Scanning Electron Microscopy (SEM) is critical in nanotechnology, materials science, and biological imaging due to its high spatial resolution and depth of focus. Signal-to-noise ratio (SNR) is an essential parameter in SEM because it directly impacts the quality and interpretability of the images. SEM is widely used in various scientific disciplines, but its utility can be compromised by noise, which degrades image clarity. This review explores multiple aspects of the SEM imaging process, from the principal operation of SEM, sources of noise in SEM, methods for SNR measurement and estimations, to various aspects that affect the SNR measurement and approaches to enhance SNR, both from a hardware and software standpoint. We review traditional and emerging techniques, focusing on their applications, advantages, and limitations. The paper aims to provide a comprehensive understanding of SNR optimization in SEM for researchers and practitioners and to encourage further research in the field.

Adaptive physics-informed super-resolution diffusion is developed for non-invasive virtual diagnostics of the 6D phase space density of charged particle beams. An adaptive variational autoencoder (VAE) embeds initial beam condition images and scalar measurements to a low-dimensional latent space from which a 326 pixel 6D tensor representation of the beam's 6D phase space density is generated. Projecting from a 6D tensor generates physically consistent 2D projections. Physics-guided super-resolution diffusion transforms low-resolution images of the 6D density to high resolution 256x256 pixel images. Un-supervised adaptive latent space tuning enables tracking of time-varying beams without knowledge of time-varying initial conditions. The method is demonstrated with experimental data and multi-particle simulations at the HiRES UED. The general approach is applicable to a wide range of complex dynamic systems evolving in high-dimensional phase space. The method is shown to be robust to distribution shift without re-training.

Electron beam accelerators are essential in many scientific and technological fields. Their operation relies heavily on the stability and precision of the electron beam. Traditional diagnostic techniques encounter difficulties in addressing the complex and dynamic nature of electron beams. Particularly in the context of free-electron lasers (FELs), it is fundamentally impossible to measure the lasing-on and lasingoff electron power profiles for a single electron bunch. This is a crucial hurdle in the exact reconstruction of the photon pulse profile. To overcome this hurdle, we developed a machine learning model that predicts the temporal power profile of the electron bunch in the lasing-off regime using machine parameters that can be obtained when lasing is on. The model was statistically validated and showed superior predictions compared to the state-of-the-art batch calibrations. The work we present here is a critical element for a virtual pulse reconstruction diagnostic (VPRD) tool designed to reconstruct the power profile of individual photon pulses without requiring repeated measurements in the lasing-off regime. This promises to significantly enhance the diagnostic capabilities in FELs at large.

Sub-atomically focused electron beams in scanning transmission electron microscopes (STEMs) can induce a broad spectrum of chemical changes, including defect formation, reconfiguration of chemical bonds, and dopant insertion. Several groups have shown the feasibility of direct atomic manipulation via electron beam stimulation, which holds great promise for a number of downstream applications such as material design, solid-state quantum computers, and others (Jesse et al, 2018; Susi et al, 2017b; Dyck et al, 2017; Tripathi et al, 2018; Dyck et al, 2018). One of the challenges for advances in this space is that these types of atomic manipulation rely on manual control by highly-trained experts, which is expensive and slow. The ability to accurately automate this type of beam control could thereby result in tremendous impact on the feasibility of atomic manipulation for real use cases. A critical requirement for this automation is accurate estimation of the transition dynamics of atoms when stimulated by focused electron beams.

Optimization of accelerator performance parameters is limited by numerous trade-offs and finding the appropriate balance between optimization goals for an unknown system is challenging to achieve. Here we show that multi-objective Bayesian optimization can map the solution space of a laser wakefield accelerator in a very sample-efficient way. Using a Gaussian mixture model, we isolate contributions related to an electron bunch at a certain energy and we observe that there exists a wide range of Pareto-optimal solutions that trade beam energy versus charge at similar laser-to-beam efficiency. However, many applications such as light sources require particle beams at a certain target energy. Once such a constraint is introduced we observe a direct trade-off between energy spread and accelerator efficiency. We furthermore demonstrate how specific solutions can be exploited using \emph{a posteriori} scalarization of the objectives, thereby efficiently splitting the exploration and exploitation phases.

We pose that microscopy offers an ideal real-world experimental environment for the development and deployment of active Bayesian and reinforcement learning methods. Indeed, the tremendous progress achieved by machine learning (ML) and artificial intelligence over the last decade has been largely achieved via the utilization of static data sets, from the paradigmatic MNIST to the bespoke corpora of text and image data used to train large models such as GPT3, DALLE and others. However, it is now recognized that continuous, minute improvements to state-of-the-art do not necessarily translate to advances in real-world applications. We argue that a promising pathway for the development of ML methods is via the route of domain-specific deployable algorithms in areas such as electron and scanning probe microscopy and chemical imaging. This will benefit both fundamental physical studies and serve as a test bed for more complex autonomous systems such as robotics and manufacturing. Favorable environment characteristics of scanning and electron microscopy include low risk, extensive availability of domain-specific priors and rewards, relatively small effects of exogeneous variables, and often the presence of both upstream first principles as well as downstream learnable physical models for both statics and dynamics. Recent developments in programmable interfaces, edge computing, and access to APIs facilitating microscope control, all render the deployment of ML codes on operational microscopes straightforward. We discuss these considerations and hope that these arguments will lead to creating a novel set of development targets for the ML community by accelerating both real-world ML applications and scientific progress.

Since the early 1930s, electron microscopy has provided unprecedented access to the world of the extraordinarily small, revealing intricate details that are otherwise impossible to discern with conventional light microscopy. But to achieve high resolution over a large sample area, the energy of the electron beams needs to be cranked up, which is costly and detrimental to the sample under observation. Texas A&M University researchers may have found a new method to improve the quality of low-resolution electron micrographs without compromising the integrity of samples. By training deep neural networks on pairs of images from the same sample but at different physical resolutions, they have found that details in lower-resolution images can be enhanced further. "Normally, a high-energy electron beam is passed through the sample at locations where greater image resolution is desired. But with our image processing techniques, we can super-resolve an entire image by using just a few smaller-sized, high-resolution images," said Yu Ding, Professor in the Department of Industrial and Systems Engineering.

Machine learning has been used by scientists in the US to reduce unwanted fluctuations in photon beams from a synchrotron light source. The technique does this by stabilizing the synchrotron's electron beam and offers a way around an important barrier to the development of next-generation facilities. The work was done by Simon Leemann and colleagues at the Lawrence Berkeley National Laboratory (LBNL) in California and could allow emerging analysis techniques that require high beam stability – such as X-ray photon correlation spectroscopy (XPCS) – to be implemented on synchrotons. Synchrotron light sources are extremely useful scientific instruments because they deliver bright, high-quality beams of coherent electromagnetic radiation from infrared wavelengths up to soft X-rays. The light is produced by accelerating electrons in a storage ring using powerful magnets – taking advantage of the fact that an accelerated electron emits electromagnetic radiation.

Synchrotron light sources are powerful facilities that produce light in a variety of "colors," or wavelengths--from the infrared to X-rays--by accelerating electrons to emit light in controlled beams. Synchrotrons like the Advanced Light Source at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) allow scientists to explore samples in a variety of ways using this light, in fields ranging from materials science, biology, and chemistry to physics and environmental science. Researchers have found ways to upgrade these machines to produce more intense, focused, and consistent light beams that enable new, and more complex and detailed studies across a broad range of sample types. Many of these synchrotron facilities deliver different types of light for dozens of simultaneous experiments. And little tweaks to enhance light-beam properties at these individual beamlines can feed back into the overall light-beam performance across the entire facility.

This image shows the profile of an electron beam at Berkeley Lab's Advanced Light Source synchrotron, represented as pixels measured by a charged coupled device (CCD) sensor. When stabilized by a machine-learning algorithm, the beam has a horizontal size dimension of 49 microns (root mean squared) and vertical size dimension of 48 microns (root mean squared). Demanding experiments require that the corresponding light-beam size be stable on time scales ranging from less than seconds to hours to ensure reliable data. Synchrotron light sources are powerful facilities that produce light in a variety of "colors," or wavelengths – from the infrared to X-rays – by accelerating electrons to emit light in controlled beams. Synchrotrons like the Advanced Light Source at the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) allow scientists to explore samples in a variety of ways using this light, in fields ranging from materials science, biology, and chemistry to physics and environmental science.