Pablo Villanueva Perez
Senior lecturer
Research
Our research focuses on the development of X-ray techniques to explore nature in 3D and 4D (3D+time), from the microscale down to the nanoscale, and from seconds down to femtoseconds. The unique penetration power of X-rays allows the study of the inner structure of matter in a non-destructive manner. Furthermore, their short wavelength allows the study from the macroscopic down to the atomic scale. These properties, together with the advent of high-brilliance sources, such as diffraction-limited storage rings (MAX IV) and X-ray free-electron lasers (European XFEL), offers the possibility to develop novel X-ray microscopes to explore nature in ways not possible before.
We are frequent users of the MAX IV synchrotron facility and the European XFEL.
Our research topics include:
- Simulation of X-ray instruments at high-brilliance sources
- Conceptual design and implementation of X-ray microscopes
- Coherent X-ray imaging
- Phase retrieval
- Fast reconstruction algorithms based on machine learning and other state-of-the-art approaches.
Some ongoing research projects are described below:
Projects
3D and 4D AI+Physics X-ray imaging reconstruction from sparse projections
X-rays have been widely used in scientific research and industry to study the structure and composition of materials. Among X-ray techniques, X-ray tomography is a commonly used 3D imaging technique in which a sample is scanned from different angles by rotating it. However, this process is typically slow and unsuitable for capturing fast, sensitive dynamics. To overcome these limitations, state-of-the-art single-shot 3D imaging techniques have been developed to capture multiple projections simultaneously from different directions [1, 2], but reconstructing time-resolved 3D movies from sparse experimental data remains a significant challenge. To address this problem, we developed two unsupervised deep learning reconstruction algorithms: ONIX (Optimized Neural Implicit X-ray Imaging) [3] and 4D-ONIX [4]. These algorithms combine advanced computer vision and AI methods with the physics of X-ray imaging and offer the potential to reconstruct high-quality 3D and 4D (dynamic 3D) structure and dynamics of the sample from ultra-sparse projections, as few as two projections spaced 24° apart. These approaches allow researchers to visualize dynamic phenomena, such as droplet collisions and metal melting, up to 1,000 times faster than conventional methods. They provide a powerful tool for exploring the structure and dynamics of various samples and open new spatiotemporal frontiers in materials science and fluid dynamics.
References
[1] Villanueva-Perez, Pablo, et al. "Hard x-ray multi-projection imaging for single-shot approaches." Optica 5.12 (2018): 1521-1524.
[2] Liang, Xiaoyu, et al. "Sub-millisecond 4D X-ray tomography achieved with a multibeam X-ray imaging system." Applied Physics Express 16.7 (2023): 072001.
[3] Zhang, Yuhe, et al. "ONIX: An X‐ray deep‐learning tool for 3D reconstructions from sparse views." Applied Research 2.4 (2023): e202300016.
[4] Zhang, Yuhe, et al. "4D-ONIX: A deep learning approach for reconstructing 3D movies from sparse X-ray projections." arXiv preprint arXiv:2401.09508 (2024).
[5] Makowska, Malgorzata G., et al. "Operando tomographic microscopy during laser-based powder bed fusion of alumina." Communications Materials 4.1 (2023):73.
[6]Malgorzata Makowska. High-resolution time-resolved tomography of Selective Laser Melting of alumina, 2023 (on doi.psi.ch).
X-ray Multibeam ptychography
Multibeam ptychography is an innovative X-ray imaging technique that extends the capabilities of single-beam ptychography to overcome limitations in speed and field of view. While traditional ptychography offers high-resolution and quantitative phase contrast imaging, it is constrained by slow data acquisition over large areas. By dividing the X-ray beam into multiple coherent probes, multibeam ptychography enables simultaneous imaging of multiple regions, significantly improving efficiency while maintaining the resolution. This approach makes it ideal for studying a wide range of samples, from advanced materials to functional devices, enabling faster and more comprehensive measurements in cutting-edge research.
Teaching
Publications
Displaying of publications. Sorted by year, then title.
Optimizing probes for multi-beam ptychography
Runqing Yang, Pablo Villanueva-Perez, Tang Li, Mikhail Lyubomirskiy, Giovanni Fevola, et al.
(2026) Optics Express, 34 p.12463-12478
ArticleTime-resolved 3D imaging opportunities with XMPI at ForMAX
Julia Katharina Rogalinski, Zisheng Yao, Yuhe Zhang, Zhe Hu, Korneliya Gordeyeva, et al.
(2026) Journal of Synchrotron Radiation, 33 p.417-428
ArticleSuper Time-Resolved Tomography
Zhe Hu, Zisheng Yao, Kalle Josefsson, Francisco García-Moreno, Malgorzata Makowska, et al.
(2026) Advanced Science, 13
ArticleUltrasonic cavitation shock wave exfoliation dynamics of 2D materials revealed in situ by MHz XFEL imaging and multiphysics modeling
Kang Xiang, Ling Qin, Shi Huang, Hongyuan Song, Vasilii Bazhenov, et al.
(2025) Science Advances, 11 p.1-10
ArticlePhysics-informed 4D x-ray image reconstruction from ultra-sparse spatiotemporal data
Zisheng Yao, Yuhe Zhang, Zhe Hu, Robert Klöfkorn, Tobias Ritschel, et al.
(2025) Measurement Science and Technology, 36
Article4D-ONIX for reconstructing 3D movies from sparse X-ray projections via deep learning
Yuhe Zhang, Zisheng Yao, Robert Klöfkorn, Tobias Ritschel, Pablo Villanueva-Perez
(2025) Communications Engineering, 4
ArticleMulti-beam multi-slice X-ray ptychography
Mattias Åstrand, Ulrich Vogt, Runqing Yang, Pablo Villanueva Perez, Tang Li, et al.
(2025) Scientific Reports, 15
ArticleDevelopment of MHz X-ray phase contrast imaging at the European XFEL
Jayanath C.P. Koliyadu, Daniel Moško, Eleni Myrto Asimakopoulou, Valerio Bellucci, Šarlota Birnšteinová, et al.
(2025) Journal of Synchrotron Radiation, 32 p.17-28
ArticleReusability report : Unpaired deep-learning approaches for holographic image
Yuhe Zhang, Tobias Ritschel, Pablo Villanueva Perez
(2024) Nature Machine Intelligence, 6 p.284-290
ArticleTowards multiscale X-ray tomographic imaging in membrane science : A perspective
Gregor Rudolph-Schöpping, Emanuel Larsson, Torben Nilsson Pingel, Manuel Guizar-Sicairos, Pablo Villanueva-Perez, et al.
(2024) Journal of Membrane Science, 690
Review articleDevelopment towards high-resolution kHz-speed rotation-free volumetric imaging
Eleni Myrto Asimakopoulou, Valerio Bellucci, Sarlota Birnsteinova, Zisheng Yao, Yuhe Zhang, et al.
(2024) Optics Express, 32 p.4413-4426
ArticleForMAX – a beamline for multiscale and multimodal structural characterization of hierarchical materials
K. Nygård, S. A. McDonald, J. B. González, V. Haghighat, Christian Appel, et al.
(2024) Journal of Synchrotron Radiation, 31 p.363-377
Article4D-ONIX : A deep learning approach for reconstructing 3D movies from sparse X-ray projections
Yuhe Zhang, Zisheng Yao, Robert Klöfkorn, Tobias Ritschel, Pablo Villanueva Perez
(2024) arXiv.org
Preprint (in preprint archive)X-Ray Multibeam Ptychography at up to 20 keV : Nano-Lithography Enhances X-Ray Nano-Imaging
Tang Li, Maik Kahnt, Thomas L. Sheppard, Runqing Yang, Ken V. Falch, et al.
(2024) Advanced Science, 11
ArticleNew opportunities for time-resolved imaging using diffraction-limited storage rings
Zisheng Yao, Julia Rogalinski, Eleni Myrto Asimakopoulou, Yuhe Zhang, Korneliya Gordeyeva, et al.
(2024) Journal of Synchrotron Radiation, 31 p.1299-1307
ArticleDevelopment of crystal optics for X-ray multi-projection imaging for synchrotron and XFEL sources
Valerio Bellucci, Sarlota Birnsteinova, Tokushi Sato, Romain Letrun, Jayanath C.P. Koliyadu, et al.
(2024) Journal of Synchrotron Radiation, 31 p.1534-1550
ArticleONIX : an X-ray deep-learning tool for 3D reconstructions from sparse views
Yuhe Zhang, Zisheng Yao, Tobias Ritschel, Pablo Villanueva Perez
(2023) Applied Research, 2
ArticleMegahertz X-ray Multi-projection imaging
Pablo Villanueva Perez, Valerio Bellucci, Yuhe Zhang, Sarlota Birnsteinova, Rita Graceffa, et al.
(2023) arXiv.org
ArticleDeep-learning image enhancement and fibre segmentation from time-resolved computed tomography of fibre-reinforced composites
Rui Guo, Johannes Stubbe, Yuhe Zhang, Christian Matthias Schlepütz, Camilo Rojas Gomez, et al.
(2023) Composites Science and Technology, 244
ArticleRevealing the origins of vortex cavitation in a Venturi tube by high speed X-ray imaging
Hitoshi Soyama, Xiaoyu Liang, Wataru Yashiro, Kentaro Kajiwara, Eleni Myrto Asimakopoulou, et al.
(2023) Ultrasonics Sonochemistry, 101
ArticleLaser-induced, single droplet fragmentation dynamics revealed through megahertz x-ray microscopy
Fabian Reuter, Tokushi Sato, Valerio Bellucci, Sarlota Birnsteinova, Carsten Deiter, et al.
(2023) Physics of Fluids, 35
ArticleOnline dynamic flat-field correction for MHz microscopy data at European XFEL
Sarlota Birnsteinova, Danilo E Ferreira de Lima, Egor Sobolev, Henry J Kirkwood, Valerio Bellucci, et al.
(2023) Journal of Synchrotron Radiation, 30 p.1030-1037
ArticleHard X-ray stereographic microscopy for single-shot differential phase imaging
Valerio Bellucci, Marie Christine Zdora, Ladislav Mikeš, Šarlota Birnšteinová, Peter Oberta, et al.
(2023) Optics Express, 31 p.18399-18406
ArticleDose-efficient scanning Compton X-ray microscopy
Tang Li, J. Lukas Dresselhaus, Nikolay Ivanov, Mauro Prasciolu, Holger Fleckenstein, et al.
(2023) Light: Science and Applications, 12
ArticleX-ray in-line holography and holotomography at the NanoMAX beamline
Sebastian Kalbfleisch, Yuhe Zhang, Maik Kahnt, Khachiwan Buakor, Max Langer, et al.
(2022) Journal of Synchrotron Radiation, 29 p.224-229
ArticleShot-to-shot flat-field correction at X-ray free-electron lasers
Khachiwan Buakor, Yuhe Zhang, Šarlota Birnšteinova, Valerio Bellucci, Takushi Sato, et al.
(2022) Optics Express, 30 p.10633-10644
ArticleDose-efficient multimodal microscopy of human tissue at a hard X-ray nanoprobe beamline
Simone Sala, Yuhe Zhang, Nathaly De La Rosa, Till Dreier, Maik Kahnt, et al.
(2022) Journal of Synchrotron Radiation, 29
ArticleA new imaging technology based on Compton X-ray scattering
Ángela Saá Hernández, Diego González-Díaz, Pablo Villanueva, Carlos Azevedo, Marcos Seoane
(2021) Journal of Synchrotron Radiation, 28 p.1558-1572
ArticleScanning Compton X-ray microscopy
P. Villanueva-Perez, H. Fleckenstein, M. Prasciolu, K. T. Murray, M. Domaracky, et al.
(2021) Optics Letters, 46 p.1920-1923
ArticleOn the use of multilayer Laue lenses with X-ray free electron lasers
Mauro Prasciolu, Kevin T. Murray, Nikolay Ivanov, Holger Fleckenstein, Martin Domaracký, et al.
(2021) Proceedings of SPIE - The International Society for Optical Engineering
Paper in conference proceedingPyPhase - A Python package for X-ray phase imaging
Max Langer, Yuhe Zhang, Diogo Figueirinhas, Jean Baptiste Forien, Kannara Mom, et al.
(2021) Journal of Synchrotron Radiation, 28 p.1261-1266
ArticlePhaseGAN : a deep-learning phase-retrieval approach for unpaired datasets
Yuhe Zhang, Mike Andreas Noack, Patrik Vagovic, Kamel Fezzaa, Francisco Garcia-Moreno, et al.
(2021) Optics Express, 29 p.19593-19604
ArticleLow-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography
Isabelle Martiel, Chia Ying Huang, Pablo Villanueva-Perez, Ezequiel Panepucci, Shibom Basu, et al.
(2020) IUCrJ, 7 p.1131-1141
ArticleSingleshot polychromatic coherent diffractive imaging with a high-order harmonic source
Erik Malm, Hampus Wikmark, Bastian Pfau, Pablo Villanueva-Perez, Piotr Rudawski, et al.
(2020) Optics Express, 28 p.394-404
ArticleUltracompact 3D microfluidics for time-resolved structural biology
Juraj Knoška, Luigi Adriano, Salah Awel, Kenneth R. Beyerlein, Oleksandr Yefanov, et al.
(2020) Nature Communications, 11
ArticleMegahertz x-ray microscopy at x-ray free-electron laser and synchrotron sources
Patrik Vagovič, Tokushi Sato, Ladislav Mikeš, Grant Mills, Rita Graceffa, et al.
(2019) Optica, 6 p.1106-1109
ArticleAssessing lesion malignancy by scanning small-angle x-ray scattering of breast tissue with microcalcifications
C. Arboleda, V. Lutz-Bueno, Z. Wang, P. Villanueva-Perez, M. Guizar-Sicairos, et al.
(2019) Physics in Medicine and Biology, 64
ArticleEvaluation of serial crystallographic structure determination within megahertz pulse trains
Oleksandr Yefanov, Dominik Oberthür, Richard Bean, Max O Wiedorn, Juraj Knoska, et al.
(2019) Structural Dynamics, 6 p.064702
ArticleHard x-ray multi-projection imaging for single-shot approaches
P. Villanueva-Perez, B. Pedrini, R. Mokso, P. Vagovic, V. A. Guzenko, et al.
(2018) Optica, 5 p.1521-1524
LetterDose efficient compton X-ray microscopy
P. Villanueva-Perez, S. Bajt, H. N. Chapman
(2018) Optica, 5 p.450-457
ArticleX-ray focusing with efficient high-NA multilayer Laue lenses
Saša Bajt, Mauro Prasciolu, Holger Fleckenstein, Martin Domaracký, Henry N Chapman, et al.
(2018) Light, science & applications, 7 p.17162
ArticleSynchrotron-based phase contrast imaging of cardiovascular tissue in mice—grating interferometry or phase propagation?
Bram Trachet, Goran Lovric, Pablo Villanueva-Perez, Lydia Aslanidou, Mauro Ferraro, et al.
(2018) Biomedical Physics Engineering Express, 5 p.015010
ArticleModel-free classification of X-ray scattering signals applied to image segmentation
V Lutz-Bueno, C Arboleda, L Leu, MJ Blunt, A Busch, et al.
(2018) Journal of Applied Crystallography, 51
ArticlePropagation-based phase-contrast synchrotron imaging of aortic dissection in mice: from individual elastic lamella to 3D analysis
Gerlinde Logghe, Bram Trachet, Lydia Aslanidou, Pablo Villaneuva-Perez, Julie De Backer, et al.
(2018) Scientific Reports, 8
ArticleMicrostructural degradation of silicon electrodes during lithiation observed via operando X-ray tomographic imaging
Oluwadamilola O. Taiwo, Thomas M M Heenan, Donal P Finegan, Juan M. Paz-García, Stephen A. Hall, et al.
(2017) Journal of Power Sources, 342 p.904-912
ArticleContrast-transfer-function phase retrieval based on compressed sensing
Pablo Villanueva-Perez, Filippo Arcadu, Peter Cloetens, Marco Stampanoni
(2017) Optics Letters, 42 p.1133-1136
ArticleSensitivity-based optimization for the design of a grating interferometer for clinical X-ray phase contrast mammography
Carolina Arboleda, Zhentian Wang, Thomas Koehler, Gerhard Martens, Udo Van Stevendaal, et al.
(2017) Optics Express, 25 p.6349-6364
ArticleEarly Events in Dissecting Aneurysms Induced by Angiotensin-II Infusion: The Geometry-Driven Aspect of a Multifaceted Problem
Lydia Aslanidou, Bram Trachet, Mauro Ferraro, Alessandra Piersigilli, Rodrigo Fraga-Silva, et al.
(2017) Arteriosclerosis, Thrombosis, and Vascular Biology, 37 p.A474-A474
ArticleCircular Unit Cell Gratings for X-ray Dark-Field Imaging
Matias Kagias, Amogha Pandeshwar, Zhentian Wang, Pablo Villanueva-Perez, Konstantins Jefimovs, et al.
(2017) Journal of Physics: Conference Series, 849
Paper in conference proceeding2D-Omnidirectional Hard-X-Ray Scattering Sensitivity in a Single Shot
Matias Kagias, Zhentian Wang, Pablo Villanueva-Perez, Konstantins Jefimovs, Marco Stampanoni
(2016) Physical Review Letters, 116 p.093902
ArticleA generalized quantitative interpretation of dark-field contrast for highly concentrated microsphere suspensions
Spyridon Gkoumas, Pablo Villanueva-Perez, Zhentian Wang, Lucia Romano, Matteo Abis, et al.
(2016) Scientific Reports, 6 p.35259
ArticleSignal-to-noise criterion for free-propagation imaging techniques at free-electron lasers and synchrotrons
Pablo Villanueva-Perez, Bill Pedrini, Rajmund Mokso, Manuel Guizar-Sicairos, Filippo Arcadu, et al.
(2016) Optics Express, 24 p.3189-3201
ArticleDirect test of time reversal symmetry in the entangled neutral kaon system at a ϕ-factory
José Bernabéu, A Di Domenico, Pablo Villanueva-Perez
(2013) Nuclear Physics B, 868 p.102-119
ArticleConsistent probabilistic description of the neutral Kaon system
J. Bernabéu, N.E. Mavromatos, P. Villanueva-pérez
(2013) Physics Letters B, 724 p.269-273
ArticleObservation of time-reversal violation in the B 0 meson system
JP Lees, V Poireau, V Tisserand, J Garra Tico, E Grauges, et al.
(2012) Physical Review Letters, 109 p.211801
ArticleTime reversal violation from the entangled B°B° system
J Bernabeu, F Martinez-Vidal, P Villanueva-Perez
(2012) Journal of High Energy Physics, 2012 p.64
Article
PhD supervision
Main Supervisor
- Yuhe, Zhang
- Zisheng Yao
- Runqing Wang
- Julia Katherina Rogalinski
Second Supervisor
- Lars Witte (ETHZ)
- Hanna, Dierks
- Huaiyu, Chen
Postoctoral researchers
- Eleni Myrto Asimakopoulou
- Zhe Hu
Visiting researchers
- Kannara Mom
Undergraduate students
- Johannes Holst (MSc)
- Claire Brumat (BSc)
- Fredrik Olofsson (MSc)
- Maria Esther Vilar Alvarez (BSc)
- Johannes, Stubbe (MSc)
- Khachiwan, Buakor (MSc)
Financing
- European Research Council, ERC, Starting Grant 3DX-FLASH, 948426.
- European Innovation Council, EIC, HORIZON-EIC-2021-PATHFINDEROPEN-01-01, MHz–TOMOSCOPY, 101046448.
- SNF project grant 4DIAM, together with PSI (M. G. Makowska) and ETHZ (M. Baumbach and M. Afrasiabi).
- Röntgen-Ångström Cluster grant HASTE, together with DESY (M. Lyubomirskiy), KIT (T. Sheppard), and MAX IV (M. Kahnt).
- Röntgen-Ångström Cluster grant INVISION, together with European XFEL (A. Mancuso and P. Vagovic), Helmhotz-Zentrum Berlin (F. Garcia-Moreno, J. Banhart), and LTH (S. Hall, R. Mokso).
- Crafoord


