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  • Primer
  • Published:

Ptychography at all wavelengths

Nature Reviews Methods Primers volume 5, Article number: 68 (2025) Cite this article

Subjects

Abstract

Ptychography is a computational imaging technique that operates across multiple wavelength regimes, from electron (picometres) to X-ray (~0.1 nm), extreme ultraviolet (~10 nm) and visible light (micrometres). By reconstructing both amplitude and phase from diffraction patterns, ptychography enables high-resolution, quantitative imaging without conventional limitations imposed by lens-based optics. Ptychography has enabled advances across a range of scales: achieving deep-sub-angstrom resolution with electron microscopy, becoming an indispensable tool at X-ray synchrotron facilities worldwide and overcoming the trade-offs between resolution and field-of-view in optical imaging. This Primer provides a unified treatment of ptychography across these wavelength regimes. First, we discuss theoretical foundations, reconstruction algorithms, experimental considerations and wavelength-specific challenges. We then give examples of raw and processed data from various configurations and wavelengths. Next, we highlight key applications of ptychography in life sciences, materials science and industry. We also discuss data standards, open-source software implementations and best practices for ensuring reproducibility across different wavelength regimes. Finally, we consider limitations and future opportunities for ptychography. Together with accompanying datasets and code implementations, this Primer aims to serve newcomers and experienced practitioners in the field, facilitating broader adoption of ptychography across different disciplines.

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Fig. 1: Principle and implementation of conventional ptychography.
Fig. 2: Experimental configurations for ptychography.
Fig. 3: Advanced ptychography strategies.
Fig. 4: Data acquisition and reconstruction in optical ptychography.
Fig. 5: EUV ptychography with tabletop high-harmonic generation.
Fig. 6: Data acquisition and reconstruction in X-ray ptychography.
Fig. 7: Data acquisition and reconstruction in electron ptychography.
Fig. 8: Life science applications.
Fig. 9: Materials science and industrial applications.

Data availability

The experimental datasets that accompany the code implementations in the Supplementary Information are available via Figshare at https://doi.org/10.6084/m9.figshare.29205677 (ref. 207).

Code availability

To support educational efforts and research accessibility, the Supplementary Information provides simplified MATLAB codes accompanied by experimental datasets spanning the four wavelength regimes discussed in this review. These implementations are designed to illustrate core ptychographic concepts without the complexity of production-level software, serving as bridges between theoretical understanding and practical application.

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Acknowledgements

This work was partially supported by the National Institutes of Health (grant no. R01-EB034744), the UConn SPARK grant and Department of Energy (grant no. SC0025582). Q.Z. acknowledges the support of the UConn GE Fellowship.

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Author notes

  1. These authors contributed equally: Ruihai Wang, Qianhao Zhao.

Authors and Affiliations

  1. Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA

    Ruihai Wang, Qianhao Zhao, Zhixuan Hong & Guoan Zheng

  2. ZEISS Research Microscopy Solutions, Jena, Germany

    Lars Loetgering

  3. Diamond Light Source, Harwell, UK

    Frederick Allars & Andrew Maiden

  4. Electron Microscopy for Materials Science, University of Antwerp, Antwerpen, Belgium

    Timothy J. Pennycook

  5. Department of Biomedical Engineering, Duke University, Durham, NC, USA

    Roarke Horstmeyer

  6. Department of Electronic and Electrical Engineering, University of Sheffield, Sheffield, UK

    John Rodenburg & Andrew Maiden

Authors
  1. Ruihai Wang
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  2. Qianhao Zhao
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  3. Lars Loetgering
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  4. Frederick Allars
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  5. Zhixuan Hong
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  6. Timothy J. Pennycook
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  7. Roarke Horstmeyer
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  10. Guoan Zheng
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Contributions

Introduction (G.Z., R.W., Q.Z. and A.M.); Experimentation (G.Z., R.W., Q.Z., L.L., F.A., T.J.P., R.H., J.R. and A.M.); Results (G.Z., R.W., Q.Z., L.L., F.A., T.J.P., R.H., J.R. and A.M.); Applications (G.Z., R.W., Q.Z. and A.M.); Reproducibility and data deposition (G.Z., R.W., Q.Z., Z.H. and A.M.); Limitations and optimizations (G.Z., R.W., Q.Z. and A.M.); Outlook (G.Z., R.W., Q.Z. and A.M.).

Corresponding authors

Correspondence to Andrew Maiden or Guoan Zheng.

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Competing interests

J.R. is a co-founder of Phase Focus Ltd and is a named inventor on the following patents related to ptychography (US Patent, nos. 7792246, 9401042 and 9116120; WO Patent, nos. 2005/106531 and 2010/064051). A.M. is a named inventor on the following patents related to ptychography (US Patent, nos. 8942449, 10466184, 9202295, 9448160, 9401042, 9322791, 9274024, 9121764, 9087674 and 9086570; WO Patent, nos. 2014/033459, 2010/064051). R.H. is a named inventor on the following patents related to ptychography (US Patent, nos. 12237094, 10679763, 10652444, 10606055, 10419665, 10401609 and 10162161; WO Patent, no. 2014/070656). G.Z. is a named inventor on the following patents related to ptychography (US Patent, nos. 12237094, 11686933, 10679763, 10652444, 10606055, 10419665, 10401609 and 11487099; WO Patent, no. 2014/070656). The remaining authors declare no competing interests.

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Nature Reviews Methods Primers thanks Yukio Takahashi, Chao Zuo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Online tutorials: https://www.youtube.com/watch?v=9KJLWwbs_cQ

Supplementary information

Glossary

Bragg diffraction condition

The specific angle and wavelength combination at which crystal lattice reflections interfere constructively, enabling selective imaging of crystal orientations and strain.

Coherence

The degree to which different parts of a wavefield maintain fixed phase relationships.

Cost function

A mathematical metric quantifying the discrepancy between the measured and estimated diffraction patterns that algorithms minimize through iterative refinement.

Dose efficiency

The information extracted per unit of radiation damage, with ptychography achieving 10–100× improvement over conventional methods by using all of the scattered photons or electrons.

Ewald sphere

A spherical surface in reciprocal space that determines which spatial frequencies of an 3D object can be measured for a given illumination angle.

Ptychogram

A complete dataset of diffraction patterns captured at different scan positions.

Pupil function

The aperture function of an optical system, which limits what spatial frequencies pass through. In Fourier ptychography, it acts as the effective ‘probe’ by scanning through reciprocal space.

Real space

The physical coordinate system \((x,y)\) in which specimens exist.

Reciprocal space

Also known as Fourier space. The spatial frequency domain \(({k}_{x},{k}_{y})\) in which far-field diffraction patterns form.

Strain field

The spatial distribution of lattice distortions in crystalline materials, which affects properties such as carrier mobility in semiconductors.

Wavefield

The complete description of a wave containing both amplitude and phase information.

Wavevector

A vector pointing in the propagation direction of the wave. To observe fine details, waves must scatter at large angles, creating large transverse wavevector components.

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Wang, R., Zhao, Q., Loetgering, L. et al. Ptychography at all wavelengths. Nat Rev Methods Primers 5, 68 (2025). https://doi.org/10.1038/s43586-025-00438-3

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