bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principle component analysis applied to high resolution cross sectional
STEM
imaging: Quantitative analysis of
2D
heterostructures
Authors: Rooney Aidan , Kozikov Aleksey , Prestat Eric , Withers Freddie , Geim Andre , Novoselov Konstantin , Haigh Sarah 
Published: December 2016

Monolayers of 2D transition metal dichalcogenides (TMDCs) provide excellent semiconducting counterparts to insulating hexagonal boron nitride (hBN) and conductive graphene.[1] Combining all three materials in a Van der Waals vertical heterostructure allows the electronic, photovoltaic and electroluminescent properties of the TMDCs to be studied.[2] Whilst transport and optoelectronic measurements can probe the properties of exotic charge carriers, and ARPES can map the bandstructure such systems, direct high resolution imaging of the buried interfaces is only possible via high resolution cross sectional (S)TEM imaging.[3] The nature of these van der Waals interfaces not only determines the carrier injection between components[4], but also affects the bandstructure of the device and its ultimate functionality[5].
Here we present a novel strategy to denoise high resolution HAADF STEM images of cross sections using principal component analysis (PCA).[6] Cross sections are fabricated in a dual‐beam FIB‐SEM instrument using the in situ lift‐out method and polished with low energy ions to achieve electron transparency.[7] Cross sections were imaged in high resolution HAADF STEM using a probe‐side aberration corrected FEI Titan G2 80–200 kV with an X‐FEG electron source. By treating each line profile perpendicular to the fringes as a signal, components associated with noise and scattering can be separated by their variance. Removing the noise components allows us to accurately determine the separation between dissimilar crystals at these unique interfaces. More widely, the approach developed here also has application in a variety of layered material systems.
In‐situ
E
(
S
)
TEM
Observations of Single Atom Dynamics in Catalytic Reactions
Authors: Gai Pratibha , Yoshida Kenta , Ward Michael , Boyes Edward 
Published: December 2016

In heterogeneous catalysis gas (or liquid)‐solid catalyst reactions take place at the atomic level at elevated temperatures. Understanding and control of complex catalytic reactions on the atomic scale are crucial for the rational development of improved catalysts and processes. The development of the first atomic resolution environmental (scanning) transmission electron microscope (E(S)TEM) is described (1–6) including for the direct visualisation of reacting individual atoms in gas‐solid reactions in the working state in real time (3–6), opening up striking new opportunities for studies of catalysis at the atomic level. Our development of the atomic resolution ETEM (2) is now used globally. Benefits of the in‐situ studies include new knowledge, improved and more environmentally beneficial technological processes for healthcare and renewable energy as well as better or replacement mainstream technologies in the chemical and energy industries.
Examples include heterogeneous catalysis of biomass conversion into bioenergy and water gas shift (WGS) reaction (employing carbon monoxide and water) which is the basis of heterogeneous catalysis important in the generation of clean hydrogen energy for fuel cells, transportation fuels and in ammonia manufacture (7). Potential supported noble metal catalysts are examined for low temperature WGS catalysis (Fig.1) and compared with reaction data and modelling. The in‐situ observations in WGS have revealed the formation of clusters of only a few noble metal atoms resulting from single atom dynamics and the catalytic effect of low coordination surface sites. The new insights have important implications for applications of nanoparticles in chemical process technologies including for transportation fuels and emission control.
Combining Current Imaging and Electrical Probing for fast and reliable in situ Electrical Fault Isolation
Authors: Kleindiek Stephan , Rummel Andreas , Schock Klaus , Kemmler Matthias 
Published: December 2016

Within the last decades, the feature widths of semiconductor devices have become too small to be resolved by state‐of the art optical microscopes, and other imaging techniques like Scanning Electron Microscopes (SEM) or Scanning Probe Microscopes (SPM) have become indispensable. For some analyses of device failures a combination of imaging and electrical measurements is required. Nowadays, one can find nanoprobers that are either based on SPM or SEM imaging techniques. For the SPM based nanoprobers, each probe consists of an Atomic Force Microscope (AFM) equipped with a conductive tip. For the SEM based systems, nanopositioners without force feedback are placed within a SEM.
Both approaches described above have advantages and disadvantages. Landing probes on a desired device is much easier for the SEM prober, as the SEM image gives immediate visual feedback. In contrast, the AFM prober requires many subsequent AFM images by each probe in order to align the probes with respect to each other and with respect to the device, which can be very time consuming. One advantage of the conductive AFM probing is the combination of topography images with electrical transport properties, i.e. images of local resistance (analogue to Scanning Tunneling Microscope (STM)). This allows easy identification of leakages or shorts on the chip.
In this work we present a very compact nanoprober that combines the advantages of SEM and SPM nanoprobers in one system.
The setup consists of a nanoprober with eight probes and an xyz substage mounted on the stage of an SEM (Zeiss Supra 40). Positioning the probes and the sample with nanometer precision as well as the controls for all electrical measurements are provided by a unified software interface. These can be used to quickly and easily probe contacts on technologies with line widths down to 10 nm and less. The probing experiments can include transistor characterization, electron beam induced current (EBIC) imaging, among others.
In order to locate leakages or shorts as described above, a voltage biased probe is scanned at constant height over the sample surface. The resulting current flow to a second probe or to the bulk contact can be simultaneously monitored with sub‐pA resolution. A typical current image can be acquired in a few seconds in a scan range of up to 1.5 µm × 1.5 um.
Each probe (or the substage) can be selected as the “scanning” voltage source or the “stationary” current sink, which allows for a very flexible definition of the expected current path enabling a powerful method for the visualization of faults in the integrated circuits.
The combination of the SEM image (the probes can be observed while the scan takes place) and the resulting current images enables correlative microscopy. Figure 2 shows an overlay image of the SEM image with current images on a 22 nm chip. Depending on the polarity (+/‐ 1V) of the voltage biased tip, n‐MOS or p‐MOS contacts become visible in the current image.
In situ and cryo
(S)TEM
imaging of internal microgel architectures
Authors: Caumanns Tobias , Gelissen Arjan , Oppermann Alexander , Hebbeker Pascal , Tiwari Rahul , Turnhoff Sarah , Wöll Dominik , Walther Andreas , Mayer Joachim , Richtering Walter 
Published: December 2016

More than ever polymer science focuses on complex molecular structures and supramolecular assemblies. Microgels are responsive polymer materials and structures, which can be manipulated in e.g. charge or size by external parameters like pH or temperature variation. The investigated microgels are soft particulate polymer networks that can be dispersed in an aqueos medium. They reveal unique features providing new opportunities to develop smart bio‐inspired materials. In contrast to rigid colloidal particles, which lack the possibility to adapt their size and shape to enviromental requirements, microgels have switchable properties of form and function that make them very useful in a wide range of e.g. biological sciences and medical applications. They combine properties of dissolved macromolecules with those of colloidal particles.
The direct visualization of the internal structure of materials is very important to analyse the spatial distribution of different compartments and, thus, to design novel materials with tailored properties. Microgels can be prepared with various morphologies and functions in different compartments. Careful analysis of the correlation between architecture and function requires powerful methods to visualize inner structure and compartmentalization in the nanometer range.
Here, the direct visualization of different compartments within microgels using a combination of in situ and cryo transmission electron microscopy methods is shown. In particular, the challenge of determing the radial distribution of appropriately labeled compartments within single microgels and particles from 2D projections is adressed.
Microgels with core‐shell architecture were obtained by precipitation polymerization. First a particle was synthesized and purified before a shell was synthesized on top by the seed and feed method. Core and shell have oppositely charged copolymers to create a two compartment amphoteric microgel system, that is alternately stained with gold and magnetite nanoparticles. [1], [2]

For
in situ
liquid cell experiments, a thin layer of liquid was embedded between two hermetically sealed, electron transparent Si
3
N
4
‐windows. The used holder is an
in situ
‐liquid cell holder manufactured by Hummingbird Company and the microscope is a Zeiss Libra 200FE with an acceleration voltage of 200 kV. The resolution is mainly limited by the thickness of the liquid.

Figure 1 shows a comparison between
cryo
TEM and
in situ
STEM. Due to the liquid layer thickness the resolution is limited in (b). Also the Brown emotion leads to a defocused and smudged image.

Figure 2 shows the comparison of the radial distribution of nanoparticles according to the two images above calculated by a MATLAB routine. For the
cryo
TEM image in (b) the relative particle density as a function of the relative particle radius is plotted. (c) shows a 3D reconstruction of the model.
A Compressive Sensing based acquisition design for quantitative ultra‐low dose high‐resolution imaging and spectroscopy in the
STEM
Authors: Muecke‐Herzberg Dorothea , Abellan Patricia , Sarahan Michael , Godfrey Iain , Saghi Zineb , Leary Rowan , Stevens Andrew , Ma Jackie , Kutyniok Gitta , Azough Feridoon , Freer Robert , Midgley Paul , Browning Nigel , Ramasse Quentin 
Published: December 2016

Typically, the Nyquist frequency determines the sampling rate required to resolve a specific feature in a dataset. In practice this requires oversampling by twice the maximum relevant frequency. As such this provides a lower limit for the electron dose necessary to acquire the data experimentally. However, by applying the compressive sensing (CS) principles of sparsity and incoherence, this limit can be overcome and therefore a substantial reduction of the total electron dose can be achieved. CS theory then allows a recovery of the essential image information from randomly undersampled images. The theory of CS has been successfully applied in a number of areas, e.g. astronomy, MRI scanning, electron tomography [1], and most recently first experimental designs for STEM have been reported [2,3]. Despite these developments, CS acquisition schemes able to recover quantifiable information from atomically resolved images of beam‐sensitive materials, time‐changing processes and spectroscopic datasets have so far not been established for STEM.
Here we demonstrate such a CS‐based STEM acquisition implementation and benchmark its performance at atomic resolution using a variety of materials, including complex oxide ceramics with an inhomogeneous distribution of point defects as illustrated in fig. 1, but also highly beam‐sensitive catalysts with atomic resolution [4]. The implementation relies on custom‐built hardware and software which controls an electrostatic beam shutter to blank the electron beam during all but a few randomly chosen pixels through a regular image (or indeed spectrum image) acquisition. The total electron dose used to form a whole dataset can thus be tailored according to the electron damage threshold of the sample under investigation whilst maintaining all other acquisition parameters identical to regular data acquisition, allowing a seamless transition from ‘fully sampled’ to ultra‐low‐dose conditions. It will be shown that datasets acquired in this fashion down to a few % of the total incoming dose (see fig. 2) can be reconstructed to yield a truthful atomic resolution representation of the sample, using a variety of reconstruction algorithms [5,6]. We show that this implementation of CS can also be extended to 2D spectroscopy mapping and simultaneous HAADF image acquisition.. These results open the door to practical ultra‐low dose high‐resolution imaging and spectroscopy in the STEM for very beam sensitive samples, where the level of sampling can simply be chosen depending on the damage threshold of the material being investigated [7].
Visualization of 2‐dimensional potential map in multilayer organic electroluminescence materials by phase‐shifting electron holography
Authors: Sato Takeshi , Yamamoto Kazuo , Tsuchiya Miki , Ito Katsuji , Yoshimoto Noriyuki , Taniguchi Yoshifumi 
Published: December 2016

Electron holography (EH) is a TEM method which can quantitatively measure electromagnetic fields of various samples [1‐3]. In this study, we tried observing a local two‐dimensional electric distribution, formed in multilayer organic electroluminescence (OEL) quantitatively with phase‐shifting EH [4‐5] by HF‐3300EH Cold‐FE TEM operated at 300 kV equipped with multiple biprism system.
An OEL multilayer sample (CuPc/α‐NPD/Rubrene/Alq3/LiF/Ag) was fabricated on a Si substrate using a vacuum evaporation method. Each layer's thickness and the surface morphology of the OEL multilayer sample were evaluated by X‐Ray Reflectometry (XRR) and Atomic Force Microscopy (AFM), respectively.
The sample for phase‐shifting EH observation was fabricated by focused ion beam (FIB) technique. A part of the multilayer sample, which formed a multilayer structure on a Si substrate, was picked up by the microsampling technique and was fixed onto a W deposition on the mesh for TEM observation. Then, a thin film sample of thickness 450 nm was fabricated by FIB processing. Generally, the OEL sample is vulnerable to water, and the structure may change in quality in reaction to atmospheric water vapor, depending on the formed materials. Therefore, in this study, after thin film processing, contact with the atmosphere was prevented by using an air protection mesh holder.
Figure 1 shows a TEM image, and a hologram by double‐biprism EH technique [6]. The model structure of an OEL multilayer is inserted in the TEM image. Sample thickness was about 450 nm. From the TEM image, some contrast is observed in the position of the CuPc layer, but we cannot confirm the image contrast corresponding to the other layers.
Figure 2 shows the result of the visualization of the 2‐dimensional potential map of an OEL multilayer. We can clearly observe the contrast of the OEL multilayer, as shown in the reconstruction image (Figure 2b). Because the inner potential of the materials in each layer is constant, we can consider phase shifts to be an electric potential change in the sample. In the future, we will investigate the accuracy of this experimental data by comparing our data with a simulation.
Apical chitinous matrix and basal lamina ‐ the ultrastructure and formation of two distinct extracellular matrices of crustacean hindgut cells
Authors: Bogataj Urban , Mrak Polona , Štrus Jasna , Žnidaršič Nada 
Published: December 2016

Ectodermally derived gut and epidermal cells in crustaceans are covered by cuticle, a chitinous apical extracellular matrix, and at the opposite side they are underlined by a basal lamina. Thus, the same cell performs synthesis and spatiotemporal control of elaboration of two extracellular matrices that differ in ultrastructure, composition and functions. Differentiation of the extracellular matrix in epithelial tissues is an integrative part of the establishment and maintenance of the characteristic apicobasal polarized cell architecture. We present here the ultrastructural description of the hindgut cells' apical matrix differentiation during embryonic and larval development of crustacean
Porcellio scaber
. In addition, in the same developmental stages the ultrastructure of basal lamina was described.

The ultrastructural hallmarks of the hindgut cells and their extracellular matrices (ECM) in adults are: (i) apical ECM is a chitinous cuticle, consisting of distinct horizontal layers ‐ electron dense epicuticle and electron lucent procuticle (Fig. 1), (ii) extensive apical and basal plasma membrane infoldings, forming prominent membrane labyrinths, (iii) basal lamina that is forming an extensive interface surface to hemolymph space (Fig. 2). The ultrastructure of cuticle differs in the two anatomic regions of the hindgut, namely the anterior chamber and the papillate region. In the anterior chamber the epicuticle is much thinner than procuticle and lamellae are discernible in the procuticle due to helicoidally arranged chitin protein fibers (Fig. 1). In papillate region epicuticle and procuticle are of approximately equal thicknesses and no lamellae could be discerned in the procuticle.
Differentiation of the hindgut cuticular matrix during embryonic and larval development involves a sequential formation and shedding of several apical matrices, which gradually display ultrastructural features characteristic for adults. The outline of the pre‐cuticluar apical matrix in embryos is ruffled and consists of homogenous lucent material and a distal electron dense lamina. In late embryos of stage 18 the first deposition of the apical cuticle was evidenced. In marsupial larvae the cuticle follows the outline of apical hindgut surface and is already differentiated into thin electron dense epicuticle and thicker electron lucent procuticle. In the epicuticle a trilayered surface lamina and electron dense material beneath are discernible (Fig. 3). The procuticle is homogenous along the whole length of the hindgut and non‐lamellate as is characteristic in anterior chamber of adults. The basal side of the hindgut epithelium of marsupial larvae is in contact with basal lamina (Fig. 4) exhibiting fibrillary structure in certain section profiles.
Advantages and pitfalls for transmission electron microscopic studies in the identification of extracellular vesicles
Authors: Kittel Agnes , Osteikoetxea Xabier , Sódar Barbara , Pálóczy Krisztina , Baranyai Tamás , Giricz Zoltán , Buzás Edit Irén 
Published: December 2016

Although the story of extracellular vesicles (EVs), these cell‐derived submicron structures started about 70 years ago, we had to wait for the first transmission electron microscopic (TEM) evidence of their existence till 1981.
By now it has been proved that the release of membrane vesicles is a process conserved in both prokaryotes and eukaryotes. Compelling piles of evidence support the significance of exosomes, microparticles/microvesicles or ectosomes and apoptotic bodies in a broad range of biological processes including e.g. intercellular communication, signaling processes, the transfer of genetic information, and also in case of pathological events, from inflammation till tumor development. Not surprisingly, the possibility of EV‐related biomarker and therapeutic applications made this research field attractive for clinical and pharmaceutical research, too.
However, in spite of growing interest, the classification of EVs is still under debate. The numerous protocols, applied by the different research teams, made the comparison of the results more complicated; moreover several frequently used and up‐to‐date particle enumeration techniques such as nanoparticle tracking analysis or tunable resistive pulse sensing are not suitable to distinguish vesicles and e.g. protein aggregates in similar size. Falsified experimental results may occur easily, especially in case of body fluid samples or culture media, in which protein aggregates, which share biophysical parameters with EVs, may contaminate vesicle preparations.
Purity and type of the fractions should be investigated with different techniques depending on the size range of the investigated vesicle population. For detection of exosomes, the frequently used flow cytometry is not the best choice, while by means of AFM, dynamic light scattering, MS techniques or microfluidic device, mentioned only few among the applied possibilities, can reveal several features of the investigated vesicle samples. However, even the most sophisticated combination of different techniques cannot be complete without transmission electron microscopy. It is the only technique which is able to visualize vesicular and non‐vesicular particles in the whole size range of the vesicle population, and if we want to use EVs for research and therapy, we have to learn, how TEM can be applied for their accurate characterization.
In situ
TEM
observation of electromigration in Ni nanobridges
Authors: Kozlova Tatiana , Zandbergen Henny W. 
Published: December 2016

Using
in situ
scanning transmission electron microscopy (STEM) (FEI Titan microscope operating at 300 keV), a microelectromechanical system (MEMS) chip and a dedicated biasing and heating sample holders, built in‐house, we investigated electrical and thermal properties of 15‐nm‐thick Ni nanobridges. These techniques allow to visualize nanobridge morphology transformations down to atomic scale while electrical current is passed. If thin metallic wire is subjected to high current density, the material transfer can start which results in the wire break. This phenomenon is called electromigration
1
.

Ni nanobridges with a length of 500 – 1000 nm and a width 200 – 500 nm were produced by e‐beam metal evaporation onto a 100‐nm‐thick freestanding silicon nitride membrane and patterned using electron beam lithography (Fig. 1a). Contacts to the nanobridges were made with a 100‐nm‐thick layer of Au and a 3‐nm‐thick adhesion layer of Cr. Initial resistance of the structures, including bridge, contact pads and leads, is in the range of 160 – 250 Ohm. More details of the sample preparation can be found elsewhere
2
. Using electrical setup
3
,
I–V
measurements were performed in bias‐ramping mode. Voltage is gradually increased (with a speed of 15 mV/s) from 0 V to a predefined value of 500–600 mV, followed by a decrease back to 0 V, after which a new cycle with higher maximum voltage was performed (Fig. 1f).

Fig.1 shows STEM images of Ni nanobridge with 10‐nm‐thick Al
2
O
3
oxidation‐protective layer on top taken before electromigration and after each bias‐ramping cycle with maximum voltages 500 mV, 520 mV, 540 mV and 580 mV. Fig. 2f shows corresponding
I–V
curves for four voltage cycles applied in a row. Sample temperature prior to voltage apply was 100 K. During electromigration experiments in Ni material transfer was shown to be voltage polarity dependent: Voids initially form near the cathode contact pad of the bridge, as in the majority of metals due to electron‐wind force, but at the end bridge breaks near the anode side.

Also, we visualised morphological transformations in polycrystalline Ni film (deposited on top of the heater with 20‐nm‐thick windows in Si
3
N
4
membrane) during substrate heating up to 400°C (Fig. 2) and estimated the bridge temperature achieved in electromigration experiments due to the Joule heating to be around the Curie point. In order to enhance the contrast between grains, annular dark‐field STEM imaging was used
4
.

Enriched with oxygen bubbles formation was found due to Ni nanobridges oxidation after a month of their storage at atmospheric pressure. In order to prevent samples oxidation, 10‐nm‐thick Al
2
O
3
layer was used as a protective layer. The place of bridge break near the anode side was shown to be independent on the ambient pressure and substrate temperature.