8. Credits

8.1. Citations

If Algotom is useful for your project, citing the following article [C1] is very much appreciated.

C1

Nghia T. Vo, Robert C. Atwood, Michael Drakopoulos, and Thomas Connolley. Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography. Opt. Express, 29(12):17849–17874, Jun 2021. URL: http://www.opticsexpress.org/abstract.cfm?URI=oe-29-12-17849, doi:10.1364/OE.418448.

Algorithms, methods, or techniques implemented in a scientific software package are crucial for its success. This is the same for Algotom. Acknowledging algorithms you use through Algotom is also very much appreciated.

8.2. References

R1

V. Argyriou and T. Vlachos. Estimation of sub-pixel motion using gradient cross-correlation. Electronics Letters, 39:980–982, June 2003. URL: https://digital-library.theiet.org/content/journals/10.1049/el_20030666, doi:10.1049/el:20030666.

R2

Sebastien Berujon and Eric Ziegler. X-ray multimodal tomography using speckle-vector tracking. Phys. Rev. Applied, 5:044014, 2016. doi:10.1103/PhysRevApplied.5.044014.

R3

Pan Bing, Xie Hui-min, Xu Bo-qin, and Dai Fu-long. Performance of sub-pixel registration algorithms in digital image correlation. Measurement Science and Technology, 17(6):1615–1621, may 2006. URL: https://doi.org/10.1088/0957-0233/17/6/045, doi:10.1088/0957-0233/17/6/045.

R4

RN Bracewell. Strip integration in radio astronomy. Australian Journal of Physics, 9(2):198 – 217, 1956. URL: https://www.publish.csiro.au/ph/PH560198, doi:10.1071/PH560198.

R5

Tilman Donath, Felix Beckmann, and Andreas Schreyer. Automated determination of the center of rotation in tomography data. J. Opt. Soc. Am. A, 23(5):1048–1057, May 2006. URL: https://opg.optica.org/josaa/abstract.cfm?URI=josaa-23-5-1048, doi:10.1364/JOSAA.23.001048.

R6

G. H. Fisher and B. T. Welsch. Flct: a fast, efficient method for performing local correlation tracking. 2007. URL: https://arxiv.org/abs/0712.4289, doi:10.48550/ARXIV.0712.4289.

R7

R.T. Frankot and R. Chellappa. A method for enforcing integrability in shape from shading algorithms. IEEE Transactions on Pattern Analysis and Machine Intelligence, 10(4):439–451, 1988. doi:10.1109/34.3909.

R8

Dennis Ghiglia and Mark Pritt. Two-dimensional Phase Unwrapping: Theory, Algorithms, and Software. Wiley, New York, 1998.

R9

Doǧa Gürsoy, Francesco De Carlo, Xianghui Xiao, and Chris Jacobsen. TomoPy: a framework for the analysis of synchrotron tomographic data. Journal of Synchrotron Radiation, 21(5):1188–1193, 2014. doi:10.1107/S1600577514013939.

R10

Beat Münch, Pavel Trtik, Federica Marone, and Marco Stampanoni. Stripe and ring artifact removal with combined wavelet — fourier filtering. Opt. Express, 17(10):8567–8591, May 2009. URL: http://www.opticsexpress.org/abstract.cfm?URI=oe-17-10-8567, doi:10.1364/OE.17.008567.

R11

Juan Martinez-Carranza, Konstantinos Falaggis, and Tomasz Kozacki. Fast and accurate phase-unwrapping algorithm based on the transport of intensity equation. Appl. Opt., 56(25):7079–7088, 2017. doi:10.1364/AO.56.007079.

R12

M.D. Pritt and J.S. Shipman. Least-squares two-dimensional phase unwrapping using fft's. IEEE Transactions on Geoscience and Remote Sensing, 32(3):706–708, 1994. doi:10.1109/36.297989.

R13

G. N. Ramachandran and A. V. Lakshminarayanan. Three-dimensional reconstruction from radiographs and electron micrographs: application of convolutions instead of fourier transforms. Proceedings of the National Academy of Sciences, 68(9):2236–2240, 1971. URL: https://www.pnas.org/content/68/9/2236, doi:10.1073/pnas.68.9.2236.

R14

Carsten Raven. Numerical removal of ring artifacts in microtomography. Review of Scientific Instruments, 69(8):2978–2980, 1998. URL: https://aip.scitation.org/doi/10.1063/1.1149043, doi:10.1063/1.1149043.

R15

T. Simchony, R. Chellappa, and M. Shao. Direct analytical methods for solving poisson equations in computer vision problems. IEEE Transactions on Pattern Analysis and Machine Intelligence, 12(5):435–446, 1990. doi:10.1109/34.55103.

R16

Sofya Titarenko, Philip J. Withers, and Anatoly Yagola. An analytical formula for ring artefact suppression in x-ray tomography. Applied Mathematics Letters, 23(12):1489–1495, 2010. URL: https://www.sciencedirect.com/science/article/pii/S089396591000282X, doi:https://doi.org/10.1016/j.aml.2010.08.022.

R17

Wim van Aarle, Willem Jan Palenstijn, Jeroen Cant, Eline Janssens, Folkert Bleichrodt, Andrei Dabravolski, Jan De Beenhouwer, K. Joost Batenburg, and Jan Sijbers. Fast and flexible x-ray tomography using the astra toolbox. Opt. Express, 24(22):25129–25147, 2016. doi:10.1364/OE.24.025129.

R18

Nghia T. Vo, Robert C. Atwood, and Michael Drakopoulos. Radial lens distortion correction with sub-pixel accuracy for x-ray micro-tomography. Opt. Express, 23(25):32859–32868, Dec 2015. URL: http://www.opticsexpress.org/abstract.cfm?URI=oe-23-25-32859, doi:10.1364/OE.23.032859.

R19

Nghia T. Vo, Robert C. Atwood, and Michael Drakopoulos. Superior techniques for eliminating ring artifacts in x-ray micro-tomography. Opt. Express, 26(22):28396–28412, Oct 2018. URL: http://www.opticsexpress.org/abstract.cfm?URI=oe-26-22-28396, doi:10.1364/OE.26.028396.

R20

Nghia T. Vo, Robert C. Atwood, and Michael Drakopoulos. Preprocessing techniques for removing artifacts in synchrotron-based tomographic images. In Bert Müller and Ge Wang, editors, Developments in X-Ray Tomography XII, volume 11113, 309 – 328. International Society for Optics and Photonics, SPIE, 2019. doi:10.1117/12.2530324.

R21

Nghia T. Vo, Michael Drakopoulos, Robert C. Atwood, and Christina Reinhard. Reliable method for calculating the center of rotation in parallel-beam tomography. Opt. Express, 22(16):19078–19086, Aug 2014. URL: http://www.opticsexpress.org/abstract.cfm?URI=oe-22-16-19078, doi:10.1364/OE.22.019078.

R22

Nghia T. Vo, Hongchang Wang, Lingfei Hu, Tunhe Zhou, Marie-Christine Zdora, Hans Deyhle, Robert C. Atwood, and Michael Drakopoulos. Practical implementations of speckle-based phase-retrieval methods in python and gpu for tomography. In Developments in X-Ray Tomography XIV, volume 12242, 122420E. International Society for Optics and Photonics, SPIE, 2022. doi:10.1117/12.2636834.

R23

H. Wang, S. Berujon, J. Herzen, R. Atwood, D. Laundy, A. Hipp, and K. Sawhney. X-ray phase contrast tomography by tracking near field speckle. Scientific Repport, 5:8762, 2015. doi:10.1038/srep08762.

R24

Hongchang Wang and Kawal Sawhney. Hard x-ray omnidirectional differential phase and dark-field imaging. Proceedings of the National Academy of Sciences, 2021. doi:10.1073/pnas.2022319118.

R25

Marie-Christine Zdora, Pierre Thibault, Tunhe Zhou, Frieder J. Koch, Jenny Romell, Simone Sala, Arndt Last, Christoph Rau, and Irene Zanette. X-ray phase-contrast imaging and metrology through unified modulated pattern analysis. Phys. Rev. Lett., 118:203903, 2017. doi:10.1103/PhysRevLett.118.203903.