Doga Gursoy

Advanced Photon Source
Argonne National Laboratory
9700 Cass Ave, Lemont, 60439 IL, USA.
Phone: +1-630-252-0882
E-mail: dgursoy@anl.gov

"There are 10 types of people in this world, those who understand binary and those who don't."

Education

PhD in electrical engineering, Graz University of Technology, 2010.
BS & MS in electrical and electronics engineering, Middle East Technical University, 2004 & 2007.

Employment

Computational Scientist, Argonne National Laboratory, 2018-cont.
Adjunct Associate Professor, Electrical Engineering & Computer Science, Northwestern University, 2020-cont.
Adjunct Assistant Professor, Electrical Engineering & Computer Science, Northwestern University, 2017-2020
Fellow, Northwestern Argonne Institute of Science and Engineering, 2017-cont.
Assistant Computational Scientist, Argonne National Laboratory, 2015-2018
Postdoctoral Researcher, Argonne National Laboratory, 2013-2015
Postdoctoral Researcher, University of Houston, 2012-2013
Postdoctoral Researcher, Graz University of Technology, 2010-2012
Research Assistant, Graz University of Technology, 2007-2010
Research Assistant, Middle East Technical University, 2006-2007

Services

Member, Technical Committee on Computational Imaging, IEEE Signal Processing Soceity, 2021-cont.
Associate Member, Technical Committee on Computational Imaging, IEEE Signal Processing Soceity, 2020-2021
Associate Editor, IEEE Transactions on Computational Imaging, 2020-cont.
Editorial Board Member, Advanced Structural and Chemical Imaging, Springer, 2017-2020.
Area Chair, IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2022.

Journal Publications

Ge M et al. Three-dimensional imaging of grain boundaries in a mixed ionic-electronic conductor system via quantitative fluorescence x-ray tomography analysis. (in revision)
Majee S, Aslan S, Boumann C, Gursoy D. CodEx: A modular framework for joint temporal de-blurring and tomographic reconstruction. (in revision)
Yu X, Nikitin V, Ching DJ, Aslan S, Gursoy D, Bicer T. Scalable and accurate multi-GPU based image reconstruction of large-scale ptychography data. (in revision)
Gursoy D, KC Wiegart, Jacobsen C. Lensless X-ray Nanoimaging: Revolutions and Opportunities. IEEE Signal Processing Magazine (accepted).
Hidayetoglu M, Bicer T, de Gonzalo SG, Ren B, Gursoy D, Kettimuthu R, Foster I, Hwu WMW. MemXCT: design, optimization, scaling, and reproducability of x-ray tomography imaging. IEEE Transactions on Parallel and Distributed Systems, 2021.
Barutcu S, Aslan S, Katsaggelos AK, Gursoy D. Limited-angle computed tomography with deep image and physics priors. Scientific Reports, vol.11, no.1, 2021.
Aslan S, Liu Z, Nikitin V, Bicer T, Leyffer S, Gursoy D. Joint ptycho-tomography with deep generative priors. Machine Learning: Science and Technology, vol.2, no.045017, 2021.
Ganguly PS, Pelt DM, Gursoy D, De Carlo F, Batenburg KJ. Improving reproducibility in synchrotron tomography using implementation-adapted filters. Journal of Synchrotron Radiation, vol.28, no.5, 2021.
De Andrade V, Nikitin V, Wojcik M, Deriy A, Bean S, Shu D, Mooney T, Peterson K, Prabhat KC, Li K, Ali S, Fezzaa K, Gursoy D, Arico C, Ouendi S, Troadec D, Simon P, De Carlo F, Lethien C. Fast x-ray nanotomography with sub-10 nm resolution as a powerful imaging tool for nanotechnology and energy storage applications. Advanced Materials, e2008653, 2021.
Du M, Di Z, Gursoy D, Xian RP, Kozorovitskiy Y, Jacobsen C. Upscaling x-ray nanoimaging to macroscopic specimens. Journal of Applied Crystallography, vol.54, no.2, 2021.
Nikitin V, De Andrade V, Slyamov A, Gould BJ, Zhang Y, Sampathkumar V, Kasthuri N, Gursoy D, De Carlo F. Distributed optimization for nonrigid nano-tomography. IEEE Transactions on Computational Imaging, vol.7, 2021.
Prasad JA, Balwani AH, Johnson EC, Miano JD, Sampathkumar V, De Andrade V, Fezzaa K, Du M, Vescovi R, Jacobsen C, Kording KP, Gursoy D, Roncal WG, Kasthuri N, Dyer EL. A three-dimensional thalamocortical dataset for characterizing brain heterogeneity. Scientific Data, vol.7, no.1, 2020.
Du M, Gursoy D, Jacobsen C. Near, far, wherever you are: simulations on the dose efficiency of holographic and ptychographic imaging. Journal of Applied Crystallography, vol.53, no.3, 2020.
Gursoy D, Jacobsen C. Multimodal x-ray nanotomography. MRS Bulletin vol.45, no.4, 272-276, 2020.
Du M, Nashed YSG, Kandel S, Gursoy D, Jacobsen C. Three dimensions, two microscopes, one code: automatic differentiation for x-ray nanotomography beyond the depth of focus limit. Science Advances (accepted).
Victor TW, Easthon LM, O’Toole KH, Smith RJ, Ge M, Huang X, Yan H, Chu YS, Chen S, Gursoy D, Imperiali B, Allen KN, Miller LM. Lanthanide-Binding Tags (LBTs) for nanoscale x-ray imaging of proteins in cells and tissues. Journal of the American Chemical Society (accepted).
Zhengchun L, Bicer T, Kettimuthu R, Gursoy D, De Carlo F, Foster I. TomoGAN: Low-dose x-ray tomography with generative adversarial networks: Discussion. Journal of the Optical Society of America A, vol.37, no.3, pp.422-434, 2020.
Di W, Chen S, Gursoy D, Paunescu T, Leyffer S, Wild MS, Vogt S. Optimization-based simultaneous alignment and reconstruction in x-ray fluorescence tomography. Optics Letters, vol.44, no.17, pp.4331-4334, 2019.
Nikitin V, Aslan S, Yao Y, Bicer T, Leyffer S, Mokso R, Gursoy D. Photon-limited ptychography of 3D objects via Bayesian reconstruction. OSA Continuum, vol.2, no.10, pp.2948-2968, 2019.
Ching D, Aslan S, Nikitin V, Gursoy D. Time-coded aperture for x-ray imaging. Optics Letters, vol.44, no.11, pp.2803-2806, 2019.
Yuan K, Starchenko V, Lee SS, De Andrade V, Gursoy D, Sturchio NC, Fenter P. Mapping three-dimensional dissolution rates of calcite microcrystals: Effects of surface curvature and dissolved metal ions. ACS Earth and Space Chemistry, vol.3, no.5, pp.833-843, 2019.
Aslan S, Nikitin V, Ching D, Bicer T, Leyffer S, Gursoy D. Joint ptycho-tomography reconstruction through alternating direction method of multipliers. Optics Express, vol. 27, no.6, pp.9128-9143, 2019.
Larsson E, Gursoy D, De Carlo F, Lilleodden E, Storm M, Wilde F, Hug K, Müller M, Greving I. Nanoporous gold: A hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems. Journal of Synchrotron Radiation, vol.26, no.1, pp.194-204, 2019.
Ching D, Hidayetoglu M, Bicer T, Gursoy D. Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes. Applied Optics, vol.57, no.31, 2018.
Du M, Vescovi R, Fezzaa K, Jacobsen C, Gursoy D. X-ray tomography of extended objects: a comparison of data acquisition approaches. Journal of the Optical Society of America A, vol.35, no.10, 2018.
Zhao C, Wada T, De Andrade V, Gursoy D, Kato H, Chen-Wiegart YK. Imaging of 3D morphological evolution of nanoporous silicon anode in lithium ion battery by X-ray nano-tomography. Nano Energy, vol.52, pp.381-390, 2018.
Vescovi R, Du M, De Andrade V, Scullin W, Gursoy D, Jacobsen C. Tomosaic: efficient acquisition and reconstruction of teravoxeltomography data using limited-size synchrotron X-ray beams. Journal of Synchrotron Radiation, vol.25, no.5, pp.1478-1489, 2018.
Kaira CS, Yang X, De Andrade V, De Carlo F, Scullin W, Gursoy D, Chawla N. Automated correlative segmentation of large transmission X-ray microscopy tomograms using deep learning. Materials Characterization. vol.142, pp.203-210, 2018.
Hierro-Rodriguez A, Gursoy D, Phatak C, Quiros C, Sorrentino A, Alvarez-Prado LM, Velez M, Martin JI, Alameda JM, Pereiro E, Ferrer S. 3D reconstruction of magnetization from dichroic soft X-ray transmission tomography. Journal of Synchrotron Radiation, vol.25, no.4, 2018.
Pandolfi RJ, Kumar D, Freychet G, Parks H, Venkatakrishnan S, Blair A, Sahoo S, Marchesini S, Pellouchoud LA, Ren F, Fournier AP, Tassone CJ, Gursoy D, De Carlo F, Parkinson DY, N'Diaye A, Arenholz E, Fackler S, Perciano T, Ushizima D, Jiang Z, Mehta A, Fukuto M, Yager K, Strzalka J, Kline RJ, Caswell TA, Allan DB, Campbell S, Sethian J, Krishnana H, Hexemer A. Xi-cam: A versatile interface for data visualization and analysis. Journal of Synchrotron Radiation, vol.25, no.4, 2018.
Yang X, De Andrade V, De Carlo F, Dyer EL, Kasthuri N, Gursoy D. Low-dose x-ray tomography through a deep convolutional neural network. Scientific Reports, vol.8, no.1, 2018.
De Carlo F, Gursoy D, Ching DJ, Batenburg J, Ludwig W, Mancini L, Marone F, Mokso R, Pelt D, Sijbers J, Rivers M. TomoBank: A tomographic data bank for computational x-ray science. Measurement Science and Technology, vol.29, no.3, 2018.
Dyer EL, Fernandes HL, Roncal WG, Vogelstein JT, Gursoy D, Xiao X, Jacobsen C, Kording KP, Kasthuri N. Quantifying mesoscale neuroanatomy using x-ray microtomography. eNeuro, vol.4, no.5, 2017.
Gursoy D, Hong YP, He K, Hujsak K, Yoo S, Chen S, Li Y, Ge M, Miller LM, Chu YS, De Andrade V, He K, Cossairt O, Katsaggelos A, Jacobsen C. Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection. Scientific Reports, vol.7, no.11818, 2017.
Gursoy D. Direct coupling of tomography and ptychography. Optics Letters, vol.42, no.16, pp.3169-3172, 2017.
Ching D, Gursoy D. Xdesign: An open-source software package for designing x-ray imaging experiments. Journal of Synchrotron Radiation, vol.24, no.2, 2017.
Bicer T, Gursoy D, De Andrade V, Kettimuthu R, Scullin W, De Carlo F, Foster I. Trace: A high-throughput tomographic reconstruction engine for large-scale datasets. Advanced Structural and Chemical Imaging, vol.3, no.6, 2017.
Yang X, Phatak C, De Carlo F, Gursoy D. A convolutional neural network approach to calibrate rotation axis of x-ray computed tomography. Journal of Synchrotron Radiation, vol.23, no.4, 2017.
Bicer T, Gursoy D, Kettimuthu R, De Carlo F, Foster I. Optimization of tomographic reconstruction workflows on geographically distributed resources. Journal of Synchrotron Radiation, vol.23, no.4, pp.997-1005 2016.
Pelt DM, Gursoy D, Batenburg KJ, De Carlo F, Palenstijna WJ, Sijbers J. Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data. Journal of Synchrotron Radiation, vol.23, no.3, pp.842-849, 2016.
Tan O, Aydin S, Sayar GH, Gursoy D. EEG complexity and frequency in chronic residual schizophrenia. Anatolian Journal of Psychiatry, vol.17, no.5, 3pp.85-392, 2016.
Duke DJ, Swantek AB, Sovis N, Tilocco FZ, Powell CF, AL Kastengren, Gursoy D, Bicer T. Time-resolved x-ray tomography of gasoline direct injection sprays. SAE International Journal of Engines, vol.9, 2015.
Gursoy D, Bicer T, Almer J, Kettimuthu R, Stock S, De Carlo F. Maximum a posteriori crystallographic phase reconstruction in x-ray powder diffraction tomography. Philosophical Transactions A, vol.373, no.2043, 2015.
Gursoy D, Bicer T, Lanzirotti A, Newville MG, De Carlo F. Hyperspectral image reconstruction for x-ray fluorescence tomography. Optics Express, vol.23, no.7, pp.9014-9023, 2015.
Phatak C, Gursoy D. Iterative reconstruction of magnetic induction using Lorentz transmission electron tomography. Ultramicroscopy, vol.150, pp.54-64, 2015.
Gursoy D, De Carlo F, Xiao X, Jacobsen C. TomoPy: A framework for the analysis of synchrotron tomographic data. Journal of Synchrotron Radiation, vol.22, no.5, 2014.
De Carlo F, Gursoy D, Marone F, Rivers M, Parkinson YD, Khan F, Schwarz N, Vine DJ, Vogt S, Gleber SC, Narayanan S, Newville M, Lanzirotti T, Sun Y, Hong YP, Jacobsen C. Scientific Data Exchange: a schema for HDF5-based storage of raw and analyzed data. Journal of Synchrotron Radiation, vol.22, 2014.
Gursoy D, Das M. Single-step absorption and phase retrieval with polychromatic x-rays using a spectral detector. Optics Letters, vol.38, no.9, pp.1461-1463, 2013.
Maimaitijiang Y, Borsic A, Gursoy D, Adler A. An experimental clinical evaluation of EIT imaging with L1 data and image norms. Physiological Measurement, vol.34, no.9, pp.1027-1039, 2013.
Gursoy D, Maimaitijiang Y, Adler A, Scharfetter H. Enhancing impedance imaging through multimodal tomography. IEEE Transactions on Biomedical Engineering, vol.58, no.11, pp.3215-3224, 2011.
Gursoy D, Scharfetter H. Imaging artifacts in magnetic induction tomography caused by the structural incorrectness of the sensor model. Measurement Science and Technology, vol.22, no.1 015502, 2011.
Gursoy D, Scharfetter H. Anisotropic conductivity tensor imaging using magnetic induction tomography. Physiological Measurement, vol.31, no.8, pp.135-145, 2010.
Gursoy D, Scharfetter H. Magnetic induction pneumography: A planar coil system for continuous monitoring of lung function via contactless measurements. Journal of Electrical Bioimpedance, vol.1, pp.56-62, 2010.
Gursoy D, Scharfetter H. The effect of receiver coil orientations on the imaging performance of magnetic induction tomography. Measurement Science and Technology, vol.20, no.10, 105505 (9pp), 2009.
Gursoy D, Scharfetter H. Optimum receiver array design for magnetic induction tomography. IEEE Transactions on Biomedical Engineering, vol.56, no.5, pp.1435-1441, 2009.
Gursoy D, Scharfetter H. Reconstruction artefacts in magnetic induction tomography due to patient's movement during data acquisition. Physiological Measurement, vol.30, no.6, pp.165-S174, 2009.

Monologues

Modeling, system optimization and artifact reduction in magnetic induction tomography for medical applications. PhD Dissertation, 2010.
Multi-frequency contactless electrical impedance imaging using realistic head models: Single coil simulations. MS Thesis, 2007.

Patents

Das M, Gursoy D. Single step x-ray phase imaging. WO 2014047424 (A1), 2014.
Scharfetter H, Freiberger M, Gursoy D. Luminescence probing in strongly scattering objects using ionizing radiation. EP 2387940 (A1), 2011.
Scharfetter H, Gursoy D. Device and method for the tracking of object movements in magnetic induction tomography. EP 2332463 (A1), 2011.

Invited Talks

Tomography of time-evolving samples with limited measurement data. Enabling 3D Mesoscale Imaging Under Dynamic Conditions Workshop, LANL (virtual), 2021.
Computational imaging with synchrotron light, LNLS/CNPEM 29th Annual Users Meeting (RAU), Campinas, Brazil, 2019.
Computational methods and challenges in high-throughput x-ray imaging, Workshop for Computational Processing for LNLS Users, Campinas, Brazil, 2019.
High-resolution tomography and challenges in visualization, Dagstuhl Seminar Series on Visual Computing in Material Sciences, Dagstuhl, Germany, 2019.
Computed tomography at high-speeds, International Congress on X-ray Optics and Microanalysis (ICXOM), Rosemont IL, USA, 2019.
Ptycho-tomography: an emerging lensless microscopy technique for 3D imaging of materials at the nanoscale, Lund Institute of Advanced Neutron and X-ray Science (LINXS) Workshop on Inverse problems in X-ray phase retrieval and tomography, Lund, Sweden, 2019
High-speed x-ray imaging at the nanoscale, UIUC iOptics Seminar Series, Champaign IL, USA, 2018.
Towards real-time monitoring, optimization, navigation and analysis for synchrotron-based tomography experiments, SSRL/LCLS Users’ Meeting Workshop on Computational Workflows for X-ray Science, Menlo Park CA, USA, 2018.
High-speed 3D imaging with ptychography, SLAC/ALS Users’ Meeting Workshop on Ptycho-Tomography, Berkeley CA, USA, 2018.
High-speed fly-Scan volumetric imaging. Microscopy & Microanalysis Meeting, Baltimore MD, USA, 2018.
High-resolution 3D x-ray microscopy. Conference of Data Analysis (CoDA), Santa Fe NM, USA, 2018.
High-speed and high-throughput x-ray tomography, Elettra Sincrotrone Seminar Series, Trieste, Italy, 2018
Multi-channel high-resolution x-ray tomography, SIAM Conference on Imaging Science, Bologna, Italy, 2018
Challenges and opportunities in data-intnsive synchrotron-based imaging and microscopy. Workshop on Big Data by & for High-speed Imaging & Particle Tracking, Atlanta GA, USA, 2017.
Experiment design and data analysis in tomographic X-ray imaging and microscopy. Mathematical Advances in Electron Microscopy, Oaxaca, Mexico, 2017.
Iterative nanostructure reconstruction from sparse, incomplete and uncertain data. Workshop on Multi-dimensional and Multi-modal X-ray Imaging and Analysis, Brookhaven National Laboratory, Upton NY, USA, 2017.
High-resolution imaging from sparse, incomplete and uncertain data. 5th Banff Meeting on Structural Dynamics: Ultrafast Dynamics with X-Rays and Electrons, Banff Centre, Alberta, Canada, 2017.
(Webinar) Integrating multimodal imaging of materials for energy storage. Joint Center for Energy Science Research (JCESR), 2016.
Scientific computing framework for imaging and analysis: Designing x-ray imaging experiments and processing data. Three-Way Meeting, DESY, Hamburg, Germany, 2016.
(Panelist) Sustainability: How to fundamentally change science? Open Data Ecosystem for Neuro- sciences (ODEN), Washington DC, USA, 2016.
Multimodal imaging of batteries. Integrated Imaging Institute (I3), Lemont IL, USA, 2016.
How to acquire and interpret data in x-ray tomography? Center for Advanced Mathematics for Energy Research Applications (CAMERA), Berkeley CA, USA, 2016.
Computational aspects of x-ray tomography. National Energy Research Scientific Computing Center (NERSC), Berkeley CA, USA, 2016.
Current and future data analysis trends for synchrotron imaging. 23rd International Congress on X-ray Optics and Microanalysis, Upton NY, USA, 2015.
Multidimensional imaging with synchrotron light. Escaping Flatland: Imaging Biological Architecture and Events in 3-D, Marine Biological Laboratory, Woods Hole MA, USA, 2015.
Compressive sensing and its potential in nanoimaging. Joint Nanoscale Science Research Centers (NSRC) Workshop, Oak Ridge TN, USA, 2015.
Imaging artifacts in x-ray tomography. Lorentz Center Workshop, Leiden, Netherlands, 2015.
(Webinar) TomoPy: A framework for the analysis of synchrotron tomographic data. Open Technical Forum: Computing for Light and Neutron Sources, 2014.
Analysis and reconstruction of tomographic data at the Advanced Photon Source. Computational Science Center, Brookhaven National Laboratory, Upton, NY, USA, 2014.
Current status and future plans for tomographic reconstruction at the Advanced Photon Source, Workshop on Advanced Tomographic Reconstruction Methods, Berkeley CA, USA, 2013.

Advanced Structural and Chemical Imaging, Applied Physics Letters, Fundamenta Informaticae, International Journal of Imaging Systems and Technology, Inverse Problems, JOM, Journal of Infrared, Journal of Synchrotron Radiation, Millimeter, and Terahertz Waves, Measurement Science and Technology, Medical & Biological Engineering & Computing, Medical Physics, Neural Computing and Applications, Optics Express, Philosophical Transactions of the Royal Society A, Physics in Medicine and Biology, Physiological Measurement, Radiation Physics and Chemistry, Scientific Reports, Sensors and Actuators A: Physical, IEEE Nuclear Science Symposium, IEEE Transactions on Biomedical Engineering, IEEE Transactions on Computational Imaging, IEEE Transactions on Image Processing, IEEE Transactions on Medical Imaging, IEEE Sensors Journal, Turkish Journal of Electrical Engineering & Computer Sciences.

Miscellaneous

Parkinson DY, Gursoy D, Pelt DM, Venkatakrishnan S, Archibald R, Mohan KA, Bicer T, Vogelgesang M, Sethian J, Wadeson N, Basham M, Farago T. Tomographic reconstruction for synchrotron tomography
Ching D, Aslan S, Nikitin V, Wojcik WJ, Gursoy D. Evaluation of modified uniformly redundant arrays as structured illuminations for ptychography. arXiv:2004.01766, 2020.
Roncal WG, Dyer EL, Gursoy D, Kording KP, Kasthuri N. From sample to knowledge: Towards an integrated approach for neuroscience discovery. arXiv:1604.03199, 2016.
(SPIE Highlight) De Andrade V, Deriy A, Wojcik M, Gursoy D, Shu D, Fezzaa K, De Carlo F. Nanoscale 3D imaging at the Advanced Photon Source. SPIE Newsroom, 2016.
Toby BH, Gursoy D, De Carlo F, Schwarz N, Sharma H, Jacobsen C. Practices and standards for data and processing at APS. Synchrotron Radiation News, vol.28, no.2, pp.15-21, 2015.
Gursoy D. The Science of Imaging, Second Edition, CRC Press, Author: Graham Saxby. Contemporary Physics, vol. 52, no.6, pp.626, 2011.

Conferences

Nikitin V, De Andrade V, Gursoy D, De Carlo F. Reconstruction with nonrigid alignment in tomography and 3D ptychography. X-Ray Nanoimaging: Instruments and Methods V, 2021 (virtual).
Aslan S, Liu Z, Nikitin V, Bicer T, Leyffer S, Gursoy D. Deep priors for ptycho-tomography. Microscopy and Microanalysis, 2020 (virtual).
(best paper) Hidayetoglu M, Bicer T, de Gonzalo SG, Ren B, De Andrade V, Gursoy D, Kettimuthu R, Foster IT, Hwu WW. Petascale XCT: 3D image reconstruction with hierarchical communications on multi-GPU nodes. SC20: International Conference for High Performance Computing, Networking, Storage and Analysis, 2020 (virtual).
Barutcu S, Ruiz P, Schiffers F, Aslan S, Gursoy D, Cossairt O, Katsaggelos AK. Simultaneous 3D x-ray ptycho-tomography with gradient descent. 27th IEEE International Conference on Image Processing, Abu Dhabi, UAE, 2020.
Hidayetoglu M, Bicer T, Gonzalo SG, Ren B, Gursoy D, Kettimuthu R, Foster IT, Hwu WW. Memory-Centric Iterative x-ray image reconstruction. SC20: International Conference for High Performance Computing, Networking, Storage and Analysis, Denver CO, USA, 2019.
Du M, Vescovi R, Chard R, Kasthuri N, Jacobsen C, Dyer E, Gursoy D. An automated pipeline for the collection, transfer, and processing of large-scale tomography data. Biophotonics Congress: Biomedical Optics Congress, Optics and the Brain, Hollywood FL, USA, 2018.
Du M, Nashed Y, Kandel S, Gursoy D, Jacobsen C. 3D object reconstruction beyond the depth-of-focus limit using automatic differentiation. International Workshop on Phase Retrieval and Coherent Scattering, Port Jefferson NY, USA, 2018.
Tondravi M, Scullin W, Du M, Vescovi R, De Andrade V, Jacobsen C, Kording K, Gursoy D, Dyer E. A pipeline for distributed segmentation of teravoxel tomography datasets. X-Ray Microscopy Conference (XRM), Saskatoon, Canada, 2018.
Antipova O, Kemner K, Roehrig C, Vogt S, Li LX, Gursoy D. Developments of X-ray fluorescence tomography at 2-ID-E at APS for studies of composite samples. X-Ray Microscopy Conference (XRM), Saskatoon, Canada, 2018.
Hierro-Rodriguez A, Gursoy D, Phatak C, Quiros C, Sorrentino A, Alvarez-Prado LM, Velez M, Martin JI, Alameda JM, Pereiro E, Ferrer S. 3D reconstruction of magnetization from soft X-ray transmission tomography. 9th Joint European Magnetic Symposia (JEMS) Conference, Mainz, Germany, 2018.
Hierro-Rodriguez A, Gursoy D, Phatak C, Quiros C, Sorrentino A, Alvarez-Prado LM, Velez M, Martin JI, Alameda JM, Pereiro E, Ferrer S. 3D magnetic reconstruction from soft X-ray transmission tomography. International Conference on Magnetism (ICM), San Francesico CA, USA, 2018.
Gursoy D. High-speed fly-Scan volumetric imaging. Microscopy & Microanalysis Meeting, Baltimore MD, USA, 2018.
Yang X, De Andrade V, Gursoy D, De Carlo F, Schroer C. Using deep learning to reduce the radiation damage induced by x-ray microscopy. International Conference on Synchrotron Radiation Instrumentation, Taipei, Taiwan, 2018.
Yang X, De Andrade V, De Carlo F, Chawla N, Kaira CS, Scullin W, Gursoy D. Segmentation for large dataset of x-ray microscopes by using a deep convolutional neural network. TMS, Phoenix, AZ, USA, 2018.
De Andrade V, Deriy A, Wojcik M, Shu D, Gursoy D, Bean S, Bicer T, Pelt DM, Yang X, Wolf M, Glowacki A, Fezzaa K, Jacobsen C, Kaira CS,Chawla N, Ley T, Kasthuri N, De Carlo F. A full-field X-ray nano-tomography system at the Advanced Photon Source: an instrument oriented toward in-situ experiments. TMS, Phoenix, AZ, USA, 2018.
Ronaghi Z, Thomas R, Deslippe J, Bailey S, Gursoy D, Kisner T, Keskitalo R, Borrill J. Python in the NERSC exascale science applications program for data. International Conference for High Performance Computing, Networking, Storage and Analysis, Denver CO, 2017
Bicer T, Gursoy D, Kettimuthu R, Foster IT, Ren B, De Andrede V, De Carlo F. Real-Time data analysis and autonomous steering of synchrotron light source experiments, 2017.
(invited) Gursoy D, Bicer T, Ching D, De Andrade V. Sliding ordered-subset algorithm for real-time x-ray tomography. SPIE Optics+Photonics, San Diego, CA, USA, 2017.
(invited) Gursoy D, YP Hong, K He, K Hujsak, S Yoo, S Chen, V De Andrade, K He, O Cossairt, A Katsaggelos, C Jacobsen. Rapid alignment of projection images in x-ray nanotomography: extension to phase-contrast imaging. SPIE Optics+Photonics, San Diego, CA, USA, 2017.
Jacobsen C, De Andrade V, Deng J, Du M, Gursoy D, Nashed YSG, Paterka T. Wavefront reconstruction in 3D x-ray microscopy. Digital Holography and 3D Imaging Conference, Jeju Island, South Korea, 2017.
Gursoy D. Streaming reconstruction for dynamic tomography experiments. Visual Analysis of Dynamic Processes Workshop, Rigi Kulm, Switzerland, 2017.
Yang X, De Carlo F, Phatak C, De Andrade V, Gursoy D. Deep neural networks for synchrotron X-ray imaging. Electronic Imaging, Burlingame CA, USA, 2017.
(Best Paper Award) Bhimji W, Bard D, Romanus M, Paul D, Ovsyannikov A, Friesen B, Bryson M, Correa J, Lockwood GK, Tsulaia V, Byna S, Farrell S, Gursoy D, Daley C, Beckner V, Straalen BV, Wright NJ, Antypas K, Prabhat. Accelerating science with the NERSC burst buffer early user program. Cray User Meeting (CUG), London, UK, 2016.
De Andrade V, Deriy A, Wojcik M, Gursoy D, Shu D, Mooney T, Peterson K, Glowacki A, Yue K, Yang X, Vescovi R, De Carlo F. Full-field in-situ nano-tomography activity at the Advanced Photon Source. X-Ray Microscopy Conference (XRM), Oxford, UK, 2016.
Vescovi RFC, Miqueles EX, Gursoy D, De Andrade V, Dyer E, Kording K, Cardoso MB, De Carlo F, Jacobsen C, Kasthuri N. Tomosaic: Towards terabyte tomography. X-Ray Microscopy Conference (XRM), Oxford, UK, 2016.
Gursoy D, Sullivan S, Vogt S. Evaluation of contemporary data acquisition schemes for x-ray fluorescence tomography. Denver X-ray Conference, Rosemont IL, USA, 2016.
Kemner KM, O’Brien S, Douglas S, Gursoy D, Lai B, Roehrig C, Sullivan S, Vogt S. x-ray fluorescence tomographic imaging of bacteria within soil aggregates. Denver X-ray Conference, Rosemont IL, USA, 2016.
Li L, Antipova O, S. Chen S, Gursoy D, Vogt S. The development of a tomographic x-ray fluorescence microscopy at the 2-ID-E beamline. Denver X-ray Conference, Rosemont IL, USA, 2016.
De Andrade V, Deriy A, Wojcik M, Gursoy D, Shu D, Mooney T, Peterson K, Glowacki A, Yue K, De Carlo F. A new transmission x-ray microscope for in-situ nano-tomography at the Advanced Photon Source. SPIE Optics+Photonics, San Diego CA, USA, 2016.
Zhao C, Wada T, Andrade VD, Gursoy D, Thieme J, Katob H, Chen-Wiegart YK. Silicon anode morphological evolution with lithiation and delithiation. Materials Research Society Meeting (MRS), Phoenix AZ, USA, 2016.
O'Brien SL, Whiteside MD, Sholto-Douglas D, Dohnalkova A, Durall DM, Gursoy D, Jones MD, Kovarik L, Lai B, Roehrig C, Sullivan S, Vogt S, Kemner KM. Identifying microbial habitats in soil using quantum dots and x-ray fluorescence microtomography. American Geophysical Union Meeting (AGU), San Francisco CA, USA, 2016.
O'Brien SL, Whiteside MD, Sholto-Douglas D, Dohnalkova A, Durall DM, Gursoy D, Jones MD, Kovarik L, Lai B, Roehrig C, Sullivan S, Vogt S, Kemner KM. Identifying microbial habitats in soil using quantum dots and x-ray fluorescence microtomography. 101st Ecological Society of America Meeting, Fort Lauderdale, FL, 2016.
Chen Y, Wang K, Gursoy D, Soriano C, De Carlo F, Anastasio MA. Joint reconstruction of refractive and absorption properties in propagation-based x-ray phase-contrast tomography via nonlinear image reconstruction. SPIE Medical Imaging, Orlando FL, USA, 2016.
Gursoy D, De Andrade V, Kettimuthu R, De Carlo F. Compressed sensing and processing for rapid three-dimensional nanoimaging. International Conference on Synchrotron Radiation Instrumentation (SRI), New York, USA, 2015.
Bicer T, Gursoy D, Kettimuthu R, De Carlo F, Agrawal G, Foster I. Rapid tomographic image reconstruction via large-scale parallelization. Euro-Par, Vienna, Austria, 2015.
Duke DJ, Swantek AB, Sovis N, Tilocco FZ, Powell CF, Kastengren AL, Gursoy D, Bicer T. Time-resolved x-ray tomography of gasoline direct injection sprays. JSAE/SAE Powertrains, Fuels and Lubricants International Meeting, Kyoto, Japan, 2015.
De Andrade V, Wojcik M, Gursoy D, De Carlo F. Multi-scale and multi-modal analysis of metamorphic rocks coupling fluorescence and TXM techniques. American Geophysical Union (AGU) Meeting, San Francisco CA, USA, 2014.
Xiao X, Gursoy D, De Carlo F. Fast imaging and tomography applications at Advanced Photon Source. SPIE Optics+Photonics, San Diego, US, 2014.
Gursoy D, Xiao X, De Carlo F. TomoPy: A framework for the analysis of synchrotron tomographic data. SPIE Optics+Photonics, San Diego, US, 2014.
Gursoy D, De Carlo F, Xiao X. Multi-resolution tomography using an accurate forward model. SPIE Optics+Photonics, San Diego, US, 2014.
De Andrade V, Wojcik M, Gursoy D, Deriy A, De Carlo F. The TXM of APS is back. International Conference on X-ray Microscopy, Melbourne, Australia, 2014.
Maimaitijiang Y, Borsic A, Gursoy D, Adler A. Clinical imaging with electrical impedance tomography using L1 norms. International Conference on Electrical Bioimpedance (ICEBI), Heilbad Heiligenstadt, Germany, 2013.
Scharfetter H, Gursoy D. Feasibility of magnetic induction spectroscopy for skin characterization, International Conference on Electrical Bioimpedance (ICEBI), Heilbad Heiligenstadt, Germany, 2013.
Gursoy D, Scharfetter H. Incorrect sensor positioning artifacts in magnetic induction tomography. Progress in Electromagnetics Research Symposium (PIERS), Kuala Lumpur, Malaysia, 2012.
Maimaitijiang Y, Roula A, Gursoy D, Adler A. A software based framework for estimating patient displacement in magnetic induction tomography. Progress in Electromagnetics Research Symposium (PIERS), Kuala Lumpur, Malaysia, 2012.
Aydin S, Gursoy D, Sayar GH, Tan O. Alterations on EEG complexity in schizophrenia. National Biomedical Engineering Meeting (BIYOMUT), Istanbul, Turkey, 2012.
Aydin S, Sadik K, Gursoy D. Cordance calculations in schizophrenia. Medical Technologies National Conference (TIPTEKNO), Antalya, Turkey, 2012.
Maimaitijiang Y, Gursoy D, Adler A. Electrode positions and current patterns for 3D EIT. International Conference on Biomedical Applications of Electrical Impedance Tomography, Bath, UK, 2011.
Gursoy D, Maimaitijiang Y, Scharfetter H. Augmenting information content through multimodal impedance imaging. International Conference on Biomedical Applications of Electrical Impedance Tomography, Bath, UK, 2011.
Engleder S, Gursoy D, Scharfetter H, Steinbach O. A comparison of mathematical models for the forward problem of magnetic induction tomography. IGTE Symposium, Graz, Austria, 2010.
Gursoy D, Scharfetter H. Errors due to modeling mismatch between the simulated and experimental coil setup in magnetic induction tomography. Annual Meeting of German Association of Biomedical Engineering (DGBMT), Rostock, Germany, 2010.
Scharfetter H, Issa S, Gursoy D. Tracking of object movements for artefact suppression in Magnetic Induction Tomography. International Conference on Electrical Bioimpedance, Gainesville FL, USA, 2010.
Gursoy D, Scharfetter H. A non-contact method for imaging the posterior chest using magnetic induction principles to monitor pulmonary oedema. International Conference on Electrical Bioimpedance, Gainesville FL, USA, 2010.
Gursoy D, Scharfetter H. A marker belt design to eliminate the motion artifacts in magnetic induction tomography. National Biomedical Engineering Meeting, Antalya, Turkey, 2010.
Scharfetter H, Gursoy D. The effect of receiver coil orientation on the system performance of magnetic induction tomography. World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, 2009.
Gursoy D, Scharfetter H. Feasibility of lung imaging using magnetic induction tomography. World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, 2009.
Gursoy D, Scharfetter H. The effect of anisotropic tissues on the reconstructed images of magnetic induction tomography. International Conference on Biomedical Applications of Electrical Impedance Tomography, Manchester, UK, 2009.
Scharfetter H, Issa S, Gursoy D. Image reconstruction in magnetic induction tomography without using a phase reference channel. International Conference on Biomedical Applications of Electrical Impedance Tomography, Manchester, UK, 2009.
Gursoy D. A sensor optimization algorithm to increase the stability of the magnetic induction tomography inversion. Conference on Applied Inverse Problems, Vienna, Austria, 2009.
Gursoy D, Scharfetter H. Resolution and stability analysis of 16 channel magnetic induction tomography. National Biomedical Engineering Meeting, Izmir, Turkey, 2009.
Gursoy D, Scharfetter H. Reconstruction artefacts in magnetic induction tomography due to patient's movement during data acquisition. International Conference on Biomedical Applications of Electrical Impedance Tomography, Dartmouth NH, USA, 2008.

Posters

Yang X, Gursoy D, Phatak C, De Andade V, Gulsoy EB, De Carlo F. Learning from scanning transmission electron microscopy to enhance transmission x-ray microscopy. Microscopy and Microanalysis (M&M), Colombus OH, USA, 2016.
Yang X, Gursoy D, Phatak C, De Carlo F. Multimodal imaging for lithium-ion battery particles. Lorentz Center Workshop, Leiden, Netherlands, 2016.
Silverman R, Giarra M, Gursoy D, Socha JJ. Using TomoPy to reconstruct synchrotron micro-CT data. The Society for Integrative and Comparative Biology (SICB), West Palm Beach FL, USA, 2015.
Gleber SC, Gursoy D, Hong YP, Fahrni C, Jacobsen C, Vogt S. Optimizing data analysis for hard x-Rry fluorescence tomography. International Conference on X-ray Microscopy, Melbourne, Australia, 2014.
Gursoy D, De Carlo F, Xiao X, Schwarz N, Jacobsen C. TomoPy: A framework for the analysis of synchrotron tomographic data. Lorentz Center Workshop, Leiden, Netherlands, 2014.
Gursoy D, Das M. Single-step phase contrast x-ray imaging using photon counting detectors. SPIE Medical Imaging, Orlando FL, USA, 2013.
Gursoy D, Scharfetter H. Hemorrhagic stroke imaging using multi-frequency magnetic induction tomography. Imaging with Modulated/Incomplete Data Workshop, Graz, Austria, 2010.
Gursoy D, Scharfetter H. Feasibility of head imaging using multi-frequency magnetic induction tomography. National Biomedical Engineering Meeting, Izmir, Turkey, 2009.