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The development, construction, and first commissioning results of a new scanning microscope installed at the 5‐ID Submicron Resolution X‐ray Spectroscopy (SRX) beamline at NSLS‐II are reported. The developed system utilizes Kirkpatrick–Baez mirrors for X‐ray focusing. The instrument is designed to enable spectromicroscopy measurements in 2D and 3D with sub‐200 nm spatial resolution. The present paper focuses on the design aspects, optical considerations, and specifics of the sample scanning stage, summarizing some of the initial commissioning results. The development and initial commissioning of a new Kirkpatrick–Baez‐based scanning microscope installed at the Submicron Resolution X‐ray Spectroscopy beamline at NSLS‐II are reported.

Scientific imaging represents an important and accepted research tool for the analysis and understanding of complex natural systems. Apart from traditional microscopic techniques such as light and electron microscopy, new advanced techniques have been established including laser scanning microscopy (LSM), magnetic resonance imaging (MRI) and scanning transmission X-ray microscopy (STXM). These new techniques allow in situ analysis of the structure, composition, processes and dynamics of microbial communities. The three techniques open up quantitative analytical imaging possibilities that were, until a few years ago, impossible. The microscopic techniques represent powerful tools for examination of mixed environmental microbial communities usually encountered in the form of aggregates and films. As a consequence, LSM, MRI and STXM are being used in order to study complex microbial biofilm systems. This mini review provides a short outline of the more recent applications with the intention to stimulate new research and imaging approaches in microbiology.

Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries 1 and electrocatalysts 2 . Experimental characterizations of such materials by operando microscopy produce rich image datasets 3 – 6 , but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation 7 . Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces. Analysis of a large dataset of scanning transmission X-ray microscopy images of carbon-coated lithium iron phosphate nanoparticles shows that the heterogeneous reaction kinetics of battery materials can be learned from such videos pixel by pixel.

Atmospheric ice nucleation impacts the hydrological cycle and climate by modifying the radiative properties of clouds. To improve our predictive understanding of ice formation, ambient ice-nucleating particles (INPs) need to be collected and characterized. Measurements of INPs at lower latitudes in a remote marine region are scarce. The Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) campaign, in the region of the Azores islands, provided the opportunity to collect particles in the marine boundary layer (MBL) and free troposphere (FT) by aircraft during the campaign's summer and winter intensive operation period. The particle population in samples collected was examined by scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy. The identified INPs were analyzed by scanning electron microscopy with energy-dispersive X-ray analysis. We observed differences in the particle population characteristics in terms of particle diversity, mixing state, and organic volume fraction between seasons, mostly due to dry intrusion events during winter, as well as between the sampling locations of the MBL and FT. These differences are also reflected in the temperature and humidity conditions under which water uptake, immersion freezing (IMF), and deposition ice nucleation (DIN) proceed. Identified INPs reflect typical particle types within the particle population on the samples and include sea salt, sea salt with sulfates, and mineral dust, all associated with organic matter, as well as carbonaceous particles. IMF and DIN kinetics are analyzed with respect to heterogeneous ice nucleation rate coefficients, Jhet, and ice nucleation active site density, ns, as a function of the water criterion Δaw. DIN is also analyzed in terms of contact angles following classical nucleation theory. Derived MBL IMF kinetics agree with previous ACE-ENA ground-site INP measurements. FT particle samples show greater ice nucleation propensity compared to MBL particle samples. This study emphasizes that the types of INPs can vary seasonally and with altitude depending on sampling location, thereby showing different ice nucleation propensities, which is crucial information when representing mixed-phase cloud and cirrus cloud microphysics in models.

Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nanometer range and strong contrast for membranous structures without requiring labeling or chemical fixation. The short acquisition time and the relatively large field of view leads to fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D segmentation pipeline based on semisupervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells.

Formation of atmospheric ice plays a crucial role in the microphysical evolution of mixed-phase and cirrus clouds and thus climate. How aerosol particles impact ice crystal formation by acting as ice-nucleating particles (INPs) is a subject of intense research activities. To improve understanding of atmospheric INPs, we examined daytime and nighttime particles collected during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign conducted in summer 2017. Collected particles, representative of a remote marine environment, were investigated for their propensity to serve as INPs in the immersion freezing (IMF) and deposition ice nucleation (DIN) modes. The particle population was characterized by chemical imaging techniques such as computer-controlled scanning electron microscopy with energy-dispersive X-ray analysis (CCSEM/EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine-structure spectroscopy (STXM/NEXAFS). Four major particle-type classes were identified where internally mixed inorganic–organic particles make up the majority of the analyzed particles. Following ice nucleation experiments, individual INPs were identified and characterized by SEM/EDX. The identified INP types belong to the major particle-type classes consisting of fresh sea salt with organics or processed sea salt containing dust and sulfur with organics. Ice nucleation experiments show IMF events at temperatures as low as 231 K, including the subsaturated regime. DIN events were observed at lower temperatures of 210 to 231 K. IMF and DIN observations were analyzed with regard to activated INP fraction, ice-nucleation active site (INAS) densities, and a water activity-based immersion freezing model (ABIFM) yielding heterogeneous ice nucleation rate coefficients. Observed IMF and DIN events of ice formation and corresponding derived freezing rates demonstrate that the marine boundary layer aerosol particles can serve as INPs under typical mixed-phase and cirrus cloud conditions. The derived IMF and DIN parameterizations allow for implementation in cloud and climate models to evaluate predictive effects of atmospheric ice crystal formation.

Scanning fluorescence X‐ray microscopy is widely used for quantitative mapping of elemental concentrations, including in studies of essential but low‐concentration metals in cells, tissues, and organs. Practical studies often use a single incident photon energy to excite fluorescence from many elements. We present calculations of the number of incident photons per pixel required to detect a specified areal concentration of an element in the case of far‐from‐threshold excitation, along with the calculated radiation dose consequently imparted in a simple model tissue. We also show how certain approximations can lead to less accurate estimates. These calculations are not specific to one particular experiment, though we also provide a comparison with one experimental result. These results can be used to guide experimental planning for studies of the role of low‐concentration elements in biological tissues. We present calculations on the number of illuminating photons per pixel required for elemental detection using X‐ray fluorescence, even with far‐from‐threshold excitation.

Determining the particle chemical morphology is crucial for unraveling reactive uptake in atmospheric multiphase and heterogeneous chemistry. However, it remains challenging due to the complexity and inhomogeneity of aerosol particles. Using a scanning transmission X-ray microscopy (STXM) coupled with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and an environmental cell, we imaged and quantified the chemical morphology and hygroscopic behavior of individual submicron urban aerosol particles. Results show that internally mixed particles composed of organic carbon and inorganic matter (OCIn) dominated the particle population (73.1±7.4 %). At 86 % relative humidity, 41.6 % of the particles took up water, with OCIn particles constituting 76.8 % of these hygroscopic particles. Most particles exhibited a core-shell structure under both dry and humid conditions, with an inorganic core and an organic shell. Our findings provide direct observational evidence of the core-shell structure and water uptake behavior of typical urban aerosols, which underscore the importance of incorporating the core-shell structure into models for predicting the reactive uptake coefficient of heterogeneous reactions.

Atmospheric deposition is one of the main sources of dissolved iron (Fe) in the ocean surfaces. Atmospheric processes are recognized as controlling fractional Fe solubility (Fesol%) in marine aerosol particles. However, the impact of these processes on Fesol% remains unclear. One of the reasons for this is the lack of field observations focusing on the relationship between Fesol% and Fe species in marine aerosol particles. In particular, the effects of organic ligands on Fesol% have not been thoroughly investigated in observational studies. In this study, Fe species in size-fractionated aerosol particles in the Pacific Ocean were determined using X-ray absorption fine structure (XAFS) spectroscopy. The internal mixing states of Fe and organic carbon were investigated using scanning transmission X-ray microscopy (STXM). The effects of atmospheric processes on Fesol% in marine aerosol particles were investigated based on the speciation results. Iron in size-fractionated aerosol particles was mainly derived from mineral dust, regardless of aerosol diameter, because the enrichment factor of Fe was almost 1 in both coarse (PM>1.3) and fine aerosol particles (PM1.3). Approximately 80 % of the total Fe (insoluble + labile Fe) was present in PM>1.3, whereas labile Fe was mainly present in PM1.3. The Fesol% in PM>1.3 was not significantly increased (2.56±2.53 %, 0.00 %–8.50 %, n=20) by the atmospheric processes because mineral dust was not acidified beyond the buffer capacity of calcite. In contrast, mineral dust in PM1.3 was acidified beyond the buffer capacity of calcite. As a result, Fesol% in PM1.3 (0.202 %–64.7 %, n=10) was an order of magnitude higher than that in PM>1.3. The PM1.3 contained ferric organic complexes with humic-like substances (Fe(III)-HULIS, but not Fe-oxalate complexes), and the abundance correlated with Fesol%. Iron(III)-HULIS was formed during transport in the Pacific Ocean because Fe(III)-HULIS was not found in aerosol particles in Beijing and Japan. The pH estimations of mineral dust in PM1.3 established that Fe was solubilized by proton-promoted dissolution under highly acidic conditions (pH < 3.0), whereas Fe(III)-HULIS was stabilized under moderately acidic conditions (pH 3.0–6.0). Since the observed labile Fe concentration could not be reproduced by proton-promoted dissolution under moderately acidic conditions, the pH of mineral dust increased after proton-promoted dissolution. The cloud process in the marine atmosphere increases the mineral dust pH because the dust particles are covered with organic carbon and Na. The precipitation of ferrihydrite was suppressed by Fe(III)-HULIS owing to its high water solubility. Thus, the organic complexation of Fe with HULIS plays a significant role in the stabilization of Fe that was initially solubilized by proton-promoted dissolution.