Three‐dimensional bright‐field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms

Bacterial biofilms play key roles in environmental and biomedical processes, and understanding their activities requires comprehension of their nanoarchitectural characteristics. Electron microscopy (EM) is an essential tool for nanostructural analysis, but conventional EM methods are limited in that they either provide topographical information alone, or are suitable for imaging only relatively thin (<300 nm) sample volumes. For biofilm investigations, these are significant restrictions. Understanding structural relations between cells requires imaging of a sample volume sufficiently large to encompass multiple cells and the capture of both external and internal details of cell structure. An emerging EM technique with such capabilities is bright‐field scanning transmission electron microscopy (BF‐STEM) and in the present report BF‐STEM was coupled with tomography to elucidate nanostructure in biofilms formed by the polycyclic aromatic hydrocarbon‐degrading soil bacterium, Delftia acidovorans Cs1‐4. Dual‐axis BF‐STEM enabled high‐resolution 3‐D tomographic recontructions (6–10 nm) visualization of thick (1250 and 1500 nm) sections. The 3‐D data revealed that novel extracellular structures, termed nanopods, were polymorphic and formed complex networks within cell clusters. BF‐STEM tomography enabled visualization of conduits formed by nanopods that could enable intercellular movement of outer membrane vesicles, and thereby enable direct communication between cells. This report is the first to document application of dual‐axis BF‐STEM tomography to obtain high‐resolution 3‐D images of novel nanostructures in bacterial biofilms. Future work with dual‐axis BF‐STEM tomography combined with correlative light electron microscopy may provide deeper insights into physiological functions associated with nanopods as well as other nanostructures.     

Comparison of intensity distributions in tomograms from BF TEM,ADF STEM,HAADF STEM,and calculated tilt series

The three-dimensional (3D) morphology of a nanometer-sized object can be obtained using electron tomography. Variations in composition or density of the object cause variations in the reconstructed intensity. When imaging homogeneous objects, variations in reconstructed intensity are caused by the imaging technique, imaging conditions, and reconstruction. In this paper, we describe data acquisition, image processing, and 3D reconstruction to obtain and compare tomograms of magnetite crystals from bright field (BF) transmission electron microscopy (TEM), annular dark-field (ADF) scanning transmission electron microscopy (STEM), and high-angle annular dark field (HAADF) STEM tilt series. We use histograms, which plot the number of volume elements (voxels) at a given intensity vs. the intensity, to measure and quantitatively compare intensity distributions among different tomograms. In combination with numerical simulations, we determine the influence of maximum tilt angle, tilt increment, contrast changes with tilt (diffraction contrast), and the signal-to-noise ratio (SNR) as well as the choice of the reconstruction approach (weighted backprojection (WB) and sequential iterative reconstruction technique (SIRT)) on the histogram. We conclude that because ADF and HAADF STEM techniques are less affected by diffraction, and because they have a higher SNR than BF TEM, they are better suited for tomography of nanometer-sized crystals.     

Comparison of intensity distributions in tomograms from BF TEM, ADF STEM, HAADF STEM, and calculated tilt series

The three-dimensional (3D) morphology of a nanometer-sized object can be obtained using electron tomography. Variations in composition or density of the object cause variations in the reconstructed intensity. When imaging homogeneous objects, variations in reconstructed intensity are caused by the imaging technique, imaging conditions, and reconstruction. In this paper, we describe data acquisition, image processing, and 3D reconstruction to obtain and compare tomograms of magnetite crystals from bright field (BF) transmission electron microscopy (TEM), annular dark-field (ADF) scanning transmission electron microscopy (STEM), and high-angle annular dark field (HAADF) STEM tilt series. We use histograms, which plot the number of volume elements (voxels) at a given intensity vs. the intensity, to measure and quantitatively compare intensity distributions among different tomograms. In combination with numerical simulations, we determine the influence of maximum tilt angle, tilt increment, contrast changes with tilt (diffraction contrast), and the signal-to-noise ratio (SNR) as well as the choice of the reconstruction approach (weighted backprojection (WB) and sequential iterative reconstruction technique (SIRT)) on the histogram. We conclude that because ADF and HAADF STEM techniques are less affected by diffraction, and because they have a higher SNR than BF TEM, they are better suited for tomography of nanometer-sized crystals.     

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.     

Effects of specimen tilt in ADF-STEM imaging of a-Si/c-Si interfaces

Annular dark field scanning transmission electron microscopy (ADF-STEM) imaging of a crystal depends strongly on specimen orientation, but for an amorphous sample it is insensitive to orientation changes. To fully investigate the effects of specimen tilt, an interface of amorphous Si (a-Si) and crystalline Si (c-Si) was rotated systematically off a zone axis in a STEM equipped with low-angle ADF (LAADF) and high-angle ADF (HAADF) detectors. The change of relative intensity across the interface shows very different trends in the LAADF and the HAADF images upon tilting. More importantly, it is found that the HAADF signal decreases much more rapidly when tilted off a zone axis than does the LAADF signal. The high-resolution lattice fringes also disappear much faster in the HAADF image than in the LAADF image. These trends reflect the fact that the channeling peaks that are responsible for scattering into the HAADF detector decrease more quickly upon tilting than the lower angle scattering to the LAADF detector does.     

Elemental mapping with elastically scattered electrons

We describe a technique for efficient, quantitative, standardless elemental mapping using a high-angle annular detector in a scanning transmission electron microscope (STEM) to collect elastically scattered electrons. With a single crystal specimen, contrast due to thickness variations, diffraction, and channelling effects can be avoided, so that the resulting image contrast quantitatively reflects variations in impurity concentration. We compare a number of simple analytical approximations to the elastic scattering cross sections and show that a standardless analysis is possible over a wide range of atomic number and inner detector angle to an absolute accuracy of better than 20%.     

Spatially resolved diffractometry with atomic-column resolution

We demonstrate spatially resolved diffractometry in which diffraction patterns are acquired at two-dimensional positions on a specimen using scanning transmission electron microscopy (STEM), resulting in four-dimensional data acquisition. A high spatial resolution of about 0.1 nm is achieved using a stabilized STEM instrument, a spherical aberration corrector and various post-acquisition data processings. We have found a few novel results in the radial and the azimuthal scattering angle dependences of atomic-column contrast in STEM images. Atomic columns are clearly observed in dark field images obtained using the excess Kikuchi band intensity even in small solid-angle detection. We also find that atomic-column contrasts in dark field images are shifted in the order of a few tens of picometers on changing the azimuthal scattering angle. This experimental result is approximately interpretable on the basis of the impact parameter in Rutherford scattering. Spatially resolved diffractometry provides fundamental knowledge related to various STEM techniques, such as annular dark field (ADF) and annular bright field (ABF) imaging, and it is expected to become an analytical platform for advanced STEM imaging.     

Thick specimens in the CEM and STEM. Resolution and image formation.

A theory of resolution and image formation is presented for thick amorphous specimens in transmission electron microscopes. Eight modes of operation are considered, four in the scanning transmission electron microscope (STEM) and four in the conventional electron microscope (CEM). A thick specimen is defined here as one in which the resolution of detail is limited by plural scattering of the electron beam. In practice this includes films on the order of a micron in thickness. An analytic theory of plural incoherent scattering is developed which is general with respect to material and beam voltage. The theory gives the distribution of elastically scattered electrons as a function of transverse coordinate and angles, and is directly applicable to optical systems. The theory applies to all thicknesses normally encountered, and includes thin specimens as well as thick specimens. Criteria are proposed for evaluation of the quality of microscope images, and the modulation transfer function is applied to determine some practical estimates of picture quality. The STEM is found to have distinct advantages over the CEM for thick specimens. For a carbon specimen one micron thick a STEM operating in bright field at 90 keV produces an image which is roughly equivalent to that of a CEM operating in bright field at 1 MeV. Improvement can be obtained in the CEM by filtering out eneryg-loss electrons which degrade resolution due to chromatic aberration. This results in a reduction in signal intensity and usable thickness, however.     

Symmetries in BF and HAADF STEM image calculations

Reductions in bright-field (BF) scanning transmission electron microscopy (STEM) and high-angle annular dark-field (HAADF) STEM image calculations with the aid of Bloch wave symmetry are discussed under assumptions that an absorption potential is written by a local potential and a zero-order Laue zone lies parallel to the crystal surface. Translational symmetry allows us to take only partial incident beams in the first Brillouin zone instead of enormous number of partial incident beams in a large convergent disk. Two dimensional point group confines partial incident beams to an irreducible area in addition to factoring a dispersion matrix into noninteracting submatrices on a high symmetry line using the projection operator. The drastic reductions in computing time and memory enable us to readily calculate various BF STEM and HAADF STEM images. The validity and accuracy are demonstrated in comparisons with high resolution experimental BF STEM and HAADF STEM images.     

Transmission EBSD from 10 nm domains in a scanning electron microscope

The spatial resolution of electron diffraction within the scanning electron microscope (SEM) has progressed from channelling methods capable of measuring crystallographic characteristics from 10 μm regions to electron backscatter diffraction (EBSD) methods capable of measuring 120 nm particles. Here, we report a new form of low‐energy transmission Kikuchi diffraction, performed in the SEM. Transmission‐EBSD (t‐EBSD) makes use of an EBSD detector and software to capture and analyse the angular intensity variation in large‐angle forward scattering of electrons in transmission, without postspecimen coils. We collected t‐EBSD patterns from Fe–Co nanoparticles of diameter 10 nm and from 40 nm‐thick Ni films with in‐plane grain size 15 nm. The patterns exhibited contrast similar to that seen in EBSD, but are formed in transmission. Monte Carlo scattering simulations showed that in addition to the order of magnitude improvement in spatial resolution from isolated particles, the energy width of the scattered electrons in t‐EBSD is nearly two orders of magnitude narrower than that of conventional EBSD. This new low‐energy transmission diffraction approach builds upon recent progress in achieving unprecedented levels of imaging resolution for materials characterization in the SEM by adding high‐spatial‐resolution analytical capabilities.     

Contrast and resolution of scanning transmission electron microscope imaging modes

Image blurring due to delocalization of inelastic events was studied for scanning transmission electron microscopy (STEM) of unstained thin sections. The delocalization probability was obtained from the angular distribution of inelastic scattering, which was calculated from experimental electron loss spectra of organic samples. This probability was implemented in a Monte Carlo program to simulate the effects of multiple scattering and delocalization for STEM images collected by either the annular detector or the spectrometer, and images generated by a combination of these two signals. Depending on the illumination, the detector geometry and the energy-loss range selected for imaging the annular detector image is blurred by a non-negligible fraction of inelastically scattered electrons. Simultaneous acquisition of an inelastic image using a spectrometer allows the blurring to be reduced by calculation of either the ratio or the difference of the two darkfield signals. While inherent nonlinearities reduce the interpretability of ratio-contrast images, difference-contrast improves the visibility of details submerged in a diffuse background without introducing artifacts.     

Can high-angle annular dark field scattering be represented by a local operator?

High-angle annular dark field imaging has become an invaluable technique for recording atomic resolution STEM images. Many analyses of high-angle annular dark field images assume that the signal is the result of a local scattering operator and can be represented as a simple convolution of a probe function with a set of atomic columns. The apparent simplicity of the technique and the straightforward increase in signal with atomic number have lead to the belief that it is possible to quantify impurity concentrations at atomic column resolution. The limitations in these assumptions are examined on the basis of approximations starting from a complete theory for high-angle scattering based on multi phonon excitations. Not surprisingly, the accuracy of the local scattering operator approximation improves as the inner cut-off angle is increased.     

STEM imaging of thick specimens with off-axis detectors

For scanning transmission electron microscopy (STEM) images obtained with relatively small objective aperture sizes, the contrast of small objects contained within thick specimens may be considerably enhanced by using an off-axis detector aperture situated on the edge of the central beam spot. The effect is demonstrated for both crystalline and amorphous specimens. The effect arises because the detector collects part of the small angle inelastic scattering and is modified by refraction effects for specimens of rapidly changing thickness.     

Secondary electron detection in the scanning transmission electron microscope

In a dedicated scanning transmission electron microscope (STEM) secondary electron images with high spatial resolution and good contrast can be obtained. Two types of detector are described. These take into account the secondary electrons which depend on the post-specimen field strength of the objective lens. Due to the thinness of the samples and the collection geometry the images differ from those obtained in a convectional scanning microscope. Examples are given where secondary electron images augment the information obtained by the more commonly used imaging modes.     

First experimental test of a new monochromated and aberration-corrected 200 kV field-emission scanning transmission electron microscope

The first 200 kV scanning transmission electron microscope (STEM) with an imaging energy filter, a monochromator and a corrector for the spherical aberration (Cs-corrector) of the illumination system has been built and tested. The STEM/TEM concept with Koehler illumination allows to switch easily between STEM mode for analytical and TEM mode for high-resolution or in situ studies. The Cs-corrector allows the use of large illumination angles for retaining a sufficiently high beam current despite the intensity loss in the monochromator. With the monochromator on and a 3 microm slit in the dispersion plane that gives 0.26 eV full-width at half-maximum (FWHM) energy resolution we have obtained so far an electron beam smaller than 0.20 nm in diameter (FWHM as measured by scanning the spot quickly over the CCD) which contains 7 pA current and, according to simulations, should be around 0.12 nm in true size. A high-angle annular dark field (ADF) image with isotropic resolution better than 0.28 nm has been recorded with the monochromator in the above configuration and the Cs-corrector on. The beam current is still somewhat low for electron energy-loss spectroscopy (EELS) but is expected to increase substantially by optimising the condenser set-up and using a somewhat larger condenser aperture.     

Catalyst particle sizes from Rutherford scattered intensities

We show that the number of atoms in a small supported catalyst cluster can be estimated from the strength of electron scattering into a high angle annular detector in the STEM. The technique is related to the Z contrast methods developed by Crewe, Wall, Langmore and Isaacson. It works best for high atomic number catalyst particles when supported on low atomic number supports, such as Pt on γ-aluminium oxide. The method is particularly useful for detecting and measuring particles in the sub-nanometre size range where bright field images are unreliable. Unlike the Z contrast methods, a high angle annular detector is used, which avoids intensity modulations arising from Bragg reflections. The signal is mostly high angle diffuse scattering, which is predominantly Rutherford scattering, and is proportional to the number of atoms probed by the beam, weighted by their individual scattering cross-sections. Scattering strengths of individual clusters are computed from digitized high angle annular detector images. Data for Pt on γ-aluminium oxide, when plotted as imaged area^1/2 against intensity^1/3, define a straight line. Such plots provide calibration of the intensity increment per atom without the need of external calibration, although assumptions about particle morphology must be made. Reliable results require high signal-to-noise and optimum sampling of the specimen. For an STEM probe size of 0.35 nm, Pt clusters containing as few as three atoms can be detected when supported on typical, 20 nm thick, γ-aluminium oxide supports.     

Applications of medium-voltage STEM for the 3-D study of organelles within very thick sections

Scanning transmission electron microscopy at 300 kV enables the visualization of nucleolar silver-stained structures within thick sections (3–8 μm) of Epon-embedded cells at high tilt angles (–50°; + 50°). Thick sections coated with gold particles were used to determine the best conditions for obtaining images with high contrast and good resolution. For a 6-μm-thick section the values of thinning and shrinkage under the beam are 35 to 10%, respectively. At the electron density used in these experiments (100e^—/Å₂/s) it is estimated that these modifications of the section stabilized in less than 10 min. The broadening of the beam through the section was measured and calculations indicated that the subsequent resolution reached 100 nm for objects localized near the lower side of 4-μm-thick sections with a spot-size of 5·6 nm. Comparing the same biological samples, viewed alternately in CTEM and STEM, demonstrated that images obtained in STEM have a better resolution and contrast for sections thicker than 3 μm. Therefore, the visualization of densely stained structures, observed through very thick sections in the STEM mode, will be very useful in the near future for microtomographic reconstruction of cellular organelles.     

Automated electron tomography with scanning transmission electron microscopy

We report the successful implementation of a fully automated tomographic data collection system in scanning transmission electron microscopy (STEM) mode. Autotracking is carried out by combining mechanical and electronic corrections for specimen movement. Autofocusing is based on contrast difference of a focus series of a small sample area. The focus gradient that exists in normal images due to specimen tilt is effectively removed by using dynamic focusing. An advantage of STEM tomography with dynamic focusing over TEM tomography is its ability to reconstruct large objects with a potentially higher resolution.     

The application of EDXS to the biological sciences

The distribution of chemical elements in soft tissues may be faithfully preserved by very rapid freezing. Most often the material is then cryosectioned and the sections frozen-dried prior to analysis, but direct analysis in the hydrated state is an established alternative. For bulk specimens, the shape of the analysed volume is uncertain. But whichever current model is accepted, analytical spatial resolution must generally be limited to the order of 1 μm. Such specimens can be suitable for the specific analysis of cytoplasm, cell nuclei and large extracellular spaces but not for study on a finer scale. Analytical spatial resolution in the range 200–500 nm is obtainable with sections cut ～ 1 μm thick. In the frozen-hydrated state, small extracellular spaces can be analysed but multiple scattering obscures intracellular detail in the STEM image. The irradiation required for an EDXS analysis, approximately 50 nanoCoulomb (50 nanoAmpere seconds), need not produce intolerable radiation damage when spread over an area 200 nm or more in diameter. Finer structure, for example mitochondria and regions of rough or smooth endoplasmic reticulum, can be identified and analysed in frozen-dried cryosections cut ～ 100 nm thick. Recently such features have been visualized in 100 nm frozen-hydrated sections where the water is vitreous. This opens the prospect of analysing material where elemental distributions have been preserved on a very fine scale, since one might avoid even the ionic shifts from aqueous solution to supramolecular structures which must occur on freeze-drying. But radiation damage may be prohibitive when an irradiation of 50 nanoCoulomb is concentrated into a hydrated area less than 200 nm in diameter.     

The measurement and calculation of the X-ray spatial resolution obtained in the analytical electron microscope

The X-ray microanalytical spatial resolution is determined experimentally in various analytical electron microscopes by measuring the degradation of an atomically discrete composition profile across an interphase interface in a thin-foil of Ni-Cr-Fe. The experimental spatial resolutions are then compared with calculated values. The calculated spatial resolutions are obtained by the mathematical convolution of the electron probe size with an assumed beam-broadening distribution and the single-scattering model of beam broadening. The probe size is measured directly from an image of the probe in a TEM/STEM and indirectly from dark-field signal changes resulting from scanning the probe across the edge of an MgO crystal in a dedicated STEM. This study demonstrates the applicability of the convolution technique to the calculation of the microanalytical spatial resolution obtained in the analytical electron microscope. It is demonstrated that, contrary to popular opinion, the electron probe size has a major impact on the measured spatial resolution in foils < 150 nm thick.