Credits

We kindly request that you cite the following article(s):

Cite [A1] if you use TomoPy.


Cite [A2] if you use ASTRA (or the TomoPy ASTRA wrapper).


Cite [A3] if you use vector reconstructions.


Cite [A4] if you use UFO (or the TomoPY UFO wrapper).


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

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.

A4

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.

References

B1

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.

B2

Kak AC and Slaney M. Principles of computerized tomographic imaging. Volume 33. SIAM, 1988.

B3

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.

B4

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.

B5

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.

B6

Phatak C and Gürsoy D. Iterative reconstruction of magnetic induction using lorentz transmission electron tomography. Ultramicroscopy, 150:54–64, 2015.

B7

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: https://doi.org/10.1088/1361-6501/aa9c19.

B8

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.

B9

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.

B10

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.

B11

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.

B12

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.

B13

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.

B14

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.

B15

Manuel GS, Thurman ST, and Fienup JR. Efficient subpixel image registration algorithms. Optics Letters, 33(2):156–158, 2008.

B16

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.

B17

Hudson HM and Larkin RS. Accelerated image reconstruction using ordered subsets of projection data. Medical Imaging, IEEE Transactions on, 13(4):601–609, 1994.

B18

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.

B19

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.

B20

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.

B21

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.

B22

Rivers ML. Tomorecon: high-speed tomography reconstruction on workstations using multi-threading. In Proc. SPIE, volume 8506, 85060U–85060U–13. 2012.

B23

Vo N, and Atwood RC, and Drakopoulos M. Superior techniques for eliminating ring artifacts in x-ray micro-tomography. Optics Express, 26(22):28396–28412, 2018.

B24

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.

B25

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.

B26

Nghia T. Vo, Robert C. Atwood, and Michael Drakopoulos. Radial lens distortion correction with sub-pixel accuracy for x-ray micro-tomography. Optics Express, 23(25):32859–32868, 2015. doi:10.1364/OE.23.032859.

B27

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.

B28

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.