A collaborative research group led by Hiroshi Daimon, a Specially Appointed Research Fellow at the Institute for Molecular Science, National Institutes of Natural Sciences, has realized an "atom-holography microscope" capable of directly observing three-dimensional atomic arrangements in nanoscale regions by combining the electron beam of a scanning electron microscope (SEM) with CoDELMA, a newly developed two-dimensional display-type analyzer.
Specifically, as shown in Figure 2, the sample is irradiated with the electron beam of a SEM. The newly developed two-dimensional display-type analyzer CoDELMA focuses all electrons emitted from the sample over a wide angular range of ±50° onto the entrance of an energy analyzer. It then selects and extracts only electrons of a particular energy and uses a projection lens to measure their angular distribution simultaneously. Because the resulting angular-distribution pattern is a hologram, computer-based holographic reconstruction can be used to derive the three-dimensional atomic arrangement around atoms of the element of interest.
The results of this study were published online in the international scientific journal Review of Scientific Instruments on July 24, 2026.
1. Background
Information on three-dimensional atomic arrangements in nanoscale regions is essential for the development of nanoscale devices and novel functional materials. Until now, however, the only available approach was to prepare a thin section containing the region of interest and observe it using a transmission electron microscope. Moreover, the atomic images obtained in this way were only two-dimensional projections.
Atomic-resolution holography(2), which our group has developed in recent years, is a powerful research technique that enables element-specific analysis of three-dimensional atomic structures not only in crystals but also around isolated atoms such as dopants. Its measurements, however, require synchrotron radiation(3). The long interval from submitting an application to conducting an actual measurement has prevented the technique from being used in ordinary research and development settings and has limited its widespread adoption.
If atomic-resolution holography could be performed using electron-beam excitation, it would become possible to conduct such measurements anywhere without using synchrotron radiation. In addition, because an electron beam can easily be focused to a nanoscale spot, the atomic arrangements within nanoscale regions could be determined. Because no such instrument had previously existed, this study aimed to develop a new measurement instrument capable of performing atomic-resolution holography using electron-beam excitation.
2. Research Findings
A Bi2Se3 crystal was placed at the sample position shown in Figure 2 and irradiated with the nanoscale electron beam of a compact SEM. Only Kikuchi electrons(4) were selected using the energy analyzer, and their angular distribution was displayed on a screen. Figure 3(a) shows the three-dimensional atomic arrangement obtained by holographically reconstructing the resulting Kikuchi-electron hologram--the hologram shown in Figure 1. A four-layer structure labeled B1, S, B2, and B3 can be observed. These atoms represent the three-dimensional atomic arrangement around a Bi atom within the Bi2Se3 crystal structure shown in Figures 3(d) and 3(e). Figure 3(b) is a yz cross-sectional view of Figure 3(a). The z coordinates of the atoms in the B1, S, B2, and B3 layers are found to be 4.0, 4.6, 5.9, and 9.9 Å, respectively. These values agree, within an error of approximately 0.1 Å, with the literature values of 3.89, 4.51, 6.08, and 9.97 Å. Figure 3(c) is an xy cross-sectional view through the B3 plane. The in-plane xy positions of the atoms in the B3 plane correspond to position C in the top view shown in Figure 3(e). These results demonstrate that the three-dimensional atomic arrangement around a Bi atom, which has high scattering power, can be reproduced with an accuracy of approximately 0.1 Å.
3. Future Prospects and Societal Significance
This instrument does not require synchrotron radiation and can perform measurements simply by irradiating a sample with the nanoscale electron beam of a widely available SEM. This work has therefore realized a microscope--an atom-holography microscope--that can measure three-dimensional atomic arrangements in nanoscale regions anytime and anywhere. The instrument greatly expands the possibility of obtaining local atomic-arrangement information in ordinary laboratories and development settings, whereas such information was previously difficult to acquire outside large-scale facilities. Future applications are expected in the analysis and development of nanoscale devices and novel functional materials.
4. Glossary
(1) Holography and holograms
An object is illuminated with highly coherent light, known as a reference wave. The pattern produced by interference between the object wave scattered from the object and the reference wave is called a hologram. Holography is a technique in which a directly viewable three-dimensional image of the object is reconstructed simply by illuminating the hologram with the reference wave. Because holograms cannot be reproduced using ordinary printing techniques, they are used as anti-counterfeiting features on banknotes and credit cards.
(2) Atomic-resolution holography
When an atom is irradiated with X-rays, photoelectrons or fluorescent X-rays are emitted from the atom and propagate outward as spherical waves. As this direct wave propagates, it is scattered by surrounding atoms, producing scattered spherical waves centered on the scattering atoms. In the far field, the direct and scattered waves interfere with one another, producing an interference pattern that serves as a hologram. When atomic images are reconstructed from this hologram, the reconstruction is performed computationally because the atoms cannot be seen with the naked eye.
(3) Synchrotron radiation
Synchrotron radiation is extremely intense, highly directional light emitted when the trajectories of charged particles, such as electrons accelerated to nearly the speed of light, are bent by a magnetic field. It covers a broad range of wavelengths, from infrared light to X-rays. There are 11 large-scale synchrotron radiation facilities throughout Japan, and prospective users may apply for access to them.
(4) Kikuchi electrons
When electrons strike a crystal, some lose a small amount of energy through collisions with atoms and are scattered from those atoms. As these electrons propagate, they are further scattered by the ordered arrangement of atoms in the crystal, producing band-like or line-like patterns. Because Dr. Seishi Kikuchi discovered this phenomenon in 1928, the resulting pattern is called a Kikuchi pattern, and its bands are called Kikuchi bands. The electrons that produce the pattern are called Kikuchi electrons.
5. Publication Information
Journal: Review of Scientific Instruments
Article title: "Realizing an Atom-Holography Microscope"
Authors: Hiroshi Daimon, Hiroki Momono, Hiroyuki Matsuda, Fumihiko Matsui, Akiko Kubota, Kaho Hirano, Shinako Iki, Yu Masuda, Koichi Moriguchi, Keiko Ogai, Yusuke Hashimoto, and Tomohiro Matsushita
Publication date: July 24, 2026 (published online)
DOI: 10.1063/5.0331644
6. Research Team
- Institute for Molecular Science, National Institutes of Natural Sciences (Hiroshi Daimon, Hiroyuki Matsuda, Fumihiko Matsui, Akiko Kubota, Kaho Hirano, and Shinako Iki)
- National Institute of Technology, Yonago College (Hiroki Momono)
- SOKENDAI, The Graduate University for Advanced Studies (Fumihiko Matsui, concurrent appointment)
- APCO Co., Ltd. (Yu Masuda, Koichi Moriguchi, and Keiko Ogai)
- Nara Institute of Science and Technology (Yusuke Hashimoto and Tomohiro Matsushita)
