We have been developing soft X-ray emission spectroscopy instrument for electron microscope, and it has been commercialized recently as a now tool to investigate chemical bonding state from an area observed in electron microscope. Here, the fundamental features of soft X-ray emission spectroscopy and a few results are presented.

Combination of scanning transmission electron microscopy and electron energy-loss spectroscopy can achieve atomic level spectroscopy. However, it is, in principle, difficult to extract the local information with atomic resolution in the truest sense due to the physically limited special resolution caused by delocalization of inelastic scattering. Here, we introduce recent high spatial resolution elemental and electronic structure analyses including the example of pure atomic resolution for transition metal oxide.

Crystal structure analysis using scanning transmission electron microscopy（STEM）is briefly reviewed. The various imaging techniques, such as bright field（BF）, annular BF（ABF）and annular dark-field（ADF）are presented. Recent progress in STEM imaging is also described.

To apply ultrafast time-resolved electron diffraction measurements for amorphous H₂O molecules, we developed a system to deposit H₂O molecules onto ultrathin silicon nitride substrates in time-resolved electron diffraction apparatus. The subtracted electron diffraction patterns before and after the ultraviolet photoexcitation represent O-H bond dissociation via multiphoton absorption and charge transfer, which trigger ionization and intermolecular disorder in the amorphous H₂O. The results obtained in the experiments illustrate light-matter and matter-matter interactions in amorphous H₂O molecules.

Since irradiation often induces atomic configurations far from the equilibrium state, knowledge of structural changes under radiation environments is of technological importance for controlling the physical properties of materials. In addition, the processing temperature for synthesizing materials can be significantly reduced by athermal processes of irradiation. In this article, we report electron-beam-induced crystallization processes of amorphous germanium-tin and alumina studied by transmission electron microscopy. In both cases, critical fluence and flux for inducing the crystallization became small with decreasing the accelerating voltage, suggesting that electron excitation processes play an important role for the amorphous-to-crystalline phase transformation.

Epitaxial graphene growth on SiC is the only technique to obtain wafer-scale single-orientation graphene directly on the insulating substrate. It is then suitable for electronics applications. Understanding the growth mechanism of graphene is necessary for obtaining high-quality graphene. In order to improve the electronic structure of graphene, interface engineering is important. Here, recent researches including the growth mechanism and the interface engineering, mainly revealed by electron microscopy are reviewed.

The electron cryo-microscopy is one of the most powerful techniques to elucidate biological molecular structure under nearly physiological condition. By single particle analysis, many three-dimensional structures of proteins and their complexes have been resolved at atomic resolutions. Furthermore, in situ molecular behaviours in cells and tissues have also been reported at nano-meter or sub-nanometer resolutions by electron tomography. I would here review current situations of electron cryo-microscopy and the principles of their analysis and so show its possibility.

Synchrotron radiation X-rays can be focused to 100 nm order in beam size taking advantage of its high brilliance and development of X-ray optical devices. We have been performing crystal quality assessment in high-spatial-resolution by X-ray diffraction using the focused X-rays. Our main target samples are single crystalline thin films grown on substrates, nano structure like super-lattice or semiconductor devices. We report the synchrotron nanobeam X-ray diffraction system at SPring-8 and typical recent results.