- Address
- 305-0047 1-2-1 Sengen Tsukuba Ibaraki JAPAN [Access]
Accepting Students
Research
- Keywords
Electron Microscopy, Electron Energy-Loss Spectroscopy, Material Characterization
- Material evaluation using transmission electron microscopy (TEM), scanning transmission electron microscopy (STEM), and electron energy-loss spectroscopy (EELS). - Automated measurement and analysis of STEM/TEM/EELS using scripting with DigitalMicrograph (Gatan Inc.). - Unsupervised machine learning techniques for advanced electron microscopy (e.g., 4D-STEM).
PublicationsNIMS affiliated publications since 2004.
Research papers
- 木本浩司. 走査透過電子顕微鏡および電子エネルギー損失分光法による材料評価. Transactions of the Atomic Energy Society of Japan. (2019) 36-39
- 八島 正知, 林 克郎, 木本 浩司. 複合アニオン化合物の構造解析. 日本結晶学会誌. 60 [5-6] (2018) 254-259 10.5940/jcrsj.60.254 Open Access
- IROKAWA, Yoshihiro, MITSUISHI, Kazutaka, NABATAME, Toshihide, KIMOTO, Koji, KOIDE, Yasuo. Investigation of intermediate layers in oxides/GaN(0001) by electron microscopy. JAPANESE JOURNAL OF APPLIED PHYSICS. 57 [11] (2018)
Books
- 木本 浩司. 走査透過電子顕微鏡の観察法. 表面分析技術選書 透過電子顕微鏡 第2版 日本表面真空学会編. 丸善出版, 2026, 32.
- 木本 浩司, 三石 和貴, 三留 正則, 原 徹, 長井 拓郎. 物質・材料研究のための透過電子顕微鏡. 講談社, 2020, 400.
- Koji Kimoto. Scanning Transmission Electron Microscopy. Compendium of Surface and Interface Analysis. , 2018, 587-592. 10.1007/978-981-10-6156-1_95
Proceedings
- 木本浩司. 電子エネルギー損失分光法入門. 分析電子顕微鏡討論会予稿集. (2014) 7-12
- 木本浩司. 電子エネルギー損失分光法 (EELS)入門 計測と解析に役立つ基礎知識. 第24回電子顕微鏡大学講義テキスト. (2014) 119-138
- Masaaki Isobe, Koji Kimoto, Masao Arai, Taras Kolodiazhnyi, Yasushi Kanke, Eiji Takayama-Muromachi. BaIrSi2: A 5d Electron System Superconductor with a New Type of Noncentrosymmetric Crystal Structure. JPS Conference Proceedings. (2020) 011179 10.7566/jpscp.30.011179
Presentations
- Biplab Manna, CRETU, Ovidiu, SAITO, Noriko, Haruaki Suzuki, KIMOTO, Koji, HARANO, Koji. From fragile to rigid: in situ secondary building unit reorganization in metal–organic frameworks. 錯体化学Kyoto国際会議 (CCC Kyoto). 2026
- HARANO, Koji, KIMOTO, Koji. Single-molecule electron microscopy imaging and analysis through molecular isolation in nanospaces. The 21st International Microscopy Congress (IMC21). 2026
- HARANO, Koji, KIMOTO, Koji, Hao Wu, Klaus Müllen, Akimitsu Narita. Single-molecule Transmission Electron Microscopy Imaging of Laterally π-extended Polyhelicenes. Microscopy & Microanalysis 2026. 2026
Misc
- 木本 浩司. 電子エネルギー損失分光法(EELS)入門 Q&A. 第29回電子顕微鏡大学Q&A集. (2019) 70-76
- 平山 司, 木本 浩司. 特集にあたって. Microscopy. (2019) 2
- 木本浩司. 電子エネルギー損失分光法 (EELS)入門 -計測と解析に役立つ基礎知識-. 電子顕微鏡大学テキスト. (2015) 143-164
Published patent applications
- ステレオ温度波測定装置及び方法 (2025)
- 温度波の動的可視化装置及び方法 (2024)
- 微小熱伝導率測定装置及び測定方法 (2024)
Society memberships
日本顕微鏡学会
Awards
- 日本電子顕微鏡学会 論文賞 (1991),応用物理学会賞B(奨励賞) (1997),日本電子顕微鏡学会 奨励賞 (2001),日本電子顕微鏡学会 瀬藤賞/学会賞 (2008),文部科学大臣表彰 科学技術賞(研究部門)(2009) ()
Center for Basic Research on Materials
Development and Application of Transmission Electron Microscopy for Materials Characterization
Transmission Electron Microscopy (TEM), Scanning Transmission Electron Microscopy (STEM), Electron Energy-Loss Spectroscopy (EELS), 4D-STEM, Monochromator, Scripting
Overview
Advanced transmission electron microscopy (TEM) allows for various microstructural analyses, such as atomic imaging, crystallographic diffractometry, and elemental analysis. The development of spherical aberration correctors, monochromators, and high-sensitivity detectors has made it possible to evaluate and analyze samples at the atomic level. We have developed TEM techniques for high-precision and high-sensitivity measurements, as well as data analysis methods. Using STEM-EELS, we have successfully observed atomic arrangements for individual elements, single-atom dopants, and atomic displacements on the picometer scale. We are pioneering analyses that incorporate knowledge of electron diffraction by combining 4D-STEM with unsupervised machine learning. By combining these various TEM techniques to evaluate microstructures with unique physical properties and superior performance, we aim to strengthen innovation in materials science.
Novelty and originality
● High-precision, high-sensitivity, and quantitative structural analysis using advanced STEM imaging with custom software. In particular, this technique enables the detection of dopants, the observation of atomic defects, and the analysis of atomic positions with picometer precision. Additionally, it supports low-acceleration, high-resolution TEM and high-energy-resolution, high-spatial-resolution STEM using a monochromator.
● Combination of 4D-STEM and unsupervised machine learning custom software (e.g., non-negative matrix factorization). Development of automated measurement using DigitalMicorgraph (Gatan Inc.) scripts.
Details

High-Resolution, High-Sensitivity Crystal Structure Observation Using STEM:
We used STEM to observe the crystal sites occupied by single-atom dopants in Eu-doped SiAlON phosphors synthesized by Hirosaki et al. at NIMS. Although these atoms cannot be detected in conventional TEM images, Eu atoms are visible in high signal-to-noise ratio (SNR) images obtained through multiple measurements using annular dark-field (ADF) imaging. Through simulation-based analysis, we also identified the TEM sample thickness and imaging conditions, thereby determining the positions of the single-atom Eu dopants.
Quantitative measurement of ADF images provides information regarding atomic number Z. We found that as Z increases and the acceleration voltage decreases, the relationship deviates from the so-called power law for Z. By performing quantitative comparisons with simulations, it is also possible to identify atoms in ADF images.

Microstructural Analysis Using 4D-STEM and Machine Learning:
The technique of acquiring a large number of diffraction patterns while scanning the STEM probe is called 4D-STEM. We first observed atomic resolution in 2011. In 2021, we were the first to combine non-negative matrix factorization (NMF), a machine learning technique, with 4D-STEM. Furthermore, we independently developed a clustering method based on the similarity of diffraction patterns and used it to analyze the nanosized crystalline structures precipitated in metallic glasses through heat treatment (2024). Using these methods, we have also succeeded in polarity mapping of single-layer MoS₂ (2025). Some of our scripts for DigitalMicrograph (Gatan Inc.) are available on our group’s website and on GitHub.
Summary
We can analyze atomic structures with high precision and sensitivity using STEM, TEM, and EELS techniques with custom software, including machine learning.
We can analyze dopants, defects, and variations in atomic positions at the picometer level with atomic resolution.
Combining various TEM measurement techniques allows us to solve materials development problems and gain new insights.

