Journal Publications

[1] J. Gregor and E. Granum, "Finding chromosome centromeres using band pattern information," Computers in Biology and Medicine, 21: 55-67, 1991.

[2] J. Gregor and E. Granum, "String segmentation and classification by forced landmark Markov networks," Intl. J. Patt. Recogn. and Artif. Intell., 5: 413-423, 1991.

[3] J. Gregor and M.G. Thomason, "Dynamic programming alignment of sequences representing cyclic patterns," IEEE Trans. PAMI, 15: 129-135, 1993.

[4] C.E. Guthrie, J. Gregor, and M.G. Thomason, "Constrained Markov networks for automated analysis of G-banded chromosomes," Computers in Biology and Medicine, 23: 105-114, 1993.

[5] J. Gregor and M.G. Thomason, "Hybrid pattern recognition using Markov networks," IEEE Trans. PAMI, 15: 651-656, 1993.

[6] J. Gregor, "Data-driven inference of finite-state automata," Intl. J. Patt. Recogn. and Artif. Intell., 8: 305-322, 1994.

[7] J. Gregor and R.S. Harris, "String matching with left-to-right networks," Pattern Recognition Letters, 16: 213-218, 1995.

[8] F. Rannou and J. Gregor, "Equilateral polygon approximation of closed contours," Pattern Recognition, 29: 1105-1115, 1996.

[9] J. Gregor and M.G. Thomason, "Efficient dynamic programming alignment of cyclic strings by shift elimination," Pattern Recognition, 29: 1179-1185, 1996.

[10] S.P. Olesen, J. Gregor, M.G. Thomason and G. Smith, "EM-ML PET reconstruction on multiple processors with reduced communications," Intl Journal for Imaging Systems and Technology, 7: 215-223, 1996.

[11] J. Gregor and D. Huff, "A focus of attention preprocessing scheme for EM-ML PET reconstruction", IEEE Trans. Medical Imaging, 16: 218-223, 1997.

[12] J. Gregor and D. Huff, "A computational study of the focus of attention EM-ML algorithm for PET reconstruction", Parallel Computing, 24: 1481-1497, 1998. Invited paper for special issue on biomedical applications.

[13] J. Gregor and R.T. Whitaker, "Indoor scene reconstruction from sets of noisy range images", Graphical Models, 63: 304-332, 2001. Greatly extended version of conference paper [4] below.

[14] J. Gregor and F.R. Rannou, "3D Support Function Estimation and Application for Projection MRI", Intl Journal for Imaging Systems and Technology, 12:43-50, 2002.

[15] R.T. Whitaker and J. Gregor, "A maximum likelihood surface estimator for dense range data", IEEE Trans. PAMI, 24:1372-1387, 2002.

[16] J. Gregor, S. Gleason, M. Paulus, J. Cates, "Fast Feldkamp reconstruction based on focus of attention and distributed computing", Intl Journal for Imaging Systems and Technology, 12:229-234, 2002.

[17] M.G. Thomason, R. Longton, J. Gregor, G.T. Smith, and K. Hutson, "Simulation of emission tomography using grid middleware for distributed computing," Computer Methods and Programs in Biomedicine, 75:251-258, 2004.

[18] T. Benson and J. Gregor, "Distributed iterative image reconstruction for micro-CT with ordered-subsets and focus of attention problem reduction," Journal of X-Ray Systems and Technology, vol 12, pp 231-240, 2004.

[19] J.S. Wall, S.J. Kennel, M.J. Paulus, S. Gleason, J. Gregor, J. Baba, M. Schell, T. Richey, B. O'Nuallain, R. Donnell, P.N. Hawkins, D.T. Weiss and A. Solomon, "Quantitative high-resolution microradiographic imaging of amyloid deposits in a novel murine model of AA-amyloidosis," Amyloid: The Journal of Protein Folding Disorders, vol 12, pp 149-156, 2005.

[20] T. Benson and J. Gregor, "Framework for iterative conebeam micro-CT reconstruction," IEEE Transactions on Nuclear Science, vol. 52, no. 5, pp. 1335-1340, Oct. 2005. Extended version of similarly titled conference paper below.

[21] T. Benson and J. Gregor, "Three-dimensional focus of attention for iterative cone-beam micro-CT reconstruction," Physics in Medicine and Biology, vol. 51, pp. 4533-4546, 2006.

[22] J. Gregor, T. Benson, S. Gleason, M. Paulus, S. Figueroa, T. Hoffman, S. Kennel, and J. Wall, "Approximate volumetric system models for microSPECT," IEEE Transactions on Nuclear Science, vol. 53, pp. 2646-2652, Oct. 2006. Extended version of similarly titled conference paper below.

[23] J.S. Wall, M.J. Paulus, S. Gleason, J. Gregor, A. Solomon, and S.J. Kennel, "Micro-imaging of amyloid in mice," R. Wetzel and I. Keterpal (eds.), Methods in Enzymology, vol. 412, pp. 161-182, 2006.

[24] J.S. Wall, S.J. Kennel, M.J. Paulus, J. Gregor, T. Richey, J. Avenell, J. Yap, D. Townsend, D.T. Weiss, and A. Solomon, "Radioimaging of light chain amyloid with a fibril-reactive monoclonal antibody," J. Nuclear Medicine, vol. 47, pp. 2016-2024, 2006. Note: Figure made cover page!

[25] G. Mazeroff and J. Gregor, "Probabilistic suffix models for API sequence analysis of Windows XP applications", Pattern Recognition, vol. 41, pp. 90-101, 2008. On-line version available May 2007.

[26] J. Gregor and T. Benson, "Computational analysis and improvement of SIRT," IEEE Transactions on Medical Imaging, vol. 27, 918-924, 2008.

[27] B. Feng, M. Chen, B. Bai, A. Smith, D.W. Austin, R. Mintzer, D. Osborne, and J. Gregor, "Modeling of the point-spread function by geometric calculations in multi-pinhole SPECT reconstruction," IEEE Transactions on Nuclear Science, vol. 57, 173-180, Feb. 2010. Extended version of similarly titled conference paper below.

[28] M.G. Thomason and J. Gregor, "Higher order SVD of tensors for fusion of multimodal images," Journal of Electronic Imaging, vol. 20, 13023.1-9, 2011.

[29] J. Gregor, "Data-driven problem reduction for image reconstruction from projections using gift wrapping," IEEE Transactions on Nuclear Science, vol. 58, pp. 724-729, June 2011. Extended version of similarly titled conference paper below.

[30] F. Kim, D. Penumadu, J. Gregor, N. Kardjilov, and I. Manke, "High resolution neutron and x-ray imaging of granular materials," Journal of Geotechnical and Geoenvironmental Enginering, American Society of Civil Engineers, vol. 139, pp. 715-723, 2013.

[31] H. Santos-Villalobos, P. Bingham, and J. Gregor, "Iterative reconstruction of coded source neutron radiographs." IEEE Transactions on Nuclear Science, vol. 60, pp. 1624-1631, 2013 Extended version of similarly titled conference paper below.

[32] T. Toops, H. Bilheux, S. Voisin, J. Gregor, L. Walker, A. Strzelec, C. Finney, J. Pihl, B. Schillinger, and M. Schulz, "Neutron tomography of particulate filters: A non-destructive investigation tool for applied and industrial research," Nuclear Instruments and Methods in Physics Research Section A, vol. 729, pp. 581-588, 2013.

[33] S. Lee, J. Gregor, and D. Osborne, "Development and validation of a complete GATE model of the Siemens Inveon trimodal imaging platform." Journal of Molecular Imaging, vol. 12, pp. 1-9, 2013.

[34] F. Kim, D. Penumadu, J. Gregor, M. Marsh, N. Kardjilov, and I. Manke, "Characterizing partially saturated compacted sand specimen using 3D image registration of high resolution neutron and x-ray tomography." Journal of Computing in Civil Engineering. Published on-line August 2014. Print version coming.

[35] T. Toops, J. Pihl, C. Finney, J. Gregor, and H. Bilheux, "Progression of soot cake layer properties during the systematic regeneration of diesel particulate filters measured with neutron tomography," Journal of Emission Control Science and Technology, vol. 1, pp. 24-31, 2015.

[36] S. Lee, J. Gregor, D. Osborne, and J. Wall, "GATE validation of standard dual energy corrections in small animal SPECT-CT." PLoS ONE 10(4): e0122780. doi:10.1371/journal.pone.0122780.

[37] J. Gregor and J. Fessler, "A comparison of SIRT with SQS for regularized weighted least squares image reconstruction." IEEE Transactions on Computational Imaging, vol. 1, no. 1, pp. 44-55, 2015.

[38] J. Dunn and J. Gregor, “Multimodal pose estimation and registration for head tracking,” submitted to Machine Vision and Applications.

[39] J.T. Liso, H. Kodituwakku, J. Gregor, and M.G. Thomason, “RED Alert: Detecting events in large multi-dimensional network data”, submitted to Transactions on Knowledge Discovery from Data.

[40] H. Kodituwakku, J.T. Liso, and J. Gregor, “InSight2: A real-time scalable modular network situational awareness platform for research and education networks”, submitted to Computer Networks.

Conference Proceedings

[1] J. Gregor and M.G. Thomason, "A disagreement count scheme for inference of constrained Markov networks", in L. Miclet and C. de la Higuera (eds.), Grammatical Inference: Learning Syntax from Sequences (LNAI 1147), Proc. ICGI-96, Montpellier, France, pages 168-178, Springer, 1996.

[2] J. Gregor and D.C. Hensley, "Gamma-ray imaging of the Quinby sources", Proc. 5th Nondestructive Assay and Nondestructive Examination Waste Characterization Conference, Salt Lake City, Utah, pages 361-379, 1997.

[3] F. Rannou and J. Gregor, "Iterative reconstruction of three-dimensional magnetic resonance images from boron data", Int. Conf. Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Pittsburgh, PA, pages 89-92, 1997.

[4] R.T. Whitaker, J. Gregor, and P.F. Chen, "Indoor scene reconstruction from sets of noisy range images", 3DIM'99, Ottawa, Canada, pages 348-357, 1999.

[5] J. Gregor and D.C. Hensley, "Enhanced imaging algorithms for the APNea system", Proc. 7th Nondestructive Assay and Nondestructive Examination Waste Characterization Conference, Salt Lake City, Utah, pages 221-234, 2000.

[6] F. Rannou and J. Gregor, "Computational issues for 3D MRI projection image reconstruction", Proc. 22nd IEEE Engr. in Medicine and Biology Conf., Chicago, IL, July 2000. Four pages.

[7] J. Gregor and D.C. Hensley, "Algorithms for imaging neutrons with the APNea system," Spectrum2000: Int'l Conf. on Nuclear and Hazardous Waste Management, Chattanooga, TN, Sept. 2000. Eight pages.

[8] J. Gregor and F. Rannou, "A least squares framework for projection MRI reconstruction", Medical Imaging 2001: Image Processing, San Diego, CA, Feb. 2001. Proc. SPIE Vol. 4322, pp 888-897.

[9] A. Gothandaraman, R.T. Whitaker, and J. Gregor, "Total variation for the removal of blocking effects in DCT based encodings", IEEE Int. Conf. Image Proc., Thessaloniki, Greece, Oct. 2001. Four pages.

[10] G. Mazeroff, V. de Cerqueira, J. Gregor, and M.G. Thomason, "Probabilistic trees and automata for application behavior modeling", ACM Southeast Conf., Savannah, GA, pp. 435-440, Mar. 2003.

[11] V. de Cerqueira, G. Mazeroff, J. Gregor, and M.G. Thomason, "Visualization techniques for probability-weighted tree and automata-based models", ACM Southeast Conf., Savannah, GA, pp. 100-105, Mar. 2003. Award for outstanding student paper.

[12] J. Gregor, T. Benson, S. Gleason, and M. Paulus, "Support algorithms for x-ray micro-CT conebeam imaging", Int. Conf. Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Saint Malo, France, July 2003. Four pages.

[13] J. Gregor, S. Gleason, and M. Paulus, "Conebeam x-ray computed tomography with an offset detector array", IEEE Int. Conf. Image Proc., Barcelona, Spain, Sep. 2003. Four pages.

[14] M. Paulus, S. Gleason, J. Goddard, S. Kennel, J. Wall, A. Solomon, J. Gregor, and more, "Initial results with a small animal microSPECT/CT imaging system", High-resolution Molecular Imaging in Small Animals (IMI/HiRes), Madrid, Spain, Sep. 2003. Abstract.

[15] J. Gregor, S. Gleason, S. Kennel, M. Paulus, A. Solomon, P. Hawkins, and J. Wall, "A microSPECT/CT system for imaging of AA-amyloidosis in mice", Small-Animal SPECT Workshop, Tucson, AZ, Jan. 2004. Also in M. Kupinski and H. Barrett (eds.), Small-Animal SPECT Imaging, Chapter 15, Plenum US, 2005.

[16] J. Wall, M. Paulus, S. Kennel, S. Gleason, J. Baba, J. Gregor, D. Wolfenbarger, D. Weiss, A. Solomon, "Imaging of primary (AL) amyloidosis with an amyloid reactive monoclonal antibody", Xth Intl. Symp. on Amyloid and Amyloidosis, Tours, France, April 2004.

[17] J. Wall, S. Kennel, M. Paulus, S. Gleason, J. Gregor, M. Schell, T. Smith, B. O'Nuallain, P. Hawkins, and A. Solomon, "MicroSPECT/CT imaging of AA amyloidosis", Xth Intl. Symp. on Amyloid and Amyloidosis, Tours, France, April 2004.

[18] L. Arrowood, J. Carney, J. Gregor, and D. Townsend, "Use of consistency conditions on PET sinogram data to register anatomical boundaries in PET/CT imaging", Soc. Nucl. Medicine, Philadelphia, PA, June 2004. Abstract.

[19] J. Gregor, S. Gleason, S. Kennel, M. Paulus, T. Benson, and J. Wall, "Approximate volumetric system models for microSPECT", IEEE Medical Imaging Conf., Rome, Italy, pp 2575-2578, Oct. 2004.

[20] T. Benson and J. Gregor, "Framework for iterative conebeam micro-CT reconstruction", IEEE Medical Imaging Conf., Rome, Italy, Oct. 2004. Five pages.

[21] J. Gregor and Z. Liu, "A Bayesian framework for regularized SVM parameter estimation," IEEE Conf. Data Mining, Brighton, England, Nov. 2004. Seven pages.

[22] T. Benson and J. Gregor, "Distributed Image Reconstruction of Micro-CT Data: Computation and Communication Issues", Int. Conf. on Communication in Computing, Las Vegas, Nevada, June 2005.

[23] T. Benson and J. Gregor, "Three-dimensional focus of attention for iterative cone-beam micro-CT reconstruction", Int. Conf. Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Salt Lake City, Utah, July 2005. Four pages.

[24] N. Black and J. Gregor, "Monte Carlo simulation of scatter in a cone-beam micro-CT scanner", Int. Conf. Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, Salt Lake City, Utah, July 2005. Four pages.

[25] T. Benson and J. Gregor, "Modified simultaneous iterative reconstruction technique for faster parallel computation," IEEE Medical Imaging Conference, Puerto Rico, pp. 2715-2718, Oct. 2005.

[26] K. Tobin, D. Aykac, P. Govindasamy, S. Gleason, J. Gregor, T. Karnowski, J. Price, and J. Wall, "Image-based informatics for preclinical biomedical research," International Symposium on Visual Computing, Lake Tahoe, NV, Nov. 2006. Also in Lecture Notes in Computer Science 4292, pp. 824-834, Springer.

[27] T. Benson and J. Gregor, "Iterative reconstruction of cone-beam CT data on a cluster," SPIE Electronic Imaging, San Jose, Feb. 2007. Twelve pages.

[28] J. Gregor, T. Benson, and G. Bosilca, "Distributed multi-core implementation of SIRT with application to cone-beam micro-CT," International Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine, Lindau, Germany, July 2007. Four pages.

[29] J. Gregor, N. Black, and J. Wall, "Monte Carlo study of scatter and attenuation effects in connection with I-125 pinhole imaging of mice," International Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine, Lindau, Germany, July 2007. Four pages.

[30] M. Lenox, J. Gregor, and S. Siegel, "Transmission measurements using iterative cone beam reconstruction on the Inveon DPET," IEEE Medical Imaging Conference, Dresden, Germany, Oct. 2008. Four pages.

[29] B. Feng, M. Chen, B. Bai, D.W. Austin, R. Mintzer, A. Smith, and J. Gregor, "Modeling of the point-spread function by geometric calculations in multi-pinhole SPECT reconstruction," IEEE Medical Imaging Conference, Dresden, Germany, Oct. 2008. Four pages.

[30] M. Lenox and J. Gregor, "Computationally efficient iterative transmission imaging for the Inveon DPET," First Annual ORNL Biomedical Science and Engineering Conference, March 2009. Four pages.

[31] H. Rothfuss, V. Panin and J. Gregor, "Modified subset scheme for attenuation weighted reconstruction," IEEE Medical Imaging Conference, Orlando, Florida, Oct. 2009. Four pages.

[32] J. Gregor, M. Lenox, P. Bingham and L. Arrowood, "Multi-core cluster implementation of SIRT with application to cone beam micro-CT," Workshop on High-Performance Medical Imaging, IEEE Medical Imaging Conference, Orlando, Florida, pp. 4120-4125, Oct. 2009.

[33] D.W. Austin, B. Feng, M. Chen, R. Mintzer, J. Gregor, A. Stuckey, and J. Wall, "Validation of CT-based attenuation correction for multi-pinhole PSF reconstruction for small animal SPECT," IEEE Medical Imaging Conference, Knoxville, TN, Oct. 2010.

[34] J. Gregor, "Data-driven problem reduction for image reconstruction from projections using gift wrapping," IEEE Medical Imaging Conference, Knoxville, TN, Oct. 2010.

[35] M.G. Thomason and J. Gregor, "Image tensor tools: Incremental updating and imputation of missing pixel values," Future of Instrumentation International Workshop, Oak Ridge, TN, Nov. 2010.

[36] J. Gregor, "Distributed multi-core implementation of SIRT with vectorized matrix kernel for micro-CT," International Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine, Potsdam, Germany, July 2011.

[37] J. Gregor, "A priority queue approach to ordered subsets," International Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine, Potsdam, Germany, July 2011.

[38] H. Santos-Villalobos, P. Bingham, and J. Gregor, "Iterative reconstruction of coded source neutron radiographs," IEEE Nuclear Science Symposium, Anaheim, California, Oct. 2012.

[39] S. Lee, J. Gregor, and D. Osborne, "Initial validation of a complete GATE model of the Siemens Inveon trimodal imaging system," IEEE Medical Imaging Conference, Anaheim, California, Oct. 2012.

[40] H. Santos-Villalobos, P. Bingham, and J. Gregor, "Neutron imaging with coded sources: New challenges and the implementation of SIRT," SPIE Electronic Imaging, San Jose, Feb 2013.

[41] J. Gregor, C. Finney, T. Toops, "Tomographic neutron imaging using SIRT," International Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine, Lake Tahoe, CA, June 2013.

[42] L. Arrowood, S. Lee, J.Gregor, "A line process approach to penalized maximum-likelihood reconstruction for 3D SPECT," accepted for IEEE Medical Imaging Conference, Seoul, South Korea, Oct. 2013.

[43] S. Lee, J. Gregor, D. Osborne, J. Wall, "Dual istope SPECT imaging of I-123 and I-125," accepted for IEEE Medical Imaging Conference, Seoul, South Korea, Oct. 2013.

[44] P. Bingham, H. Villalobos-Santos, J. Gregor, "Magnified neutron radiography with coded sources," submitted to SPIE Electronic Imaging, San Jose, Feb. 2014.

[45] J. Gregor, "Algorithmic improvements to SIRT with application to X-ray CT of luggage," Third Intl. Conf. Image Formation in X-ray Computed Tomography, Salt Lake City, June 2014.

[46] H. Santos-Villalobos, P. Bingham, J. Gregor, "Model-based least squares reconstruction of coded source neutron radiographs: Integrating the ORNL HFIR CG1D source model," IEEE Nuclear Science Symposium, Seattle, WA, Nov 2014.

[47] S. Lee, J. Gregor, J. Wall, D. Osborne, "Micro-SPECT imaging in the presence of an X-ray CT contrast agent: Effects of attenuation and scatter and effectiveness of corrections," International Meeting on Fully 3D Image Reconstruction in Radiology and Nuclear Medicine, Newport, RI, June 2015.

[48] J. Gregor, P. Bingham, H. Santos-Villalobos, "Non-uniform neutron source approximation for the iterative reconstruction of coded source images." IS&T International Symposium on Electronic Imaging, San Jose, Feb. 2016.

[49] J. Gregor, H. Santos-Villalobos, "The unavoidable use of computational imaging on next generation biometric identification systems." IS&T International Symposium on Electronic Imaging, San Jose, Feb. 2016.

[50] J. Gregor, P. Bingham, L.F. Arrowood, "Total variation constrained weighted least squares using SIRT and proximal mappings." 4th International Conference on Image Formation in X-Ray Computed Tomography, Bamberg, Germany, July 2016.

[51] T. Tumpa, S. Acuff, J. Gregor, S. Lee, D. Hu and D. Osborne, “Respiratory motion correction using a novel positron emission particle tracking technique: A framework for individual lesion motion correction,” IEEE Engineering in Medicine and Biology Conference, Honolulu, HI, July 2018.

Book Chapters

[1] E. Granum, M.G. Thomason, and J. Gregor, "On the use of automatically inferred Markov networks for chromosome analysis," in C. Lundsteen and J. Piper (eds.), Automation of Cytogenetics, pages 233-251, Springer, Berlin, 1989. By invitation.

[2] M.G. Thomason and J. Gregor, "Inference of Markov chain models of sequences", Current Topics in Pattern Recognition Research, Research Trends, pp. 163-173, 1995. By invitation.

[3] J. Gregor, S. Gleason, S. Kennel, M. Paulus, A. Solomon, P. Hawkins, and J. Wall, "A microSPECT/CT system for imaging of AA-amyloidosis in mice," in M. Kupinski and H. Barrett (eds.), Small-Animal SPECT Imaging, Plenum US, pp 209-214, 2005.

[4] W. Allen, R. Ford, J. Gregor, G. Marin, M.G. Thomason, and J. Whittaker, "Behavioral Detection of Malicious Code," in C. Wang et al (eds.), Department of Defense Sponsored Information Security Research: New Methods for Protecting Against Cyber Threats, Wiley, pp 533-544, 2007.

[5] K. Tobin, E. Chaum, J. Gregor, T. Karnowski, J. Price, and J. Wall, "Image informatics for clinical and preclinical biomedical analysis", in G. Schaefer, A. Hassanien, and J. Jiang (eds.), Computational Intelligence in Medical Imaging, CRC Press, pp 239-290, 2009.

[6] K. Tobin, P. Bingham, and J. Gregor, "Mathematics of neutron imaging", in I. Anderson, R. McGreevy, and H. Bilheux (eds.), Neutron Imaging and Applications, Chapter 7, Springer, pp 109-128, 2009.