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Skyrmions are nanoscale spin textures that are viewed as promising candidates as information carriers in future spintronic devices 1 , 2 , 3 . Skyrmions have been observed using neutron scattering 4 , 5 and microscopy techniques 6 , 7 , 8 , 9 , 10 , 11 . Real-space imaging using electrons is a straightforward way to interpret spin configurations by detecting the phase shifts due to electromagnetic fields. Here, we report the first observation by electron holography of the magnetic flux and the three-dimensional spin configuration of a skyrmion lattice in Fe 0.5 Co 0.5 Si thin samples. The magnetic flux inside and outside a skyrmion was directly visualized and the handedness of the magnetic flux flow was found to be dependent on the direction of the applied magnetic field. The electron phase shifts φ in the helical and skyrmion phases were determined using samples with a stepped thickness t (from 55 nm to 510 nm), revealing a linear relationship ( φ  = 0.00173 t ). The phase measurements were used to estimate the three-dimensional structures of both the helical and skyrmion phases, demonstrating that electron holography is a useful tool for studying complex magnetic structures and for three-dimensional, real-space mapping of magnetic fields 12 . Electron holography is used to visualize the three-dimensional structure of a skyrmion lattice and the magnetic flux inside and outside a skyrmion.

Atomic-scale observations of a specific local area would be considerably beneficial when exploring new fundamental materials and devices. The development of hardware-type aberration correction 1 , 2 in electron microscopy has enabled local structural observations with atomic resolution 3 – 5 as well as chemical and vibration analysis 6 – 8 . In magnetic imaging, however, atomic-level spin configurations are analysed by electron energy-loss spectroscopy by placing samples in strong magnetic fields 9 – 11 , which destroy the nature of the magnetic ordering in the samples. Although magnetic-field-free observations can visualize the intrinsic magnetic fields of an antiferromagnet by unit-cell averaging 12 , directly observing the magnetic field of an individual atomic layer of a non-uniform structure is challenging. Here we report that the magnetic fields of an individual lattice plane inside materials with a non-uniform structure can be observed under magnetic-field-free conditions by electron holography with a hardware-type aberration corrector assisted by post-digital aberration correction. The magnetic phases of the net magnetic moments of (111) lattice planes formed by opposite spin orderings between Fe 3+ and Mo 5+ in a ferrimagnetic double-perovskite oxide (Ba 2 FeMoO 6 ) were successfully observed. This result opens the door to direct observations of the magnetic lattice in local areas, such as interfaces and grain boundaries, in many materials and devices. The magnetic fields of an individual lattice plane inside materials with a non-uniform structure were observed under magnetic-field-free conditions by electron holography.

It is well known that two DNA molecules are wrapped around histone octamers and folded together to form a single chromosome. However, the nucleosome fiber folding within a chromosome remains an enigma, and the higher-order structure of chromosomes also is not understood. In this study, we employed electron diffraction which provides a noninvasive analysis to characterize the internal structure of chromosomes. The results revealed the presence of structures with 100–200 nm periodic features directionally perpendicular to the chromosome axis in unlabeled isolated human chromosomes. We also visualized the 100–200 nm periodic features perpendicular to the chromosome axis in an isolated chromosome whose DNA molecules were specifically labeled with OsO4 using electron tomography in 300 keV and 1 MeV transmission electron microscopes.

In the samples collected from the asteroid Ryugu, magnetite displays natural remanent magnetization due to nebular magnetic field, whereas contemporaneously grown iron sulfide does not display stable remanent magnetization. To clarify this counterintuitive feature, we observed their nanoscale magnetic domain structures using electron holography and found that framboidal magnetites have an external magnetic field of 300 A m −1 , similar to the bulk value, and its magnetic stability was enhanced by interactions with neighboring magnetites, permitting a disk magnetic field to be recorded. Micrometer-sized pyrrhotite showed a multidomain magnetic structure that was unable to retain natural remanent magnetization over a long time due to short relaxation time of magnetic-domain-wall movement, whereas submicron-sized sulfides formed a nonmagnetic phase. These results show that both magnetite and sulfide could have formed simultaneously during the aqueous alteration in the parent body of the asteroid Ryugu.

Extraterrestrial minerals on the surface of airless Solar System bodies undergo gradual alteration processes known as space weathering over long periods of time. The signatures of space weathering help us understand the phenomena occurring in the Solar System. However, meteorites rarely retain the signatures, making it impossible to study the space weathering processes precisely. Here, we examine samples retrieved from the asteroid Ryugu by the Hayabusa2 spacecraft and discover the presence of nonmagnetic framboids through electron holography measurements that can visualize magnetic flux. Magnetite particles, which normally provide a record of the nebular magnetic field, have lost their magnetic properties by reduction via a high-velocity (>5 km s –1 ) impact of a micrometeoroid with a diameter ranging from 2 to 20 μm after destruction of the parent body of Ryugu. Around these particles, thousands of metallic-iron nanoparticles with a vortex magnetic domain structure, which could have recorded a magnetic field in the impact event, are found. Through measuring the remanent magnetization of the iron nanoparticles, future studies are expected to elucidate the nature of the nebular/interplanetary magnetic fields after the termination of aqueous alteration in an asteroid. Electron holography discovered nonmagnetic framboids and many iron nanoparticles with a vortex magnetic flux formed by magnetite reduction due to a micrometeoroid impact on asteroid Ryugu, providing a new way to study the Solar System magnetic field.