Abstract

Ptychographic X-ray computed tomography is a phase-contrast imaging technique capable of retrieving three-dimensional maps of the index of refraction of the imaged volumes with nanometric resolution. Despite its unmatched reach, its application remains prerogative of a limited number of laboratories at synchrotron sources. We present a detailed description of an experimental procedure and a data analysis pipeline which can be both exploited for ptychographic X-ray computed tomography experiments at any high-brilliance X-ray source. These have been validated at the I13-1 Coherence Branchline within the first experiment of its kind to be successfully carried out on a biological sample at Diamond Light Source.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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2018 (5)

F. Pfeiffer, “X-ray ptychography,” Nat. Photonics 12, 9–17 (2018).
[Crossref]

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. Maia, A. L. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9, 1–7 (2018).

M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
[Crossref]

D. Batey, S. Cipiccia, X. Shi, S. Williams, K. Wanelik, A. Wilson, S. Pérez-Tamarit, P. Cimavilla, M. A. Ródriguez-Pérez, and C. Rau, “Coherence Branch at I13, DLS: The Multiscale, Multimodal, Ptycho-tomographic End Station,” Microsc. Microanal. 24, 42–43 (2018).
[Crossref]

S. Sala, V. S. C. Kuppili, S. Chalkidis, D. J. Batey, X. Shi, C. Rau, and P. Thibault, “Multiscale X-ray imaging using ptychography,” J. Synchrotron Radiat. 25, 1214–1221 (2018).
[Crossref] [PubMed]

2017 (3)

M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
[Crossref] [PubMed]

J. C. da Silva, A. Pacureanu, Y. Yang, F. Fus, M. Hubert, L. Bloch, M. Salome, S. Bohic, and P. Cloetens, “High-energy cryo x-ray nano-imaging at the ID16A beamline of ESRF,” Proc. SPIE 10389, 103890F (2017).

U. Vogt, K. Parfeniukas, T. Stankevic, S. Kalbfleisch, Z. Matej, A. Björling, M. Liebi, G. Carbone, A. Mikkelsen, and U. Johansson, “First x-ray nanoimaging experiments at NanoMAX,” Proc. SPIE 10389, 103890K (2017).

2016 (3)

A. Singer, L. Boucheron, S. H. Dietze, K. E. Jensen, D. Vine, I. McNulty, E. R. Dufresne, R. O. Prum, S. G. J. Mochrie, and O. G. Shpyrko, “Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales,” Sci. Adv. 2, e1600149 (2016).
[Crossref] [PubMed]

S. Marchesini, H. Krishnan, B. J. Daurer, D. A. Shapiro, T. Perciano, J. A. Sethian, and F. R. N. C. Maia, “SHARP: a distributed GPU-based ptychographic solver,” J. Appl. Crystallogr. 49, 1245–1252 (2016).
[Crossref]

B. Enders and P. Thibault, “A computational framework for ptychographic reconstructions,” Proc. R. Soc. A 472, 1–19 (2016).
[Crossref]

2015 (3)

2014 (3)

M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, and O. Bunk, “X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,” Sci. Rep. 4, 1–5 (2014).

D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
[Crossref]

D. A. Shapiro, Y. S. Yu, T. Tyliszczak, J. Cabana, R. Celestre, W. Chao, K. Kaznatcheev, A. L. Kilcoyne, F. Maia, S. Marchesini, Y. S. Meng, T. Warwick, L. L. Yang, and H. A. Padmore, “Chemical composition mapping with nanometre resolution by soft X-ray microscopy,” Nat. Photonics 8, 765–769 (2014).
[Crossref]

2013 (4)

A. M. Maiden, G. R. Morrison, B. Kaulich, A. Gianoncelli, and J. M. Rodenburg, “Soft X-ray spectromicroscopy using ptychography with randomly phased illumination,” Nat. Commun. 4, 1666–1669 (2013).
[Crossref]

T. B. Edo, D. J. Batey, A. M. Maiden, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Sampling in x-ray ptychography,” Phys. Rev. A 87, 1–8 (2013).
[Crossref]

P. Thibault and A. Menzel, “Reconstructing state mixtures from diffraction measurements supplement,” Nature 494, 68–71 (2013).
[Crossref] [PubMed]

J. Marchal, I. Horswell, B. Willis, R. Plackett, E. N. Gimenez, J. Spiers, D. Ballard, P. Booker, J. A. Thompson, P. Gibbons, S. R. Burge, T. Nicholls, J. Lipp, and N. Tartoni, “EXCALIBUR: a small-pixel photon counting area detector for coherent X-ray diffraction - front-end design, fabrication and characterisation,” J. Phys. Conf. Ser. 425, 062003 (2013).
[Crossref]

2012 (4)

A. Limaye, “Drishti: a volume exploration and presentation tool,” Proc. SPIE 8506, 85060X (2012).
[Crossref]

P. Thibault and M. Guizar-Sicairos, “Maximum-likelihood refinement for coherent diffractive imaging,” New J. Phys. 14, 063004 (2012).
[Crossref]

A. Diaz, P. Trtik, M. Guizar-Sicairos, A. Menzel, P. Thibault, and O. Bunk, “Quantitative x-ray phase nanotomography,” Phys. Rev. B 85, 1–4 (2012).
[Crossref]

A. Schropp, R. Hoppe, J. Patommel, D. Samberg, F. Seiboth, S. Stephan, G. Wellenreuther, G. Falkenberg, and C. G. Schroer, “Hard x-ray scanning microscopy with coherent radiation: Beyond the resolution of conventional x-ray microscopes,” Appl. Phys. Lett. 100, 10–13 (2012).
[Crossref]

2011 (4)

C. Rau, U. Wagner, Z. Pešić, and A. De Fanis, “Coherent imaging at the Diamond beamline I13,” Phys. Status Solidi A 208, 2522–2525 (2011).
[Crossref]

Y. Takahashi, A. Suzuki, N. Zettsu, Y. Kohmura, Y. Senba, H. Ohashi, K. Yamauchi, and T. Ishikawa, “Towards high-resolution ptychographic x-ray diffraction microscopy,” Phys. Rev. B 83, 1–5 (2011).
[Crossref]

M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S. C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft X-ray ptychography,” Phys. Rev. Lett. 107, 1–4 (2011).
[Crossref]

M. Guizar-Sicairos, A. Diaz, M. Holler, M. S. Lucas, A. Menzel, R. a. Wepf, and O. Bunk, “Phase tomography from x-ray coherent diffractive imaging projections,” Opt. Express 19, 21345–21357 (2011).
[Crossref] [PubMed]

2010 (1)

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467, 436–439 (2010).
[Crossref] [PubMed]

2009 (2)

P. Thibault, M. Dierolf, O. Bunk, A. Menzel, and F. Pfeiffer, “Probe retrieval in ptychographic coherent diffractive imaging,” Ultramicroscopy 109, 338–343 (2009).
[Crossref] [PubMed]

A. M. Maiden and J. M. Rodenburg, “An improved ptychographical phase retrieval algorithm for diffractive imaging,” Ultramicroscopy 109, 1256–1262 (2009).
[Crossref] [PubMed]

2007 (1)

J. M. Rodenburg, A. C. Hurst, A. G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs, and I. Johnson, “Hard-X-ray lensless imaging of extended objects,” Phys. Rev. Lett. 98, 1–4 (2007).
[Crossref]

2004 (2)

H. M. L. Faulkner and J. M. Rodenburg, “Movable aperture lensless transmission microscopy: a novel phase retrieval algorithm,” Phys. Rev. Lett. 93, 023903 (2004).
[Crossref] [PubMed]

J. M. Rodenburg and H. M. L. Faulkner, “A phase retrieval algorithm for shifting illumination,” Appl. Phys. Lett. 85, 4795–4797 (2004).
[Crossref]

1997 (1)

H. N. Chapman, “Phase-retrieval X-ray microscopy by Wigner-distribution deconvolution: signal processing,” Scanning Microsc. 11, 67–80 (1997).

1996 (1)

H. N. Chapman, “Phase-retrieval X-ray microscopy by Wigner-distribution deconvolution,” Ultramicroscopy 66, 153–172 (1996).
[Crossref]

1994 (1)

H. Ghiradella, “Structure of butterfly scales: patterning in an insect cuticle,” Microsc. Res. Tech. 27, 429–438 (1994).
[Crossref] [PubMed]

Aeppli, G.

M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
[Crossref] [PubMed]

Allner, S.

Ballard, D.

J. Marchal, I. Horswell, B. Willis, R. Plackett, E. N. Gimenez, J. Spiers, D. Ballard, P. Booker, J. A. Thompson, P. Gibbons, S. R. Burge, T. Nicholls, J. Lipp, and N. Tartoni, “EXCALIBUR: a small-pixel photon counting area detector for coherent X-ray diffraction - front-end design, fabrication and characterisation,” J. Phys. Conf. Ser. 425, 062003 (2013).
[Crossref]

Batey, D.

D. Batey, S. Cipiccia, X. Shi, S. Williams, K. Wanelik, A. Wilson, S. Pérez-Tamarit, P. Cimavilla, M. A. Ródriguez-Pérez, and C. Rau, “Coherence Branch at I13, DLS: The Multiscale, Multimodal, Ptycho-tomographic End Station,” Microsc. Microanal. 24, 42–43 (2018).
[Crossref]

Batey, D. J.

S. Sala, V. S. C. Kuppili, S. Chalkidis, D. J. Batey, X. Shi, C. Rau, and P. Thibault, “Multiscale X-ray imaging using ptychography,” J. Synchrotron Radiat. 25, 1214–1221 (2018).
[Crossref] [PubMed]

D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
[Crossref]

T. B. Edo, D. J. Batey, A. M. Maiden, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Sampling in x-ray ptychography,” Phys. Rev. A 87, 1–8 (2013).
[Crossref]

Beckers, M.

M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S. C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft X-ray ptychography,” Phys. Rev. Lett. 107, 1–4 (2011).
[Crossref]

Björling, A.

U. Vogt, K. Parfeniukas, T. Stankevic, S. Kalbfleisch, Z. Matej, A. Björling, M. Liebi, G. Carbone, A. Mikkelsen, and U. Johansson, “First x-ray nanoimaging experiments at NanoMAX,” Proc. SPIE 10389, 103890K (2017).

Bloch, L.

J. C. da Silva, A. Pacureanu, Y. Yang, F. Fus, M. Hubert, L. Bloch, M. Salome, S. Bohic, and P. Cloetens, “High-energy cryo x-ray nano-imaging at the ID16A beamline of ESRF,” Proc. SPIE 10389, 103890F (2017).

J. C. da Silva, J. Haubrich, G. Requena, M. Hubert, A. Pacureanu, L. Bloch, Y. Yang, and P. Cloetens, “High energy near- and far-field ptychographic tomography at the ESRF,” Proc. SPIE 10391, 1039106 (2017).

Bohic, S.

J. C. da Silva, A. Pacureanu, Y. Yang, F. Fus, M. Hubert, L. Bloch, M. Salome, S. Bohic, and P. Cloetens, “High-energy cryo x-ray nano-imaging at the ID16A beamline of ESRF,” Proc. SPIE 10389, 103890F (2017).

Booker, P.

J. Marchal, I. Horswell, B. Willis, R. Plackett, E. N. Gimenez, J. Spiers, D. Ballard, P. Booker, J. A. Thompson, P. Gibbons, S. R. Burge, T. Nicholls, J. Lipp, and N. Tartoni, “EXCALIBUR: a small-pixel photon counting area detector for coherent X-ray diffraction - front-end design, fabrication and characterisation,” J. Phys. Conf. Ser. 425, 062003 (2013).
[Crossref]

Boon, J. J.

Boucheron, L.

A. Singer, L. Boucheron, S. H. Dietze, K. E. Jensen, D. Vine, I. McNulty, E. R. Dufresne, R. O. Prum, S. G. J. Mochrie, and O. G. Shpyrko, “Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales,” Sci. Adv. 2, e1600149 (2016).
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M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
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M. Guizar-Sicairos, J. J. Boon, K. Mader, A. Diaz, A. Menzel, and O. Bunk, “Quantitative interior x-ray nanotomography by a hybrid imaging technique,” Optica 2, 259–266 (2015).
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M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, and O. Bunk, “X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,” Sci. Rep. 4, 1–5 (2014).

A. Diaz, P. Trtik, M. Guizar-Sicairos, A. Menzel, P. Thibault, and O. Bunk, “Quantitative x-ray phase nanotomography,” Phys. Rev. B 85, 1–4 (2012).
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M. Guizar-Sicairos, A. Diaz, M. Holler, M. S. Lucas, A. Menzel, R. a. Wepf, and O. Bunk, “Phase tomography from x-ray coherent diffractive imaging projections,” Opt. Express 19, 21345–21357 (2011).
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J. M. Rodenburg, A. C. Hurst, A. G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs, and I. Johnson, “Hard-X-ray lensless imaging of extended objects,” Phys. Rev. Lett. 98, 1–4 (2007).
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Cloetens, P.

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J. M. Rodenburg, A. C. Hurst, A. G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs, and I. Johnson, “Hard-X-ray lensless imaging of extended objects,” Phys. Rev. Lett. 98, 1–4 (2007).
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M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
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J. C. da Silva, J. Haubrich, G. Requena, M. Hubert, A. Pacureanu, L. Bloch, Y. Yang, and P. Cloetens, “High energy near- and far-field ptychographic tomography at the ESRF,” Proc. SPIE 10391, 1039106 (2017).

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Diaz, A.

M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
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M. Guizar-Sicairos, J. J. Boon, K. Mader, A. Diaz, A. Menzel, and O. Bunk, “Quantitative interior x-ray nanotomography by a hybrid imaging technique,” Optica 2, 259–266 (2015).
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M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, and O. Bunk, “X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,” Sci. Rep. 4, 1–5 (2014).

A. Diaz, P. Trtik, M. Guizar-Sicairos, A. Menzel, P. Thibault, and O. Bunk, “Quantitative x-ray phase nanotomography,” Phys. Rev. B 85, 1–4 (2012).
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M. Guizar-Sicairos, A. Diaz, M. Holler, M. S. Lucas, A. Menzel, R. a. Wepf, and O. Bunk, “Phase tomography from x-ray coherent diffractive imaging projections,” Opt. Express 19, 21345–21357 (2011).
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M. Stockmar, M. Hubert, M. Dierolf, B. Enders, R. Clare, S. Allner, A. Fehringer, I. Zanette, J. Villanova, J. Laurencin, P. Cloetens, F. Pfeiffer, and P. Thibault, “X-ray nanotomography using near-field ptychography,” Opt. Express 23, 12720–12731 (2015).
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M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467, 436–439 (2010).
[Crossref] [PubMed]

P. Thibault, M. Dierolf, O. Bunk, A. Menzel, and F. Pfeiffer, “Probe retrieval in ptychographic coherent diffractive imaging,” Ultramicroscopy 109, 338–343 (2009).
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A. Singer, L. Boucheron, S. H. Dietze, K. E. Jensen, D. Vine, I. McNulty, E. R. Dufresne, R. O. Prum, S. G. J. Mochrie, and O. G. Shpyrko, “Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales,” Sci. Adv. 2, e1600149 (2016).
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Dinapoli, R.

M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
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J. M. Rodenburg, A. C. Hurst, A. G. Cullis, B. R. Dobson, F. Pfeiffer, O. Bunk, C. David, K. Jefimovs, and I. Johnson, “Hard-X-ray lensless imaging of extended objects,” Phys. Rev. Lett. 98, 1–4 (2007).
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M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
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D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
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Farmand, M.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. Maia, A. L. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9, 1–7 (2018).

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Fus, F.

J. C. da Silva, A. Pacureanu, Y. Yang, F. Fus, M. Hubert, L. Bloch, M. Salome, S. Bohic, and P. Cloetens, “High-energy cryo x-ray nano-imaging at the ID16A beamline of ESRF,” Proc. SPIE 10389, 103890F (2017).

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Guizar-Sicairos, M.

M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
[Crossref] [PubMed]

M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
[Crossref]

M. Guizar-Sicairos, J. J. Boon, K. Mader, A. Diaz, A. Menzel, and O. Bunk, “Quantitative interior x-ray nanotomography by a hybrid imaging technique,” Optica 2, 259–266 (2015).
[Crossref]

M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, and O. Bunk, “X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,” Sci. Rep. 4, 1–5 (2014).

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A. Diaz, P. Trtik, M. Guizar-Sicairos, A. Menzel, P. Thibault, and O. Bunk, “Quantitative x-ray phase nanotomography,” Phys. Rev. B 85, 1–4 (2012).
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M. Guizar-Sicairos, A. Diaz, M. Holler, M. S. Lucas, A. Menzel, R. a. Wepf, and O. Bunk, “Phase tomography from x-ray coherent diffractive imaging projections,” Opt. Express 19, 21345–21357 (2011).
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M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, and O. Bunk, “X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,” Sci. Rep. 4, 1–5 (2014).

Hartmann, J.

M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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J. C. da Silva, J. Haubrich, G. Requena, M. Hubert, A. Pacureanu, L. Bloch, Y. Yang, and P. Cloetens, “High energy near- and far-field ptychographic tomography at the ESRF,” Proc. SPIE 10391, 1039106 (2017).

Holler, M.

M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
[Crossref] [PubMed]

M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
[Crossref]

M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe, and O. Bunk, “X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution,” Sci. Rep. 4, 1–5 (2014).

M. Guizar-Sicairos, A. Diaz, M. Holler, M. S. Lucas, A. Menzel, R. a. Wepf, and O. Bunk, “Phase tomography from x-ray coherent diffractive imaging projections,” Opt. Express 19, 21345–21357 (2011).
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D. Batey, S. Cipiccia, X. Shi, S. Williams, K. Wanelik, A. Wilson, S. Pérez-Tamarit, P. Cimavilla, M. A. Ródriguez-Pérez, and C. Rau, “Coherence Branch at I13, DLS: The Multiscale, Multimodal, Ptycho-tomographic End Station,” Microsc. Microanal. 24, 42–43 (2018).
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D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
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D. Batey, S. Cipiccia, X. Shi, S. Williams, K. Wanelik, A. Wilson, S. Pérez-Tamarit, P. Cimavilla, M. A. Ródriguez-Pérez, and C. Rau, “Coherence Branch at I13, DLS: The Multiscale, Multimodal, Ptycho-tomographic End Station,” Microsc. Microanal. 24, 42–43 (2018).
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M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S. C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft X-ray ptychography,” Phys. Rev. Lett. 107, 1–4 (2011).
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M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S. C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft X-ray ptychography,” Phys. Rev. Lett. 107, 1–4 (2011).
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Samberg, D.

A. Schropp, R. Hoppe, J. Patommel, D. Samberg, F. Seiboth, S. Stephan, G. Wellenreuther, G. Falkenberg, and C. G. Schroer, “Hard x-ray scanning microscopy with coherent radiation: Beyond the resolution of conventional x-ray microscopes,” Appl. Phys. Lett. 100, 10–13 (2012).
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M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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A. Schropp, R. Hoppe, J. Patommel, D. Samberg, F. Seiboth, S. Stephan, G. Wellenreuther, G. Falkenberg, and C. G. Schroer, “Hard x-ray scanning microscopy with coherent radiation: Beyond the resolution of conventional x-ray microscopes,” Appl. Phys. Lett. 100, 10–13 (2012).
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A. Schropp, R. Hoppe, J. Patommel, D. Samberg, F. Seiboth, S. Stephan, G. Wellenreuther, G. Falkenberg, and C. G. Schroer, “Hard x-ray scanning microscopy with coherent radiation: Beyond the resolution of conventional x-ray microscopes,” Appl. Phys. Lett. 100, 10–13 (2012).
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M. Beckers, T. Senkbeil, T. Gorniak, M. Reese, K. Giewekemeyer, S. C. Gleber, T. Salditt, and A. Rosenhahn, “Chemical contrast in soft X-ray ptychography,” Phys. Rev. Lett. 107, 1–4 (2011).
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M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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Shapiro, D. A.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. Maia, A. L. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9, 1–7 (2018).

S. Marchesini, H. Krishnan, B. J. Daurer, D. A. Shapiro, T. Perciano, J. A. Sethian, and F. R. N. C. Maia, “SHARP: a distributed GPU-based ptychographic solver,” J. Appl. Crystallogr. 49, 1245–1252 (2016).
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S. Sala, V. S. C. Kuppili, S. Chalkidis, D. J. Batey, X. Shi, C. Rau, and P. Thibault, “Multiscale X-ray imaging using ptychography,” J. Synchrotron Radiat. 25, 1214–1221 (2018).
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A. Singer, L. Boucheron, S. H. Dietze, K. E. Jensen, D. Vine, I. McNulty, E. R. Dufresne, R. O. Prum, S. G. J. Mochrie, and O. G. Shpyrko, “Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales,” Sci. Adv. 2, e1600149 (2016).
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J. Marchal, I. Horswell, B. Willis, R. Plackett, E. N. Gimenez, J. Spiers, D. Ballard, P. Booker, J. A. Thompson, P. Gibbons, S. R. Burge, T. Nicholls, J. Lipp, and N. Tartoni, “EXCALIBUR: a small-pixel photon counting area detector for coherent X-ray diffraction - front-end design, fabrication and characterisation,” J. Phys. Conf. Ser. 425, 062003 (2013).
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Stephan, S.

A. Schropp, R. Hoppe, J. Patommel, D. Samberg, F. Seiboth, S. Stephan, G. Wellenreuther, G. Falkenberg, and C. G. Schroer, “Hard x-ray scanning microscopy with coherent radiation: Beyond the resolution of conventional x-ray microscopes,” Appl. Phys. Lett. 100, 10–13 (2012).
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Strobridge, F. C.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. Maia, A. L. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9, 1–7 (2018).

Suzuki, A.

Y. Takahashi, A. Suzuki, N. Zettsu, Y. Kohmura, Y. Senba, H. Ohashi, K. Yamauchi, and T. Ishikawa, “Towards high-resolution ptychographic x-ray diffraction microscopy,” Phys. Rev. B 83, 1–5 (2011).
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Y. Takahashi, A. Suzuki, N. Zettsu, Y. Kohmura, Y. Senba, H. Ohashi, K. Yamauchi, and T. Ishikawa, “Towards high-resolution ptychographic x-ray diffraction microscopy,” Phys. Rev. B 83, 1–5 (2011).
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J. Marchal, I. Horswell, B. Willis, R. Plackett, E. N. Gimenez, J. Spiers, D. Ballard, P. Booker, J. A. Thompson, P. Gibbons, S. R. Burge, T. Nicholls, J. Lipp, and N. Tartoni, “EXCALIBUR: a small-pixel photon counting area detector for coherent X-ray diffraction - front-end design, fabrication and characterisation,” J. Phys. Conf. Ser. 425, 062003 (2013).
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S. Sala, V. S. C. Kuppili, S. Chalkidis, D. J. Batey, X. Shi, C. Rau, and P. Thibault, “Multiscale X-ray imaging using ptychography,” J. Synchrotron Radiat. 25, 1214–1221 (2018).
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A. Diaz, P. Trtik, M. Guizar-Sicairos, A. Menzel, P. Thibault, and O. Bunk, “Quantitative x-ray phase nanotomography,” Phys. Rev. B 85, 1–4 (2012).
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M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467, 436–439 (2010).
[Crossref] [PubMed]

P. Thibault, M. Dierolf, O. Bunk, A. Menzel, and F. Pfeiffer, “Probe retrieval in ptychographic coherent diffractive imaging,” Ultramicroscopy 109, 338–343 (2009).
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Thompson, J. A.

J. Marchal, I. Horswell, B. Willis, R. Plackett, E. N. Gimenez, J. Spiers, D. Ballard, P. Booker, J. A. Thompson, P. Gibbons, S. R. Burge, T. Nicholls, J. Lipp, and N. Tartoni, “EXCALIBUR: a small-pixel photon counting area detector for coherent X-ray diffraction - front-end design, fabrication and characterisation,” J. Phys. Conf. Ser. 425, 062003 (2013).
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M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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A. Diaz, P. Trtik, M. Guizar-Sicairos, A. Menzel, P. Thibault, and O. Bunk, “Quantitative x-ray phase nanotomography,” Phys. Rev. B 85, 1–4 (2012).
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Tsai, E. H.

M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
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M. Guizar-Sicairos, M. Holler, A. Diaz, J. C. da Silva, E. H. R. Tsai, O. Bunk, C. Martinez-Perez, P. C. J. Donoghue, C. H. Wellman, and A. Menzel, “Ptychographic nanotomography at the Swiss Light Source,” Proc. SPIE 9592, 95920A (2015).
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Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. Maia, A. L. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9, 1–7 (2018).

D. A. Shapiro, Y. S. Yu, T. Tyliszczak, J. Cabana, R. Celestre, W. Chao, K. Kaznatcheev, A. L. Kilcoyne, F. Maia, S. Marchesini, Y. S. Meng, T. Warwick, L. L. Yang, and H. A. Padmore, “Chemical composition mapping with nanometre resolution by soft X-ray microscopy,” Nat. Photonics 8, 765–769 (2014).
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Vine, D.

A. Singer, L. Boucheron, S. H. Dietze, K. E. Jensen, D. Vine, I. McNulty, E. R. Dufresne, R. O. Prum, S. G. J. Mochrie, and O. G. Shpyrko, “Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales,” Sci. Adv. 2, e1600149 (2016).
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U. Vogt, K. Parfeniukas, T. Stankevic, S. Kalbfleisch, Z. Matej, A. Björling, M. Liebi, G. Carbone, A. Mikkelsen, and U. Johansson, “First x-ray nanoimaging experiments at NanoMAX,” Proc. SPIE 10389, 103890K (2017).

Waag, A.

M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
[Crossref]

Wagner, U.

D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
[Crossref]

T. B. Edo, D. J. Batey, A. M. Maiden, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Sampling in x-ray ptychography,” Phys. Rev. A 87, 1–8 (2013).
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C. Rau, U. Wagner, Z. Pešić, and A. De Fanis, “Coherent imaging at the Diamond beamline I13,” Phys. Status Solidi A 208, 2522–2525 (2011).
[Crossref]

Waigh, T. A.

D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
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T. B. Edo, D. J. Batey, A. M. Maiden, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Sampling in x-ray ptychography,” Phys. Rev. A 87, 1–8 (2013).
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Wanelik, K.

D. Batey, S. Cipiccia, X. Shi, S. Williams, K. Wanelik, A. Wilson, S. Pérez-Tamarit, P. Cimavilla, M. A. Ródriguez-Pérez, and C. Rau, “Coherence Branch at I13, DLS: The Multiscale, Multimodal, Ptycho-tomographic End Station,” Microsc. Microanal. 24, 42–43 (2018).
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Warwick, T.

Y. S. Yu, M. Farmand, C. Kim, Y. Liu, C. P. Grey, F. C. Strobridge, T. Tyliszczak, R. Celestre, P. Denes, J. Joseph, H. Krishnan, F. R. Maia, A. L. Kilcoyne, S. Marchesini, T. P. C. Leite, T. Warwick, H. Padmore, J. Cabana, and D. A. Shapiro, “Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography,” Nat. Commun. 9, 1–7 (2018).

D. A. Shapiro, Y. S. Yu, T. Tyliszczak, J. Cabana, R. Celestre, W. Chao, K. Kaznatcheev, A. L. Kilcoyne, F. Maia, S. Marchesini, Y. S. Meng, T. Warwick, L. L. Yang, and H. A. Padmore, “Chemical composition mapping with nanometre resolution by soft X-ray microscopy,” Nat. Photonics 8, 765–769 (2014).
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M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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J. C. da Silva, A. Pacureanu, Y. Yang, F. Fus, M. Hubert, L. Bloch, M. Salome, S. Bohic, and P. Cloetens, “High-energy cryo x-ray nano-imaging at the ID16A beamline of ESRF,” Proc. SPIE 10389, 103890F (2017).

J. C. da Silva, J. Haubrich, G. Requena, M. Hubert, A. Pacureanu, L. Bloch, Y. Yang, and P. Cloetens, “High energy near- and far-field ptychographic tomography at the ESRF,” Proc. SPIE 10391, 1039106 (2017).

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D. A. Shapiro, Y. S. Yu, T. Tyliszczak, J. Cabana, R. Celestre, W. Chao, K. Kaznatcheev, A. L. Kilcoyne, F. Maia, S. Marchesini, Y. S. Meng, T. Warwick, L. L. Yang, and H. A. Padmore, “Chemical composition mapping with nanometre resolution by soft X-ray microscopy,” Nat. Photonics 8, 765–769 (2014).
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M. Kahnt, G. Falkenberg, J. Garrevoet, J. Hartmann, T. Krause, M. Niehle, M. Scholz, M. Seyrich, A. Trampert, A. Waag, H.-H. Wehmann, F. Wittwer, H. Zhou, M. Hanke, and C. G. Schroer, “Simultaneous hard X-ray ptychographic tomography and X-ray fluorescence tomography of isolated hollow core-shell GaN rods,” Microsc. Microanal. 24, 34–35 (2018).
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J. Synchrotron Radiat. (1)

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D. Batey, S. Cipiccia, X. Shi, S. Williams, K. Wanelik, A. Wilson, S. Pérez-Tamarit, P. Cimavilla, M. A. Ródriguez-Pérez, and C. Rau, “Coherence Branch at I13, DLS: The Multiscale, Multimodal, Ptycho-tomographic End Station,” Microsc. Microanal. 24, 42–43 (2018).
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A. M. Maiden, G. R. Morrison, B. Kaulich, A. Gianoncelli, and J. M. Rodenburg, “Soft X-ray spectromicroscopy using ptychography with randomly phased illumination,” Nat. Commun. 4, 1666–1669 (2013).
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D. A. Shapiro, Y. S. Yu, T. Tyliszczak, J. Cabana, R. Celestre, W. Chao, K. Kaznatcheev, A. L. Kilcoyne, F. Maia, S. Marchesini, Y. S. Meng, T. Warwick, L. L. Yang, and H. A. Padmore, “Chemical composition mapping with nanometre resolution by soft X-ray microscopy,” Nat. Photonics 8, 765–769 (2014).
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F. Pfeiffer, “X-ray ptychography,” Nat. Photonics 12, 9–17 (2018).
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Nature (3)

M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, “Ptychographic X-ray computed tomography at the nanoscale,” Nature 467, 436–439 (2010).
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M. Holler, M. Guizar-Sicairos, E. H. Tsai, R. Dinapoli, E. Müller, O. Bunk, J. Raabe, and G. Aeppli, “High-resolution non-destructive three-dimensional imaging of integrated circuits,” Nature 543, 402–406 (2017).
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P. Thibault and M. Guizar-Sicairos, “Maximum-likelihood refinement for coherent diffractive imaging,” New J. Phys. 14, 063004 (2012).
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Opt. Express (2)

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Phys. Rev. A (2)

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D. J. Batey, T. B. Edo, C. Rau, U. Wagner, Z. D. Pešić, T. A. Waigh, and J. M. Rodenburg, “Reciprocal-space up-sampling from real-space oversampling in x-ray ptychography,” Phys. Rev. A 89, 1–5 (2014).
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P. Li, “Investigations and improvements in ptychographic imaging,” Phd thesis, University of Sheffield (2016).

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Figures (6)

Fig. 1
Fig. 1 (a) Transmitted light micrograph and (b) horizontal refraction image of a wing scale from a pansy butterfly mounted on holder.
Fig. 2
Fig. 2 Horizontal section of ptychographic X-ray computed tomography (PXCT) experimental setup including beam-shaping slits, central stop (CS), Fresnel focusing zone plate (FZP), order sorting aperture (OSA), translation and rotation sample stages (sample) and detector.
Fig. 3
Fig. 3 (a) Phase part of the object and (b) complex-valued wavefront of the dominant mode (96.5% of total power) of the probe, both obtained from a ptychographic reconstruction run on a Siemens star test pattern. In (b) amplitude is mapped to brightness and phase to hue according to the colour wheel.
Fig. 4
Fig. 4 Phase images of the apical region of a wing scale from a pansy butterfly collected at different sample orientations: (a) 0° and (b) 146°.
Fig. 5
Fig. 5 Schematic representation of PXCT data analysis pipeline. The ptychographic pipeline is aimed at obtaining 2D projections of the transmission function of the imaged object, starting from the raw data recorded by the detector for each ptychographic scan. The tomographic pipeline is aimed at obtaining a stack of 2D tomograms (i.e. a whole volume) starting from the whole set of 2D projections obtained from the ptychographic pipeline. Tomographic consistency is the iterative algorithm exploited for horizontal alignment of the partial local tomography data set.
Fig. 6
Fig. 6 (a-c) Phase tomograms at different heights, including two tips of the apical region of a wing scale from a pansy butterfly. (d) 3D rendering obtained from a stack of 750 such phase tomograms using Drishti [41]. Regions to which tomograms from (a), (b) and (c) refer are annotated in (d).

Equations (2)

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O ( x , y , z ) = e i k   [ n ( x , y , z ) 1 ] d z = e k β ( x , y , z ) d z e i k δ ( x , y , z ) d z
ξ t = 1 2 λ R D

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