We kindly request that you cite the following article(s) [A1] if you use TomoPy (and also cite [A2] if you use ASTRA or [A3] if you use UFO). For vector reconstructions please additionally cite [A4].

[A1]Gürsoy D, De Carlo F, Xiao X, and Jacobsen C. Tomopy: a framework for the analysis of synchrotron tomographic data. Journal of Synchrotron Radiation, 21(5):1188–1193, 2014.
[A2]Pelt D, Gürsoy D, Palenstijn WJ, Sijbers J, De Carlo F, and Batenburg KJ. Integration of tomopy and the astra toolbox for advanced processing and reconstruction of tomographic synchrotron data. Journal of Synchrotron Radiation, 23(3):842–849, 2016.
[A3]Vogelgesang M, Chilingaryan S, Rolo T dos Santos, and Kopmann A. Ufo: a scalable gpu-based image processing framework for on-line monitoring. In Proceedings of The 14th IEEE Conference on High Performance Computing and Communication & The 9th IEEE International Conference on Embedded Software and Systems (HPCC-ICESS), 824–829. 6 2012.
[A4]Hierro-Rodriguez A, Gürsoy D, Phatak C, Quiros C, Sorrentino A, Alvarez-Prado LM, Velez M, Martin JI, Alameda JM, Pereiro E, and Ferrer S. 3d reconstruction of magnetization from dichroic soft x-ray transmission tomography. Journal of Synchrotron Radiation, 2018.


[B1]Patterson BM, Cordes NL, Henderson K, Williams JJ, Stannard T, Singh SS, Ovejero AR, Xiao X, Robinson M, and Chawla N. In situ x-ray synchrotron tomographic imaging during the compression of hyper-elastic polymeric materials. Journal of Materials Science, 51(1):171–187, 2016.
[B2]Phatak C and Gürsoy D. Iterative reconstruction of magnetic induction using lorentz transmission electron tomography. Ultramicroscopy, 150:54–64, 2015.
[B3]Gürsoy D, Biçer T, Lanzirotti A, Newville MG, and De Carlo F. Hyperspectral image reconstruction for x-ray fluorescence tomography. Optics Express, 23(7):9014–9023, 2015.
[B4]Gürsoy D, Biçer T, Almer JD, Kettimuthu R, Stock SR, and De Carlo F. Maximum a posteriori estimation of crystallographic phases in x-ray diffraction tomography. Philosophical Transactions A, 2015.
[B5]Duke DJ, Swantek AB, Sovis N, Tilocco FZ, Powell CF, AL Kastengren, Gürsoy D, and Biçer T. Time-resolved x-ray tomography of gasoline direct injection sprays. SAE International Journal of Engines, 2015.
[B6]Kamke FA, McKinley PE, Ching DJ, Zauner M, and Xiao X. Micro x-ray computed tomography of adhesive bonds in wood. Wood and Fiber Science, 2016.
[B7]Birkbak ME, Leemreize H, Frohlich S, Stock SR, and Birkedal H. Diffraction scattering computed tomography: a window into the structures of complex nanomaterials. Nanoscale, 2015.
[B8]Miller SM, Xiao X, and Faber KT. Freeze-cast alumina pore networks: effects of freezing conditions and dispersion medium. Journal of the European Ceramic Society, 35(13):3595––3605, 2015.
[B9]Roncal WG, Dyer EL, Gürsoy D, Kording K, and Kasthuri N. From sample to knowledge: towards an integrated approach for neuroscience discovery. arXiv, 2016.


[C1]Bergamaschi A, Medjoubi K, Messaoudi C, Marco S, and Somogyi A. Mmx-i: data-processing software for multimodal x-ray imaging and tomography. Journal od Synchrotron Radiation, 23:783–794, 2016.
[C2]Kak AC and Slaney M. Principles of computerized tomographic imaging. Volume 33. SIAM, 1988.
[C3]Dempster AP, Laird NM, and Rubin DB. Maximum likelihood from incomplete data via the em algorithm. journal of the Royal Statistical Society, Series B, 39(1):1–38, 1977.
[C4]Münch B, Trtik P, Marone F, and Stampanoni M. Stripe and ring artifact removal with combined wavelet–fourier filtering. Optics Express, 17(10):8567–8591, 2009.
[C5]Dowd BA, Campbell GH, Marr RB, Nagarkar VV, Tipnis SV, Axe L, and Siddons DP. Developments in synchrotron x-ray computed microtomography at the national synchrotron light source. In Proc. SPIE, volume 3772, 224–236. 1999.
[C6]Francesco De Carlo, Doga Gursoy, Daniel Jackson Ching, Kees Joost Batenburg, Wolfgang Ludwig, Lucia Mancini, Federica Marone, Rajmund Mokso, Daniel M. Pelt, Jan Sijbers, and Mark Rivers. Tomobank: a tomographic data repository for computational x-ray science. Measurement Science and Technology, 2017. URL:
[C7]Antonin Chambolle and Thomas Pock. A first-order primal-dual algorithm for convex problems with applications to imaging. Journal of mathematical imaging and vision, 40(1):120–145, 2011.
[C8]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 AK, and Jacobsen C. Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection. Scientific Reports, 2017.
[C9]Paganin D, Mayo SC, Gureyev TE, Miller PR, and Wilkins SW. Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object. Journal of Microscopy, 206(1):33–40, 2002.
[C10]Tilman D, Felix B, and Andreas S. Automated determination of the center of rotation in tomography data. Journal of the Optical Society of America A, 23(5):1048–1057, 2006.
[C11]Miqueles EX, Rinkel J, O’Dowd F, and Bermúdez JSV. Generalized titarenko’s algorithm for ring artefacts reduction. Journal of Synchrotron Radiation, 21(6):1333–1346, 2014.
[C12]Brun F, Pacile S, Accardo A, Kourousias G, Dreossi D, Mancini L, Tromba G, and Pugliese R. Enhanced and flexible software tools for x-ray computed tomography at the italian synchrotron radiation facility elettra. Fundamenta Informaticae, 141(2-3):233–243, 2015.
[C13]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, and Jacobsen C. Scientific data exchange: a schema for hdf5-based storage of raw and analyzed data. Journal of Synchrotron Radiation, 21(6):1224–1230, 2014.
[C14]Manuel GS, Thurman ST, and Fienup JR. Efficient subpixel image registration algorithms. Optics Letters, 33(2):156–158, 2008.
[C15]Toby HB, Gürsoy D, De Carlo F, Schwarz N, Sharma H, and Jacobsen CJ. Practices and standards for data and processing at the APS. Synchrotron Radiation News, 28(2):15–21, 2015.
[C16]Hudson HM and Larkin RS. Accelerated image reconstruction using ordered subsets of projection data. Medical Imaging, IEEE Transactions on, 13(4):601–609, 1994.
[C17]Chang J-H, Anderson JMM, and Votaw JT. Regularized image reconstruction algorithms for positron emission tomography. Medical Imaging, IEEE Transactions on, 23(9):1165–1175, 2004.
[C18]Mertens JCE and Chawla JJWN. A method for zinger artifact reduction in high-energy x-ray computed tomography. Nuclear Instruments and Methods in Physics Research Section A, 800:82–92, 2015.
[C19]Vogelgesang M, Rota L, Ardila Perez Luis E, Caselle M, Chilingaryan S, and Kopmann A. High-throughput data acquisition and processing for real-time x-ray imaging. In Proc. SPIE, volume 9967, 996715–996715–9. 2016. doi:10.1117/12.2237611.
[C20]De Jonge MD, Ryan CG, and Jacobsen C. X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens. Journal of Synchrotron Radiation, 21(5):1031–1047, 2014.
[C21]Rivers ML. Tomorecon: high-speed tomography reconstruction on workstations using multi-threading. In Proc. SPIE, volume 8506, 85060U–85060U–13. 2012.
[C22]Vo N, Drakopoulos M, Atwood RC, and Reinhard C. Reliable method for calculating the center of rotation in parallel-beam tomography. Optics Express, 22(16):19078–19086, 2014.
[C23]Biçer T, Gürsoy D, Kettimuthu R, De Carlo F, Agrawal G, and Foster IT. Rapid tomographic image reconstruction via large-scale parallelization. In Lecture Notes in Computer Science, volume 9233, 289–302. 2015.
[C24]Bhimji W, Bard D, Roumanus M, Paul D, Ovsyannikov A, Friesen B, Bryson M, Correa, Lockwood GK, Tsulaia V, Byna S, Farrell S, Gürsoy D, Daley C, Beckner V, Van Straalen B, Wright NJ, Antypas K, and Prabhat M. Accelerating science with the nersc burts buffer early user program. In Cray User Group Conference. 2016.
[C25]Xu W and Feng D. Studying performance of a penalized maximum likelihood method for pet reconstruction on nvidia gpu and intel xeon phi coprocessor. Proc. 4th Intl Conf. Image Formation in X-ray Computed Tomography, pages 191–194, 2016.