in Biomedical Engineering 29(1):1-16.  doi:10.1002/cnm.2489
  • Kleese van Dam K, JP Carson, AL Corrigan, DR Einstein, ZC Guillen, BS Heath, AP Kuprat, IT Lanekoff, CS Lansing, J Laskin, D Li, Y Liu, MJ Marshall, EA Miller, G Orr, P Pinheiro da Silva, S Ryu, CJ Szymanski, and M Thomas. 2013. "Velo and REXAN - Integrated Data Management and High Speed Analysis for Experimental Facilities." In Proceedings of the IEEE 8th International Conference on EScience, October 8-12, 2012, Chicago, Illinois.  IEEE Press, Los Alamitos, CA.  doi: 10.1109/eScience.2012.6404463
  • Lanekoff IT, M Thomas, JP Carson, JN Smith, C Timchalk, and J Laskin. 2013. "Imaging Nicotine in Rat Brain Tissue by Use of Nanospray Desorption Electrospray Ionization Mass Spectrometry." Analytical Chemistry 85(2):882-889.  doi:10.1021/ac302308p

2012

  • Carson JP, AP Kuprat, SM Colby, CA Davis, C Basciano, K Greene, JT Feo, and A Kennedy. 2012. "Detecting Distance between Injected Microspheres and Target Tumor via 3D Reconstruction of Tissue Sections." In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 28 - September 1, San Diego, California, pp. 1149-1152.  IEEE, Piscataway, NJ.  doi:10.1109/EMBC.2012.6346139
  • Corley RA, S Kabilan, AP Kuprat, JP Carson, KR Minard, RE Jacob, C Timchalk, RW Glenny, S Pipavath, TC Cox, C Wallis, R Larson, M Fanucchi, E Postlewait, and DR Einstein. 2012. "COMPARATIVE COMPUTATIONAL MODELING OF AIRFLOWS AND VAPOR DOSIMETY IN THE RESPIRATORY TRACTS OF RAT, MONKEY, AND HUMAN." Toxicological Sciences 128(2):500-516.  doi:10.1093/toxsci/kfs168
  • Freed AD, DR Einstein, JP Carson, and RE Jacob. 2012. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System, Phase II: Dodecahedral Micro-Model. PNNL-21287, Pacific Northwest National Laboratory, Richland, WA. 
  • Lanekoff IT, BS Heath, AV Liyu, M Thomas, JP Carson, and J Laskin. 2012. "An Automated Platform for High-Resolution Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry." Analytical Chemistry 84(19):8351-8356. 
  • Minard KR, AP Kuprat, S Kabilan, RE Jacob, DR Einstein, JP Carson, and RA Corley. 2012. "Phase-Contrast MRI and CFD Modeling of Apparent 3He Gas Flow in Rat Pulmonary Airways." Journal of Magnetic Resonance 221:129-138.  doi:10.1016/j.jmr.2012.05.007
  • Neradilek MB, N Polissar, DR Einstein, RW Glenny, KR Minard, JP Carson, X Jiao, RE Jacob, TC Cox, E Postlewait, and RA Corley. 2012. "BRANCH-BASED MODEL FOR THE DIAMETERS OF THE PULMONARY AIRWAYS: ACCOUNTING FOR DEPARTURES FROM SELF-CONSISTENCY AND REGISTRATION ERRORS." The Anatomical Record 295(6):1027-1044.  doi:10.1002/ar.22476
  • Thomas M, BS Heath, J Laskin, D Li, EC Liu, KL Hui, AP Kuprat, K Kleese van Dam, and JP Carson. 2012. "Visualization of High Resolution Spatial Mass Spectrometric Data during Acquisition." In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 28 - September 1, San Diego, California, pp. 5545-5548.  IEEE, Piscataway, NJ.  doi:10.1109/EMBC.2012.6347250

2011

  • Kindle LM, I Kakadiaris, T Ju, and JP Carson. 2011. "A semiautomated approach for artefact removal in serial tissue cryosections." Journal of Microscopy 241(2):200-206.  doi:10.1111/j.1365-2818.2010.03424.x
  • Enlow MA, T Ju, I Kakadiaris, and JP Carson. 2011. "Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain." In Proceedings of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2011), August 30-September 3, 2011, Boston, Massachusetts, pp. 8086-8089.  IEEE, Piscataway, NJ. 
  • Kurkure U, YH Le, N Paragios, JP Carson, T Ju, and I Kakadiaris. 2011. "Landmark/Image-based Deformable Registration of Gene Expression Data." In IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2011), June 20-25, 2011, Colorado Springs, Colorado, pp. 1089-1096.  IEEE Computer Society, Los Alamitos, CA.  doi:10.1109/CVPR.2011.5995708
  • Kurkure U, YH Le, N Paragios, T Ju, JP Carson, and I Kakadiaris. 2011. "Markov Random Field-Based Fitting of a Subdivision-Based Geometric Atlas." In IEEE International Conference on Computer Vision (ICCV), November 6-13, 2011, Barcelona, Spain, pp. 2540-2547.  IEEE, Piscataway, NJ.  doi:10.1109/ICCV.2011.6126541

2010

  • Carson JP, T Ju, M Bello, C Thaller, J Warren, I Kakadiaris, W Chiu, and G Eichele. 2010. "Automated pipeline for atlas-based annotation of gene expresssion patterns: application to postnatal day 7 mouse brain." Methods, A Companion to Methods in Enzymology 50(2):85-95. 
  • Carson JP, DR Einstein, KR Minard, M Fanucchi, C Wallis, and RA Corley. 2010. "High resolution lung airway cast segmentation with proper topology suitable for computational fluid dynamic simulations." Computerized Medical Imaging and Graphics 34(7):572-857.  doi:10.1016/j.compmedimag.2010.03.001
  • Carson JP, AP Kuprat, X Jiao, F del Pin, and DR Einstein. 2010. "An Anisotropic Fluid-Solid Model of the Mouse Heart." In Computers in Cardiology 2009, Park City, Utah September 13-16, 2009, vol. 36, pp. 377-380.  Computers in Cardiology and IEEE, Piscataway, NJ. 
  • Carson JP, AP Kuprat, X Jiao, V Dyedov, F del Pin, JM Guccione, MB Ratcliffe, and DR Einstein. 2010. "Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations." Biomechanics and Modeling in Mechanobiology 9(2):187-201.  doi:10.1007/S10237-009-0170-5
  • Ju T, JP Carson, L Liu, J Warren, M Bello, and I Kakadiaris. 2010. "Subdivision meshes for organizing spatial biomedical data. ." Methods 50(2):70-76.  doi:10.1016/J.YMETH.2009.07.012

2009

  • Einstein DR, F del Pin, X Jiao, AP Kuprat, JP Carson, K Kunzelman, RP Cochran, JM Guccione, and MB Ratcliffe. 2009. "Fluid-Structure Interactions of the Mitral Valve and Left Heart: Comprehensive Strategies, Past, Present and Future." International Journal for Numerical Methods in Biomedical Engineering 26(3-4):348-380.  doi:10.1002/cnm.1280
  • Jacob RE, JP Carson, KM Gideon, BG Amidan, CL Smith, and KM Lee. 2009. "Comparison of Two Quantitative Methods of Discerning Airspace Enlargement in Smoke-Exposed Mice." PLoS One 4(8):E6670.  doi:10.1371/journal.pone.0006670
  • Dyedov V, DR Einstein, X Jiao, AP Kuprat, JP Carson, and F del Pin. 2009. "Variational Generation of Prismatic Boundary-Layer Meshes for Biomedical Computing." International Journal for Numerical Methods in Engineering 79(8):907-945.  doi:10.1002/nme.2583
  • Jiao X, DR Einstein, V Dyedov, and JP Carson. 2009. "Automatic Identification and Truncation of Boundary Outlets in Complex Imaging-Derived Biomedical Geometries." Medical & Biological Engineering & Computing 47(9):989-999.  doi:10.1007/s11517-009-0501-9

2008

  • Einstein DR, B Neradilak, N Pollisar, KR Minard, C Wallis, M Fanucchi, JP Carson, AP Kuprat, S Kabilan, R Jacob, and R Corley. 2008. "An Automated Self-similarity Analysis of the Pulmonary Tree of the Sprague-Dawley Rat." The Anatomical Record 291(12):1628-1648.  doi:10.1002/ar.20771
  • Gatchel JR, K Watase, C Thaller, JP Carson, P Jafar-Nejad, CA Shaw, T Zu, HT Orr, and HY Zoghbi. 2008. "The insulin-like growth factor pathway is altered in Spinocerebellar ataxia type 1 and type 7." Proceedings of the National Academy of Sciences of the United States of America 105(4):1291-1296.  doi:10.1073/pnas.0711257105

2007

  • Bello M, T Ju, JP Carson, J Warren, W Chiu, and I Kakadiaris. 2007. "Learning-based Segmentation Framework for Tissue Images Containing Gene Expression Data." IEEE Transactions on Medical Imaging 26(5):728-744.  doi:10.1109/TMI.2007.895462
  • Visel A, JP Carson, J Oldekamp, M Warnecke, V Jakubcakova, X Zhou, C Shaw, G Alvarez-Bolado, and G Eichele. 2007. "Regulatory pathway analysis by high-throughput in situ hybridization." PLoS Genetics 3(10):paper no. e178.  doi:10.1371/journal.pgen.0030178

2006

  • Ju T, J Warren, JP Carson, M Bello, I Kakadiaris, W Chiu, C Thaller, and G Eichele. 2006. "3D volume reconstruction of a mouse brain histological sections using warp filtering." Journal of Neuroscience Methods 156(1-2):84-100.  doi:10.1016/j.jneumeth.2006.02.020

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