Electron-beam (e-beam) irradiation damage is often regarded as a severe limitation to atomic-scale study of two-dimensional (2D) materials using electron microscopy techniques. However, energy transferred from the e-beam can also provide a way to modify 2D materials via defect engineering when the interaction of the beam with the sample is precisely controlled. In this article, we discuss the atomic geometry, formation mechanism, and properties of several types of structural defects, ranging from zero-dimensional point defects to extended domains, induced by an e-beam in a few representative 2D materials, including graphene, hexagonal boron nitride, transition-metal dichalcogenides, and phosphorene. We show that atomic as well as line defects and even novel nanostructures can be created and manipulated in 2D materials by an e-beam in a controllable manner. Phase transitions can also be induced. The e-beam in a (scanning) transmission electron microscope not only resolves the intrinsic atomic structure of materials with defects, but also provides new opportunities to modify the structure with subnanometer precision.

Beam damage is a major limitation in electron microscopy that becomes increasingly severe at higher resolution. One possible route to circumvent radiation damage, which forms the basis for single-particle electron microscopy and related techniques, is to distribute the dose over many identical copies of an object. For the acquisition of low-dose data, ideally no dose should be applied to the region of interest before the acquisition of data. We present an automated approach that can collect large amounts of data efficiently by acquiring images in a user-defined area-of-interest with atomic resolution. We demonstrate that the stage mechanics of the Nion UltraSTEM, combined with an intelligent algorithm to move the sample, allow the automated acquisition of atomically resolved images from micron-sized areas of a graphene substrate. Moving the sample stage automatically in a regular pattern over the area-of-interest enables the collection of data from pristine sample regions without exposing them to the electron beam before recording an image. Therefore, it is possible to obtain data with minimal dose (no prior exposure during focusing), which is only limited by the minimum signal needed for data processing. This enables us to minimize beam-induced damage in the sample and to acquire large data sets within a reasonable amount of time.

Recently, transmission electron microscopy (TEM) and related techniques have brought unique insights to graphene research, demonstrating remarkable flexibility in characterizations ranging from atomic ordering to charge distribution. Such TEM studies have helped advance areas including the understanding of graphene growth and the effects of defects and dopants on the mechanical and electrical properties of graphene. Electron microscopy has proved particularly useful in determining the structure of crystals and grain boundaries across six orders of magnitude—from the shapes, arrangements, and stacking sequences of grains to the atomic arrangements at grain boundaries. Meanwhile, graphene is becoming a promising two-dimensional laboratory bench for electron microscopy, for example, turning graphene into a medium for nanosculpting by transforming buckyballs into graphene and vice versa. Finally, graphene has been used as an ultrathin support membrane for TEM, enabling studies of the motion of single atoms, direct imaging of two-dimensional amorphous materials, and even formation of nano-aquaria for imaging bacteria or nanoparticles in liquid media. Rapid developments in the fields of both electron microscopy and graphene will continue to provide a rich ground for future insights.