Two methods are especially suited for tomographic imaging with histological detail of macroscopic samples that consist of multiple tissue types (bone, muscle, nerve or fat): Light sheet (based) fluorescence microscopy (LSFM) and micro-computed tomography (micro-CT). Micro-CT requires staining with heavy chemical elements (and thus fixation and sometimes dehydration) in order to make soft tissue imageable when measured alongside denser structures. LSMF requires fixation, decalcification, dehydration, clearing and staining with a fluorescent dye. The specimen preparation of both imaging methods is prone to shrinkage, which is often not mentioned, let alone quantified. In this paper the presence and degree of shrinkage are quantitatively identified for the selected preparation methods/stains. LSFM delivers a volume shrinkage of 17% for bone, 56% for muscle and 62% for brain tissue. The three most popular micro-CT stains (phosphotungstic acid, iodine with potassium iodide, and iodine in absolute ethanol) deliver a volume shrinkage ranging from 10 to 56% for muscle and 27–66% for brain, while bone does not shrink in micro-CT preparation.

A multicomponent Fe-Cu based steel is studied using atom-probe tomography. The precipitates are identified using two different methodologies and subsequent morphological and compositional results are compared. The precipitates are first identified using a maximum separation distance algorithm, the envelope method, and then by a concentration threshold method, an isoconcentration surface. We discuss in detail the proper selection of the parameters needed to delineate precipitates utilizing both methods. The results of the two methods exhibit a difference of 44 identified precipitates, which can be attributed to differences in the basis of both methods and the sensitivity of our results to user-prescribed parameters. The morphology of the precipitates, characterized by four different precipitate radii and precipitate size distribution functions (PSDs), are compared and evaluated. A variation of less than ∼8% is found between the different radii. Two types of concentration profiles are compared, giving qualitatively similar results. Both profiles show Cu-rich precipitates containing Fe with elevated concentrations of Ni, Al, and Mn near the heterophase interfaces. There are, however, quantitative disagreements due to differences in the basic foundations of the two analysis methods.

This review traces the development of X-ray mapping from its beginning 50 years ago through current analysis procedures that can reveal otherwise obscure elemental distributions and associations. X-ray mapping or compositional imaging of elemental distributions is one of the major capabilities of electron beam microanalysis because it frees the operator from the necessity of making decisions about which image features contain elements of interest. Elements in unexpected locations, or in unexpected association with other elements, may be found easily without operator bias as to where to locate the electron probe for data collection. X-ray mapping in the SEM or EPMA may be applied to bulk specimens at a spatial resolution of about 1 μm. X-ray mapping of thin specimens in the TEM or STEM may be accomplished at a spatial resolution ranging from 2 to 100 nm, depending on specimen thickness and the microscope. Although mapping has traditionally been considered a qualitative technique, recent developments demonstrate the quantitative capabilities of X-ray mapping techniques. Moreover, the long-desired ability to collect and store an entire spectrum at every pixel is now a reality, and methods for mining these data are rapidly being developed.

Observation of growth, synthesis, dynamics, and electrochemical reactions in the liquid state is an important yet largely unstudied aspect of nanotechnology. The only techniques that can potentially provide the insights necessary to advance our understanding of these mechanisms is simultaneous atomic-scale imaging and quantitative chemical analysis (through spectroscopy) under environmental conditions in the transmission electron microscope. In this study we describe the experimental and technical conditions necessary to obtain electron energy loss (EEL) spectra from a nanoparticle in colloidal suspension using aberration-corrected scanning transmission electron microscopy (STEM) combined with the environmental liquid stage. At a fluid path length below 400 nm, atomic resolution images can be obtained and simultaneous compositional analysis can be achieved. We show that EEL spectroscopy can be used to quantify the total fluid path length around the nanoparticle and demonstrate that characteristic core-loss signals from the suspended nanoparticles can be resolved and analyzed to provide information on the local interfacial chemistry with the surrounding environment. The combined approach using aberration-corrected STEM and EEL spectra with the in situ fluid stage demonstrates a plenary platform for detailed investigations of solution-based catalysis.

Detection of Förster resonance energy transfer (FRET) between cyan and yellow fluorescent proteins is a key method for quantifying dynamic processes inside living cells. To compare the different cyan and yellow fluorescent proteins, FRET efficiencies were measured for a set of the possible donor:acceptor pairs. FRET between monomeric Cerulean and Venus is more efficient than the ECFP:EYFP pair and has a 10% greater Förster distance. We also compared several live cell microscopy methods for measuring FRET. The greatest contrast for changes in intramolecular FRET is obtained using a combination of ratiometric and spectral imaging. However, this method is not appropriate for establishing the presence of FRET without extra controls. Accurate FRET efficiencies are obtained by fluorescence lifetime imaging microscopy, but these measurements are difficult to collect and analyze. Acceptor photobleaching is a common and simple method for measuring FRET efficiencies. However, when applied to cyan to yellow fluorescent protein FRET, this method becomes prone to an artifact that leads to overestimation of FRET efficiency and false positive signals. FRET was also detected by measuring the acceptor fluorescence anisotropy. Although difficult to quantify, this method is exceptional for screening purposes, because it provides high contrast for discriminating FRET.Note: M. Rizzo and K. Segawa performed this research at Vanderbilt University (same address as Piston). W. Zipfel performed research at Cornell University.

The helium ion microscope is a unique imaging instrument. Based on an atomic level imaging system using the principle of field ion microscopy, the helium ion source has been shown to be incredibly stable and reliable, itself a remarkable engineering feat. Here we show that the image contrast is fundamentally different to other microscopes such as the scanning electron microscope (SEM), although showing many operational similarities due to the physical ion interaction mechanisms with the sample. Secondary electron images show enhanced surface contrast due the small surface interaction volume as well as elemental contrast differences, such as for nanowires imaged on a substrate. We present images of nanowires and nanoparticles for comparison with SEM imaging. Applications of Rutherford backscattered ion imaging as a unique and novel imaging mechanism are described. The advantages of the contrast mechanisms offered by this instrument for imaging nanomaterials are clearly apparent due to the high resolution and surface sensitivity afforded in the images. Future developments of the helium ion microscope should yield yet further improvements in imaging and provide a platform for continued advances in microscope science and nanoscale research.

As a major improvement in three-dimensional (3D) atom probe, the range of applicable material classes has recently been broadened by the establishment of laser-assisted atom probes (LA-3DAP). Meanwhile, measurements of materials of low conductivity, such as dielectrics, ceramics, and semiconductors, have widely been demonstrated. However, besides different evaporation probabilities, heterogeneous dielectric properties are expected to give rise to additional artifacts in the 3D volume reconstruction on which the method is based. In this article, these conceivable artifacts are discussed based on a numeric simulation of the field evaporation. Sample tips of layer- or precipitate-type geometry are considered. It is demonstrated that dielectric materials tend to behave similarly to metals of reduced critical evaporation field.

A luminescence database for minerals and materials has been complied from the literature, the aim being to create a resource that will aid in the analysis of luminescence spectral of ionic species in minerals and materials. The database is based on a range of excitation techniques and records both major and minor lines, and their activators. The luminescence techniques included in the database are cathodoluminescence, ion luminescence, and photoluminescence. When combined with other traditional X-ray measurements collected on the same region, use of the luminescence database will give additional insight into the chemistry of minerals and materials.

Through recent years, off-axis electron holography has helped us to understand and to overcome some experimental restrictions in transmission electron microscopy. With development of powerful electron microscopes, slow-scan CCD cameras, and computers, holography is not an academic technique anymore used by specialized laboratories. Holography has proven its wide range of applications in solving real-world problems in materials science and biology. At medium resolution, that is, on nanometer scale, holography allows access to large area phase contrast produced by magnetic fields and electric potentials. In the high-resolution domain, holography unveils its power by unscrambling amplitude and phase of the electron wave, resulting in an improved lateral resolution up to the information limit. Holography is a thoroughly quantitative method, and, in combination with the perfect zero-loss filtering inherent to this method, the interpretation of the reconstructed data is strongly simplified. After outlining the basics of holography, in this tutorial we focus on development of a step-by-step procedure for recording and reconstruction of holograms. At the end, some recent applications are discussed.

The high beam current and subangstrom resolution of aberration-corrected scanning transmission electron microscopes has enabled electron energy loss spectroscopy (EELS) mapping with atomic resolution. These spectral maps are often dose limited and spatially oversampled, leading to low counts/channel and are thus highly sensitive to errors in background estimation. However, by taking advantage of redundancy in the dataset map, one can improve background estimation and increase chemical sensitivity. We consider two such approaches—linear combination of power laws and local background averaging—that reduce background error and improve signal extraction. Principal component analysis (PCA) can also be used to analyze spectrum images, but the poor peak-to-background ratio in EELS can lead to serious artifacts if raw EELS data are PCA filtered. We identify common artifacts and discuss alternative approaches. These algorithms are implemented within the Cornell Spectrum Imager, an open source software package for spectroscopic analysis.

Localization microscopy techniques based on localizing single fluorophore molecules now routinely achieve accuracies better than 30 nm. Unlike conventional optical microscopies, localization microscopy experiments do not generate an image but a list of discrete coordinates of estimated fluorophore positions. Data display and analysis therefore generally require visualization methods that translate the position data into conventional images. Here we investigate the properties of several widely used visualization techniques and show that a commonly used algorithm based on rendering Gaussians may lead to a 1.44-fold loss of resolution. Existing methods typically do not explicitly take sampling considerations into account and thus may produce spurious structures. We present two additional visualization algorithms, an adaptive histogram method based on quad-trees and a Delaunay triangulation based visualization of point data that address some of these deficiencies. The new visualization methods are designed to suppress erroneous detail in poorly sampled image areas but avoid loss of resolution in well-sampled regions. A number of criteria for scoring visualization methods are developed as a guide for choosing among visualization methods and are used to qualitatively compare various algorithms.

Spectrum simulation is a useful practical and pedagogical tool. Particularly with complex samples or trace constituents, a simulation can help to understand the limits of the technique and the instrument parameters for the optimal measurement. DTSA-II, software for electron probe microanalysis, provides both easy to use and flexible tools for simulating common and less common sample geometries and materials. Analytical models based on ϕ(ρz) curves provide quick simulations of simple samples. Monte Carlo models based on electron and X-ray transport provide more sophisticated models of arbitrarily complex samples. DTSA-II provides a broad range of simulation tools in a framework with many different interchangeable physical models. In addition, DTSA-II provides tools for visualizing, comparing, manipulating, and quantifying simulated and measured spectra.

Aberration correctors using hexapole fields have proven useful to correct for the spherical aberration in electron microscopy. We investigate the limits of the present design for the hexapole corrector with respect to minimum probe size for the scanning transmission electron microscope and discuss several ways in which the design could be improved by rather small and incremental design changes for the next generation of advanced probe-forming systems equipped with a gun monochromator.

X-ray cone-beam reconstruction from incomplete projection data has important practical applications, especially in microtomography. We developed expectation maximization (EM)-type and algebraic reconstruction technique (ART)-type iterative cone-beam reconstruction algorithms for metal artifact reduction and local reconstruction from truncated data. These iterative algorithms are adapted from the emission computerized tomography (CT) EM formula and the ART. A key step in our iterative algorithms is introduction of a projection mask and computation of a 3-D spatially varying relaxation factor that allows compensation for beam divergence and data incompleteness. The algorithms are simulated with projection data synthesized from mathematical phantoms. In simulation, the EM-type and ART-type iterative algorithms are demonstrated to be effective for metal artifact reduction and local region reconstruction. They perform similarly in terms of visual quality, image noise, and discrepancy between measured and reprojected data. The EM-type and ARTtype iterative cone-beam reconstruction algorithms have potential for metal artifact reduction and local region reconstruction in X-ray CT.

We have investigated the changes produced in single-element and two-layer transmission electron microscope (TEM) specimens irradiated by an intense nanometer-sized electron probe, such as that produced in a field-emission or aberration-corrected TEM. These changes include hole formation and the accumulation of material within the irradiated area. The results are discussed in terms of mechanisms, including electron-beam sputtering and surface diffusion. Strategies for minimizing the effect of the beam are considered.

A numerical model has been developed to simulate images obtained from the three-dimensional atom probe. This model was used to simulate the artefacts commonly observed in two-phase materials. This model takes into account the dynamic evolution of the atomic-scale shape of the specimen during field evaporation. This article reviews the model and its applications to some specific cases. Local magnification effects were studied as a function of the size, the shape, and the orientation of precipitated phases embedded in the matrix. Small precipitates produce large aberrations in good agreement with experiments. The magnification from such precipitates, as measured from the simulation, is only found to match the theoretical value for mesoscopic scale precipitates (size similar to the specimen size). Orientation effects are also observed in excellent agreement with experiments. The measured thickness of a grain-boundary-segregated film in the simulation is found to decrease with the angle between the normal to the grain boundary and the tip axis. Depth scaling artefacts caused by variation in the evaporation field of atoms in multilayer structures were successfully simulated and again showed good agreement with effects observed experimentally.

In situ nanoindentation of a 30 nm Cu/20 nm Nb multilayer film in a transmission electron microscope revealed confined layer slip as the dominant deformation mechanism. Dislocations were observed to nucleate from the Cu-Nb interfaces in both layers. Dislocation glide was confined by interfaces to occur within each layer, without transmission across interfaces. Cu and Nb layers co-deformed to large plastic strains without cracking. These microscopy observations provide insights in the unit mechanisms of deformation, work hardening, and recovery in nanoscale metallic multilayers.

Nanostructure evolution during low temperature aging of three binary Fe-Cr alloys has been investigated by atom probe tomography. A new method based on radial distribution function (RDF) analysis to quantify the composition wavelength and amplitude of spinodal decomposition is proposed. Wavelengths estimated from RDF have a power-law type evolution and are in reasonable agreement with wavelengths estimated using other more conventional methods. The main advantages of the proposed method are the following: (1) Selecting a box size to generate the frequency diagram, which is known to generate bias in the evaluation of amplitude, is avoided. (2) The determination of amplitude is systematic and utilizes the wavelength evaluated first to subsequently evaluate the amplitude. (3) The RDF is capable of representing very subtle decomposition, which is not possible using frequency diagrams, and thus a proposed theoretical treatment of the experimental RDF creates the possibility to determine amplitude at very early stages of spinodal decomposition.

Programmed cell death or apoptosis occurs in many tissues during normal development and in the normal homeostasis of adult tissues. Apoptosis also plays a significant role in abnormal development and disease. Increased interest in apoptosis and cell death in general has resulted in the development of new techniques and the revival of old ones. Each assay has its advantages and disadvantages that can render it appropriate and useful for one application, but inappropriate or difficult to use in another. Understanding the strengths and limitations of the assays would allow investigators to select the best methods for their needs.

For the transmission electron aberration-corrected microscope (TEAM) initiative of five U.S. Department of Energy laboratories in the United States, a correction system for the simultaneous compensation of the primary axial aberrations, the spherical aberration Cs, and the chromatic aberration Cc has been developed and successfully installed. The performance of the resulting Cc /Cs-corrected TEAM instrument has been investigated thoroughly. A significant improvement of the linear contrast transfer can be demonstrated. The information about the instrument one obtains using Young's fringe method is compared for uncorrected, Cs-corrected, and Cc /Cs-corrected instruments. The experimental results agree well with simulations. The conclusions might be useful to others in understanding the process of image formation in a Cc /Cs-corrected transmission electron microscope.