Pragmatic reconstruction methods in atom probe tomography

Data collected in atom probe tomography have to be carefully analysed in order to give reliable composition data accurately and precisely positioned in the probed volume. Indeed, the large analysed surfaces of recent instruments require reconstruction methods taking into account not only the tip geometry but also accurate knowledge of geometrical projection parameters. This is particularly crucial in the analysis of multilayers materials or planar interfaces. The current work presents a simulation model that enables extraction of the two main projection features as a function of the tip and atom probe instrumentation geometries. Conversely to standard assumptions, the image compression factor and the field factor vary significantly during the analysis. An improved reconstruction method taking into account the intrinsic shape of a sample containing planar features is proposed to overcome this shortcoming.     

Morphology visualization of irregular shape bacteria by electron holography and tomography

In the current work, irregular morphology of Staphylococcus aureus bacteria has been visualized by phase retrieval employing off‐axis electron holography (EH) and 3D reconstruction electron tomography using high‐angle annular dark field scanning transmission electron microscopy (HAADF‐STEM). Bacteria interacting with gold nanoparticles (AuNP) acquired a shrunken or irregular shape due to air dehydration processing. STEM imaging shows the attachment of AuNP on the surface of cells and suggests an irregular 3D morphology of the specimen. The phase reconstruction demonstrates that off‐axis electron holography can reveal with a single hologram the morphology of the specimen and the distribution of the functionalized AuNPs. In addition, EH reduces significantly the acquisition time and the cumulative radiation damage (in three orders of magnitude) over biological samples in comparison with multiple tilted electron expositions intrinsic to electron tomography, as well as the processing time and the reconstruction artifacts that may arise during tomogram reconstruction.     

Tomography experiment of an integrated circuit specimen using 3 MeV electrons in the transmission electron microscope

The possibility of utilizing high-energy electron tomography to characterize the micron-scale three dimensional (3D) structures of integrated circuits has been demonstrated experimentally. First, electron transmission through a tilted SiO(2) film was measured with an ultrahigh-voltage electron microscope (ultra-HVEM) and analyzed from the point of view of elastic scattering of electrons, showing that linear attenuation of the logarithmic electron transmission still holds valid for effective specimen thicknesses up to 5 microm under 2 MV accelerating voltages. Electron tomography of a micron-order thick integrated circuit specimen including the Cu/via interconnect was then tried with 3 MeV electrons in the ultra-HVEM. Serial projection images of the specimen tilted at different angles over the range of +/-90 degrees were acquired, and 3D reconstruction was performed with the images by means of the IMOD software package. Consequently, the 3D structures of the Cu lines, via and void, were revealed by cross sections and surface rendering.     

Improvements in planar feature reconstructions in atom probe tomography

Standard atom probe tomography spatial reconstruction techniques have been reasonably successful in reproducing single crystal datasets. However, artefacts persist in the reconstructions that can be attributed to the incorrect assumption of a spherical evaporation surface. Using simulated and experimental field evaporation, we examine the expected shape of the evaporating surface and propose the use of a variable point projection position to mitigate to some degree these reconstruction artefacts. We show initial results from an implementation of a variable projection position, illustrating the effect on simulated and experimental data, while still maintaining a spherical projection surface. Specimen shapes during evaporation of model structures with interfaces between regions of low- and high-evaporation-field material are presented. Use of two-and three-dimensional projection-point maps in the reconstruction of more complicated datasets is discussed.     

Some aspects of the field evaporation behaviour of GaSb

In-depth analysis of pulsed laser atom probe tomography (APT) data on the field evaporation of the III-V semiconductor material GaSb reveals strong variations in charge states, relative abundances of different cluster ions, multiplicity of detector events and spatial correlation of evaporation events, as a function of the effective electric field at the specimen surface. These variations are discussed in comparison with the behaviour of two different metallic specimen materials, an Al-6XXX series alloy and pure W, studied under closely related experimental conditions in the same atom probe instrument. It is proposed that the complex behaviour of GaSb originates from a combination of spatially correlated evaporation events and the subsequent field induced dissociation of cluster ions, the latter contributing to inaccuracies in the overall atom probe composition determination for this material.     

A reproducible method for damage-free site-specific preparation of atom probe tips from interfaces

Atom probe tomography (APT) is a mass spectrometry method with atomic-scale spatial resolution that can be used for the investigation of a wide range of materials. The main limiting factor with respect to the type of problems that can be addressed is the small volume investigated and the randomness of common sample preparation methods. With existing site-specific specimen preparation methods it is still challenging to rapidly and reproducibly produce large numbers of successful samples from specifically selected grain boundaries or interfaces for systematic studies. A new method utilizing both focused ion beam (FIB) and transmission electron microscopy (TEM) is presented that can be used to reproducibly produce damage-free atom probe samples with features of interest at any desired orientation with an accuracy of better than 50 nm from samples that require very little prior preparation.     

Impact of laser pulsing on the reconstruction in an atom probe tomography

The implementation of fast pulsed laser has significantly improved the performance of the atom probe technique by enabling near-atomic-scale three-dimensional analysis of poorly conducting materials. This has broadened the range of applications for the atom probe, addressing a major limitation of the technique. Despite this, the implications of lasing on the tomographic reconstruction of atom probe data have yet to be fully characterised. Here, we demonstrate how changes in the shape of the specimen surface, induced by laser pulsing, affect the ion trajectories, and hence the projection parameters used to build the three-dimensional map.     

3-D reconstruction of the atomic positions in a simulated gold nanocrystal based on discrete tomography: prospects of atomic resolution electron tomography

A novel reconstruction procedure is proposed to achieve atomic resolution in electron tomography. The method exploits the fact that crystals are discrete assemblies of atoms (atomicity). This constraint enables us to obtain a three-dimensional (3-D) reconstruction of test structures from less than 10 projections even in the presence of noise and defects. Phase contrast transmission electron microscopy (TEM) images of a gold nanocrystal were simulated in six different zone axes. The discrete number of atoms in every column is determined by application of the channelling theory to reconstructed electron exit waves. The procedure is experimentally validated by experiments with gold samples. Our results show that discrete tomography recovers the shape of the particle as well as the position of its 309 atoms from only three projections.

Experiments on a nanocrystal that contains several missing atoms, both on the surface and in the core of the nanocrystal, while considering a high noise level in each simulated image were performed to prove the stability of the approach to reconstruct defects. The algorithm is well capable of handling structural defects in a highly noisy environment, even if this causes atom count “errors” in the projection data.     

Macroscopic electrical field distribution and field-induced surface stresses of needle-shaped field emitters

One major concern since the development of the field ion microscope is the mechanical strength of the specimens. The macroscopic shape of the imaging tip greatly influences field-induced stresses and there is merit in further study of this phenomenon from a classical perspective. Understanding the geometrical, as opposed to localized electronic, factors that affect the stress might improve the quality and success rate of atom probe experiments. This study uses macroscopic electrostatic principles and finite element modelling to investigate field-induced stresses in relation to the shape of the tip. Three two-dimensional idealized models are considered, namely hyperbolic, parabolic and sphere-on-orthogonal-cone; the shapes of which are compared to experimental tips prepared by electro-polishing. Three dimensional morphologies of both a nano-porous and single-crystal aluminium tip are measured using electron tomography to quantitatively test the assumption of cylindrical symmetry for electro-polished tips. The porous tip was prepared and studied to demonstrate a fragile specimen for which such finite element studies could determine potential mechanical failure, prior to any exhaustive atom probe investigation.     

Accurate structure determination from image reconstruction in ADF STEM

Annular dark-field (ADF) imaging in a scanning transmission electron microscope results in direct structure images of the atomic configuration of the specimen. Since such images are almost perfectly incoherent they can be treated as a convolution between a point-spread function, which is simply the intensity of the illuminating electron probe, and a sharply peaked object function that represents the projected structure of the specimen. Knowledge of the object function for an image region of perfect crystal allows the point-spread function to be directly determined for that image. We examine how the object function for an image can then be reconstructed using a Wiener filter, the CLEAN algorithm and a maximum entropy reconstruction. Prior information is required to perform a reconstruction, and we discuss what nature of prior information is suitable for ADF imaging.     

Evolution of tip shape during field evaporation of complex multilayer structures

Atom-probe tomography analysis of complex multilayer structures is a promising avenue for studying interfacial properties. However, significant artefacts in the three-dimensional reconstructed data arise due to the field evaporation process. To clarify the origin and impact of these artefacts for a FeCoB/FeCo/MgO/FeCo/IrMn multilayer, tip shapes were observed by transmission electron microscopy and compared to those obtained by finite difference modelling of electric fields and evaporation processes. It was found that the emitter shape is not spherical and its surface morphology evolves during successive evaporation of the different layers. This evolving morphology contributes to the artefacts generally observed in the reconstructed atom-probe data for multilayer structures because algorithms for three-dimensional reconstruction are based on the assumption that the shape of the emitter during field evaporation is spherical. Some proposed improvements to data reconstruction are proposed.     

STEM tomography for thick biological specimens

Scanning transmission electron microscopy (STEM) tomography was applied to biological specimens such as yeast cells, HEK293 cells and primary culture neurons. These cells, which were embedded in a resin, were cut into 1-microm-thick sections. STEM tomography offers several important advantages including: (1) it is effective even for thick specimens, (2) 'dynamic focusing', (3) ease of using an annular dark field (ADF) mode and (4) linear contrasts. It has become evident that STEM tomography offers significant advantages for the observation of thick specimens. By employing STEM tomography, even a 1-microm-thick specimen (which is difficult to observe by conventional transmission electron microscopy (TEM)) was successfully analyzed in three dimensions. The specimen was tilted up to 73 degrees during data acquisition. At a large tilt angle, the specimen thicknesses increase dramatically. In order to observe such thick specimens, we introduced a special small condenser aperture that reduces the collection angle of the STEM probe. The specimen damage caused by the convergent electron beam was expected to be the most serious problem; however, the damage in STEM was actually smaller than that in TEM. In this study, the irradiation damage caused by TEM- and STEM-tomography in biological specimens was quantitatively compared.     

Molecular dynamics simulation of the contact process in AFM surface observations

In the present work, several molecular dynamics simulations have been performed to clarify dynamically the contact mechanism between the specimen surface and probe tip in surface observations by an atomic force microscope (SFM) or friction force microscope (FFM). In the simulation, a three‐dimensional model is proposed where the specimen and the probe are assumed to consist of monocrystalline copper and rigid diamond or a carbon atom, respectively. The effect of the cantilever stiffness of the AFM/FFM is also taken into consideration. The surface observation process is simulated on a well‐defined Cu{100} surface. From the simulation results it has been verified that the surface images and the two‐dimensional atomic‐scale stick‐slip phenomenon, just as is the case for real AFM/FFM surface observations, can be detected from the spring force acting on the cantilever. From the evaluation of the behaviour of specimen surface atoms, the importance of the specimen stiffness in deciding the cantilever properties can also be understood. The influence of the probe tip shape on the force images is also evaluated. From the results it can be verified that the behaviour of the specimen surface atoms as well as the solid surface images in AFM/FFM surface observations can be understood using the molecular dynamics simulation of the model presented.     

Investigations of field-evaporated end forms in voltage- and laser-pulsed atom probe tomography

Atom Probe Tomography (APT) consists of analyzing a needle-shaped specimen on an atom-by-atom basis. In recent years, instruments have become commercially available, enabling the sequential analysis of the same specimen in both laser- and voltage-pulsed modes. In this contribution, a comparison of field evaporated end-forms as a function of the voltage and laser power is presented for silicon. Electron microscopy is utilized for visual inspection of the final tip end-forms. The field of evaporation for silicon is calculated based on these radius measurements for voltage and laser pulsing. Electron microscopy and analysis of the atom probe data show that the specimen end-forms for both pulsing modes can be different. We have observed two effects on the shape of a field-ion emitter when irradiated by a focused laser beam. One is a change in the 3-dimensional topology of the emitter due to different crystallographic orientations. Secondly, exposure to focused laser beam from one side may lead to a non-hemispherical tip shape especially when reasonably high laser energy is utilized. For comparison purposes to the laser mode, the voltage pulse evaporated tip end form is also analyzed for different specimen temperatures. Consequently, evaporation fields are calculated for different temperatures and laser conditions for silicon.     

Formation and reduction of streak artefacts in electron tomography

We have analysed the formation of streak artefacts in the reconstruction based on the filtered back projection algorithm in electron tomography (ET) and accordingly applied an adaptive interpolation technique to artefact reduction. In the adaptive interpolation to recover the missing information, the edge positions in a projection curve were tracked to reduce the interpolation error. A simulation was used to demonstrate the effectiveness of the artefact reduction. Furthermore, image reconstruction of integrated circuit specimens in the ET experiments with the ultra‐high voltage electron microscope show that the strong streak artefacts can be reduced effectively by our artefact reduction technique.     

Nanoscale scanning transmission electron tomography

Electron tomography enables the study of complex three‐dimensional objects with nanometre resolution. In materials science, scanning transmission electron microscopy provides images with minimal coherent diffraction effects and with high atomic number contrast that makes them ideal for electron tomographic reconstruction. In this study, we reviewed the topic of scanning transmission electron microscopy‐based tomography and illustrated the power of the technique with a number of examples with critical dimensions at the nanoscale.     

Atom probe tomography and transmission electron microscopy characterisation of precipitation in an Al-Cu-Li-Mg-Ag alloy

State-of-the art atom probe tomography (APT) combined with transmission electron microscopy (TEM) were used to investigate the microstructure at different stages of the ageing process of an alloy of composition (at%) Al-1.68%Cu-4.62%Li-0.33%Mg-0.1%Ag. These alloys were shown to exhibit a complex microstructure of T₁ plates and several metastable phases, including θ′ and S. We will highlight the early stages of clustering, precipitate interactions and possible solute segregation at the matrix/precipitate interfaces and detail the chemical composition of the different phases.     

Modification of a TEM-goniometer specimen holder to enable beam current measurements in a (S)TEM for use in quantitative X-ray microanalysis

In order to have available a specimen holder suited to measure the beam current as is often required in quantitative electron probe X-ray microanalysis, the rod of a low background beryllium specimen holder of a transmission electron microscope was modified. The tip was electrically insulated from the mass of the microscope and connected electrically to the central contact of a BNC connector mounted on the specimen holder handle. With this modified specimen holder the current absorbed by the specimen and/or the specimen holder could be measured easily and accurately. The modified specimen holder has been used to measure the beam current stability of an analytical electron microscope under various conditions. Data were obtained for tungsten as well as lanthanum hexaboride cathodes. Small changes to other types of specimen tips made it possible to exchange these for the low background tip.     

Formation and elimination of surface ion milling defects in cadmium telluride,zinc sulphide and zinc selenide

The nature of damage produced by low energy Ar⁺ ion and Ar atom milling in the II–VI semiconductors CdTe, ZnS and ZnSe is studied in detail by conventional and high resolution transmission electron microscopy. It is demonstrated that the damage consists of dense arrays of small dislocation loops near to each milled surface. When ion or atom milling of this type is used for thin specimen preparation prior to microscopy the loop arrays can seriously obscure images and so complicate their interpretation. This problem concerning the presence of artifactual defects can be greatly reduced by the use of reactive I⁺ ion milling for specimen thinning and, in the case of CdTe, spurious dislocation loop formation can be completely suppressed.     

Local crystal structure analysis with several picometer precision using scanning transmission electron microscopy

We report a local crystal structure analysis with a high precision of several picometers on the basis of scanning transmission electron microscopy (STEM). Advanced annular dark-field (ADF) imaging has been demonstrated using software-based experimental and data-processing techniques, such as the improvement of signal-to-noise ratio, the reduction of image distortion, the quantification of experimental parameters (e.g., thickness and defocus) and the resolution enhancement by maximum-entropy deconvolution. The accuracy in the atom position measurement depends on the validity of the incoherent imaging approximation, in which an ADF image is described as the convolution between the incident probe profile and scattering objects. Although the qualitative interpretation of ADF image contrast is possible for a wide range of specimen thicknesses, the direct observation of a crystal structure with deep-sub-angstrom accuracy requires a thin specimen (e.g., 10 nm), as well as observation of the structure image by conventional high-resolution transmission electron microscopy.