zref.bib

@article{Bergamaschi:16,
author = {Bergamaschi A and Medjoubi K and Messaoudi C and Marco S and Somogyi A},
title = {MMX-I: data-processing software for multimodal x-ray imaging and tomography},
journal = {Journal od Synchrotron Radiation},
year = {2016},
volume = {23},
pages = {783--794}
}

@inproceedings{Bhimji:16,
author = {Bhimji W and Bard D and Roumanus M and Paul D and Ovsyannikov A and Friesen B and Bryson M and Correa and Lockwood GK and Tsulaia V and Byna S and Farrell S and G\"{u}rsoy D and Daley C and Beckner V and Van Straalen B and Wright NJ and Antypas K and Prabhat M},
title = {Accelerating science with the NERSC burts buffer early user program},
booktitle = {Cray User Group Conference},
year = {2016}
}

@article{Brun:15,
author = {Brun F and Pacile S and Accardo A and Kourousias G and Dreossi D and Mancini L and Tromba G and Pugliese R},
journal = {Fundamenta Informaticae},
title = {Enhanced and flexible software tools for x-ray computed tomography at the Italian synchrotron radiation facility Elettra},
year = {2015},
volume = {141},
number = {2-3},
pages = {233--243}
}

@inproceedings{Bicer:15,
author = {Bi\c{c}er T and G\"{u}rsoy D and Kettimuthu R and De Carlo F and Agrawal G and Foster IT},
title = {Rapid tomographic image reconstruction via large-scale parallelization},
booktitle = {Lecture Notes in Computer Science},
year = {2015},
volume = {9233},
pages = {289--302}
}

@article{Chang:04,
author = {Chang J-H and Anderson JMM and Votaw JT},
journal = {Medical Imaging, IEEE Transactions on},
title = {Regularized image reconstruction algorithms for positron emission tomography},
year = {2004},
volume = {23},
number = {9},
pages = {1165--1175}
}

@article{DeCarlo:14a,
author = {De Carlo F and Gursoy D and Marone F and Rivers M and Parkinson YD and Khan F and Schwarz N and Vine DJ and Vogt S and Gleber SC and Narayanan S and Newville M and Lanzirotti T and Sun Y and Hong YP and Jacobsen C},
title = {Scientific Data Exchange: a schema for HDF5-based storage of raw and analyzed data},
journal = {Journal of Synchrotron Radiation},
year = {2014},
volume = {21},
number = {6},
pages = {1224--1230}
}

@article{DeCarlo:17,
  author={Francesco De Carlo and Doga Gursoy and Daniel Jackson Ching and Kees Joost Batenburg and Wolfgang Ludwig and Lucia Mancini and Federica Marone and Rajmund Mokso and Daniel M. Pelt and Jan Sijbers and Mark Rivers},
  title={TomoBank: A tomographic data repository for computational X-ray science},
  journal={Measurement Science and Technology},
  url={https://doi.org/10.1088/1361-6501/aa9c19},
  year={2017}
}

@article{Dempster:77,
author = {Dempster AP and Laird NM and Rubin DB},
title = {Maximum likelihood from incomplete data via the EM algorithm},
journal = {journal of the Royal Statistical Society, Series B},
year = {1977},
volume = {39},
number = {1},
pages = {1--38}
}

@article{DeJonge:14,
author = {De Jonge MD and Ryan CG and Jacobsen C},
title = {X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens},
journal = {Journal of Synchrotron Radiation},
year = {2014},
volume = {21},
number = {5},
pages = {1031--1047}
}

@article{Donath:06,
author = {Tilman D and Felix B and Andreas S},
title = {Automated determination of the center of rotation in tomography data},
journal = {Journal of the Optical Society of America A},
year = {2006},
volume = {23},
number = {5},
pages = {1048--1057}
}

@inproceedings{Dowd:99,
author = {Dowd BA and Campbell GH and Marr RB and Nagarkar VV and Tipnis SV and Axe L and Siddons DP},
title = {Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source},
booktitle = {Proc. SPIE},
year = {1999},
volume = {3772},
pages = {224--236}
}

@article{Guizar:08,
author = {Manuel GS and Thurman ST and Fienup JR},
title = {Efficient subpixel image registration algorithms},
journal = {Optics Letters},
year = {2008},
volume = {33},
number = {2},
pages = {156--158}
}

@article{Gursoy:17,
author = {Gursoy D and Hong YP and He K and Hujsak K and Yoo S and Chen S and Li Y and Ge M and Miller LM and Chu YS and De Andrade V and He K and Cossairt O and Katsaggelos AK and Jacobsen C},
title = {Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection},
journal = {Scientific Reports},
volume = {7},
number = {11818},
year = {2017}
}

@article{Hudson:94,
author = {Hudson HM and Larkin RS},
journal = {Medical Imaging, IEEE Transactions on},
title = {Accelerated image reconstruction using ordered subsets of projection data},
year = {1994},
volume = {13},
number = {4},
pages = {601--609}
}

@book{Kak:98,
  title = {Principles of computerized tomographic imaging},
  author = {Kak AC and Slaney M},
  year = {1988},
  volume = {33},
  publisher = {SIAM}
}

@article{Mertens:15,
author = {Mertens JCE and Chawla JJWN},
title = {A method for zinger artifact reduction in high-energy x-ray computed tomography},
journal = {Nuclear Instruments and Methods in Physics Research Section A},
year = {2015},
volume = {800},
pages = {82--92}
}

@article{Miqueles:14,
author = {Miqueles EX and Rinkel J and O'Dowd F and Berm{\'{u}}dez JSV},
title = {Generalized Titarenko's algorithm for ring artefacts reduction},
journal = {Journal of Synchrotron Radiation},
year = {2014},
volume = {21},
number = {6},
pages = {1333--1346}
}

@article{Munch:09,
author = {M\"{u}nch B and Trtik P and Marone F and Stampanoni M},
title = {Stripe and ring artifact removal with combined wavelet--Fourier filtering},
journal = {Optics Express},
year = {2009},
volume = {17},
number = {10},
pages = {8567--8591}
}

@article {Paganin:02,
author = {Paganin D and Mayo SC and Gureyev TE and Miller PR and Wilkins SW},
title = {Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object},
journal = {Journal of Microscopy},
year = {2002},
volume = {206},
number = {1},
pages = {33--40}
}

@inproceedings{Rivers:06,
author = {Rivers ML},
title = {tomoRecon: High-speed tomography reconstruction on workstations using multi-threading},
booktitle = {Proc. SPIE},
year = {2012},
volume = {8506},
pages = {85060U-85060U-13}
}

@article{Toby:15,
author = {Toby HB and G\"{u}rsoy D and De Carlo F and Schwarz N and Sharma H and Jacobsen CJ},
title = {Practices and Standards for Data and Processing at the {APS}},
journal = {Synchrotron Radiation News},
year = {2015},
volume = {28},
number = {2},
pages = {15--21}
}

@inproceedings{Vogelgesang:16,
author = {Vogelgesang M and Rota L and Ardila Perez Luis E and Caselle M and Chilingaryan S and Kopmann A},
title = {High-throughput data acquisition and processing for real-time x-ray imaging},
booktitle = {Proc. SPIE},
volume = {9967},
pages = {996715-996715-9},
year = {2016},
doi = {10.1117/12.2237611}
}

@article{Vo:14,
author = {Vo N and Drakopoulos M and Atwood RC and Reinhard C},
title = {Reliable method for calculating the center of rotation in parallel-beam tomography},
journal = {Optics Express},
year = {2014},
volume = {22},
number = {16},
pages = {19078--19086}
}

@article{Xu:16,
author = {Xu W and Feng D},
title = {Studying Performance of A Penalized Maximum Likelihood Method for PET Reconstruction on Nvidia GPU and Intel Xeon Phi Coprocessor},
journal = {Proc. 4th Intl Conf. Image Formation in X-ray Computed Tomography},
year = {2016},
pages = {191--194}
}

@article{Chambolle:11,
title={A first-order primal-dual algorithm for convex problems with applications to imaging},
author={Chambolle, Antonin and Pock, Thomas},
journal={Journal of mathematical imaging and vision},
volume={40},
number={1},
pages={120--145},
year={2011},
publisher={Springer}
}

@article{Vo:18,
author = {Vo N and and Atwood RC and Drakopoulos M},
title = {Superior techniques for eliminating ring artifacts in X-ray micro-tomography},
journal = {Optics Express},
year = {2018},
volume = {26},
number = {22},
pages = {28396--28412}
}

@article{Vo:15,
author = {Nghia T. Vo and Robert C. Atwood and Michael Drakopoulos},
title = {Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography},
journal = {Optics Express},
year = {2015},
volume = {23},
number = {25},
pages = {32859--32868},
doi = {10.1364/OE.23.032859},
}

@article{Phatak:15,
author = {Phatak C and G\"{u}rsoy D},
title = {Iterative reconstruction of magnetic induction using Lorentz transmission electron tomography},
journal = {Ultramicroscopy},
year = {2015},
volume = {150},
pages = {54--64}
}