References

[1]	Stefano Agostinelli and Gabriella Paoli. An object oriented fully 3d tomography visual toolkit. Computer Methods and Programs in Biomedicine, 65(1):61 – 69, 2001. URL: http://www.sciencedirect.com/science/article/pii/S0169260700001012, doi:http://dx.doi.org/10.1016/S0169-2607(00)00101-2.

[2]	R Bayford, Y Hanquan, K Boone, and D S Holder. Experimental validation of a novel reconstruction algorithm for electrical impedance tomography based on backprojection of lagrange multipliers. Physiological Measurement, 16(3A):A237, 1995. URL: http://stacks.iop.org/0967-3334/16/i=3A/a=022.

[3]

Antoine Bergamaschi, Kadda Medjoubi, Cédric Messaoudi, Sergio Marco, and Andrea Somogyi. \it MMX-I: data-processing software for multimodal X-ray imaging and tomography. Journal of Synchrotron Radiation, 23(3):783–794, May 2016. URL: http://dx.doi.org/10.1107/S1600577516003052, doi:10.1107/S1600577516003052.

[4]	Xia C, Zhu K, Cao Y, Sun H, Kou B, and Wang Y. X-ray tomography study of the random packing structure of ellipsoids. Soft Matter, 10(7):990–996, 2014.

[5]

Lotfi Chaâri, Jean-Christophe Pesquet, Amel Benazza-Benyahia, and Philippe Ciuciu. A wavelet-based regularized reconstruction algorithm for \SENSE\ parallel \MRI\ with applications to neuroimaging. Medical Image Analysis, 15(2):185 – 201, 2011. URL: http://www.sciencedirect.com/science/article/pii/S1361841510001052, doi:http://dx.doi.org/10.1016/j.media.2010.08.001.

[6]	X. L. Dean-Ben, A. Buehler, V. Ntziachristos, and D. Razansky. Accurate model-based reconstruction algorithm for three-dimensional optoacoustic tomography. IEEE Transactions on Medical Imaging, 31(10):1922–1928, Oct 2012. doi:10.1109/TMI.2012.2208471.

[7]

James T. Dobbins. Effects of undersampling on the proper interpretation of modulation transfer function, noise power spectra, and noise equivalent quanta of digital imaging systems. Medical Physics, 22(2):171–181, 1995. URL: http://scitation.aip.org/content/aapm/journal/medphys/22/2/10.1118/1.597600, doi:http://dx.doi.org/10.1118/1.597600.

[8]

Saul N. Friedman, George S. K. Fung, Jeffrey H. Siewerdsen, and Benjamin M. W. Tsui. A simple approach to measure computed tomography (ct) modulation transfer function (mtf) and noise-power spectrum (nps) using the american college of radiology (acr) accreditation phantom. Medical Physics, 40(5):, 2013. URL: http://scitation.aip.org/content/aapm/journal/medphys/40/5/10.1118/1.4800795, doi:http://dx.doi.org/10.1118/1.4800795.

[9]

B. Kelly Han, Katharine L.R. Grant, Ross Garberich, Martin Sedlmair, Jana Lindberg, and John R. Lesser. Assessment of an iterative reconstruction algorithm (safire) on image quality in pediatric cardiac \CT\ datasets. Journal of Cardiovascular Computed Tomography, 6(3):200 – 204, 2012. URL: http://www.sciencedirect.com/science/article/pii/S1934592512001402, doi:http://dx.doi.org/10.1016/j.jcct.2012.04.008.

[10]	Beverley F Holman, Vesna Cuplov, Brian F Hutton, Ashley M Groves, and Kris Thielemans. The effect of respiratory induced density variations on non-tof pet quantitation in the lung. Physics in Medicine and Biology, 61(8):3148, 2016. URL: http://stacks.iop.org/0031-9155/61/i=8/a=3148.

[11]

J. Hsieh, E. Chao, J. Thibault, B. Grekowicz, A. Horst, S. McOlash, and T. J. Myers. A novel reconstruction algorithm to extend the ct scan field-of-view. Medical Physics, 31(9):2385–2391, 2004. URL: http://scitation.aip.org/content/aapm/journal/medphys/31/9/10.1118/1.1776673, doi:http://dx.doi.org/10.1118/1.1776673.

[12]

Jiang Hsieh, John Londt, Melissa Vass, Jay Li, Xiangyang Tang, and Darin Okerlund. Step-and-shoot data acquisition and reconstruction for cardiac x-ray computed tomography. Medical Physics, 33(11):4236–4248, 2006. URL: http://scitation.aip.org/content/aapm/journal/medphys/33/11/10.1118/1.2361078, doi:http://dx.doi.org/10.1118/1.2361078.

[13]	J. D. Hunter. Matplotlib: a 2d graphics environment. Computing In Science & Engineering, 9(3):90–95, 2007.

[14]

S Jan, G Santin, D Strul, S Staelens, K Assié, D Autret, S Avner, R Barbier, M Bardiès, P M Bloomfield, D Brasse, V Breton, P Bruyndonckx, I Buvat, A F Chatziioannou, Y Choi, Y H Chung, C Comtat, D Donnarieix, L Ferrer, S J Glick, C J Groiselle, D Guez, P-F Honore, S Kerhoas-Cavata, A S Kirov, V Kohli, M Koole, M Krieguer, D J van der Laan, F Lamare, G Largeron, C Lartizien, D Lazaro, M C Maas, L Maigne, F Mayet, F Melot, C Merheb, E Pennacchio, J Perez, U Pietrzyk, F R Rannou, M Rey, D R Schaart, C R Schmidtlein, L Simon, T Y Song, J-M Vieira, D Visvikis, R Van de Walle, E Wieërs, and C Morel. Gate: a simulation toolkit for pet and spect. Physics in Medicine and Biology, 49(19):4543, 2004. URL: http://stacks.iop.org/0031-9155/49/i=19/a=007.

[15]	K. P. Kostli, D. Frauchiger, J. J. Niederhauser, G. Paltauf, H. P. Weber, and M. Frenz. Optoacoustic imaging using a three-dimensional reconstruction algorithm. IEEE Journal of Selected Topics in Quantum Electronics, 7(6):918–923, Nov 2001. doi:10.1109/2944.983294.

[16]

Arjun S. Kumar, Pratiti Mandal, Yongjie Zhang, and Shawn Litster. Image segmentation of nanoscale zernike phase contrast x-ray computed tomography images. Journal of Applied Physics, 117(18):, 2015. URL: http://scitation.aip.org/content/aip/journal/jap/117/18/10.1063/1.4919835, doi:http://dx.doi.org/10.1063/1.4919835.

[17]

Thomas Köhler, Bernhard Brendel, and Ewald Roessl. Iterative reconstruction for differential phase contrast imaging using spherically symmetric basis functions. Medical Physics, 38(8):4542–4545, 2011. URL: http://scitation.aip.org/content/aapm/journal/medphys/38/8/10.1118/1.3608906, doi:http://dx.doi.org/10.1118/1.3608906.

[18]

Yijin Liu, Florian Meirer, Phillip A. Williams, Junyue Wang, Joy C. Andrews, and Piero Pianetta. \it TXM-Wizard: a program for advanced data collection~and evaluation in full-field transmission X-ray microscopy. Journal of Synchrotron Radiation, 19(2):281–287, Mar 2012. URL: http://dx.doi.org/10.1107/S0909049511049144, doi:10.1107/S0909049511049144.

[19]	Stefano Marchesini, Hari Krishnan, David A. Shapiro, Talita Perciano, James A. Sethian, Benedikt J. Daurer, and Filipe R. N. C. Maia. SHARP: a distributed, GPU-based ptychographic solver. Report LBNL-1003977, 2016. doi:10.1107/S1600576716008074.

[20]	F. Marone and M. Stampanoni. Regridding reconstruction algorithm for real-time tomographic imaging. Journal of Synchrotron Radiation, 19(6):1029–1037, Nov 2012. URL: http://dx.doi.org/10.1107/S0909049512032864, doi:10.1107/S0909049512032864.

[21]	Willem Jan Palenstijn, K Joost Batenburg, and Jan Sijbers. The astra tomography toolbox. In 13th International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE, volume 2013. 2013.

[22]	Al-Raoush R and Willson CS. Extraction of physically realistic pore network properties from three-dimensional synchrotron x-ray microtomography images of unconsolidated porous media systems. Journal of Hydrology, 300(1):44–64, 2005.

[23]	Al-Raoush R, Thompson K, and Willson CS. Comparison of network generation techniques for unconsolidated porous media. Soil Science Society of America Journal, 67(6):1687–1700, 2003.

[24]	Ranadhir Roy, Alan B Thompson, Anuradha Godavarty, and Eva M Sevick-Muraca. Tomographic fluorescence imaging in tissue phantoms: a novel reconstruction algorithm and imaging geometry. IEEE transactions on medical imaging, 24(2):137–154, 2005.

[25]	H. R. Sheikh and A. C. Bovik. Image information and visual quality. IEEE Transactions on Image Processing, 15(2):430–444, Feb 2006. doi:10.1109/TIP.2005.859378.

[26]	A Sufian, AR Russell, AJ Whittle, and M Saadatfar. Pore shapes, volume distribution and orientations in monodisperse granular assemblies. Granular Matter, 17(6):727–742, 2015.

[27]	Kris Thielemans, Charalampos Tsoumpas, Sanida Mustafovic, Tobias Beisel, Pablo Aguiar, Nikolaos Dikaios, and Matthew W Jacobson. Stir: software for tomographic image reconstruction release 2. Physics in Medicine and Biology, 57(4):867, 2012. URL: http://stacks.iop.org/0031-9155/57/i=4/a=867.

[28]	Bradley E. Treeby and B. T. Cox. K-wave: matlab toolbox for the simulation and reconstruction of photoacoustic wave fields. Journal of Biomedical Optics, 15(2):021314–021314–12, 2010. URL: http://dx.doi.org/10.1117/1.3360308, arXiv:, doi:10.1117/1.3360308.

[29]

Matthias Vogelgesang, Tomas Farago, Thilo F. Morgeneyer, Lukas Helfen, Tomy dos Santos Rolo, Anton Myagotin, and Tilo Baumbach. Real-time image-content-based beamline control for smart 4D X-ray imaging. Journal of Synchrotron Radiation, 23(5):, Sep 2016. URL: http://dx.doi.org/10.1107/S1600577516010195, doi:10.1107/S1600577516010195.

[30]	Zhou Wang and Alan C Bovik. Modern image quality assessment. Synthesis Lectures on Image, Video, and Multimedia Processing, 2(1):1–156, 2006.

[31]	Zhou Wang, Eero P Simoncelli, and Alan C Bovik. Multiscale structural similarity for image quality assessment. In Signals, Systems and Computers, 2004. Conference Record of the Thirty-Seventh Asilomar Conference on, volume 2, 1398–1402. Ieee, 2003.

[32]	Jie Wu and Jiabi Chen. A phase retrieval algorithm for x-ray phase contrast imaging. Optik - International Journal for Light and Electron Optics, 124(9):864 – 866, 2013. URL: http://www.sciencedirect.com/science/article/pii/S0030402612001635, doi:http://dx.doi.org/10.1016/j.ijleo.2012.02.030.

[33]

Zhaozheng Yin, Takeo Kanade, and Mei Chen. Understanding the phase contrast optics to restore artifact-free microscopy images for segmentation. Medical Image Analysis, 16(5):1047 – 1062, 2012. URL: http://www.sciencedirect.com/science/article/pii/S1361841512000035, doi:http://dx.doi.org/10.1016/j.media.2011.12.006.

[34]	Daniele Zanaga, Folkert Bleichrodt, Thomas Altantzis, Naomi Winckelmans, Willem Jan Palenstijn, Jan Sijbers, Bart de Nijs, Marijn A van Huis, Ana Sánchez-Iglesias, Luis M Liz-Marzán, and others. Quantitative 3d analysis of huge nanoparticle assemblies. Nanoscale, 8(1):292–299, 2016.