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

Hints of Growth Mechanism Left in Supercrystals

Supercrystals of DNA-functionalized nanoparticles are visualized in three dimensions using X-ray ptychographic tomography, and their reciprocal spaces are mapped with small-angle X-ray scattering in order to better understand their internal defect structures. X-ray ptychographic tomography reveals various types of defects in an assembly that otherwise exhibits a single crystalline diffraction pattern. On average, supercrystals composed of smaller nanoparticles are smaller in size than supercrystals composed of larger particles. Additionally, supercrystals composed of small nanoparticles are typically aggregated into larger "necklace-like" structures. Within these larger structures, some but not all pairs of connected domains are coherent in their relative orientations. In contrast, supercrystals composed of larger nanoparticles with longer DNA ligands typically form faceted crystals. The combination of these two complementary X-ray techniques reveals that the crystalline assemblies grow by aggregation of smaller assemblies followed by rearrangement of nanoparticles.

The probe profile and lateral resolution of scanning transmission electron microscopy of thick specimens

Lateral profiles of the electron probe of scanning transmission electron microscopy (STEM) were simulated at different vertical positions in a micrometers-thick carbon sample. The simulations were carried out using the Monte Carlo method in CASINO software. A model was developed to fit the probe profiles. The model consisted of the sum of a Gaussian function describing the central peak of the profile and two exponential decay functions describing the tail of the profile. Calculations were performed to investigate the fraction of unscattered electrons as a function of the vertical position of the probe in the sample. Line scans were also simulated over gold nanoparticles at the bottom of a carbon film to calculate the achievable resolution as a function of the sample thickness and the number of electrons. The resolution was shown to be noise limited for film thicknesses less than 1 μm. Probe broadening limited the resolution for thicker films. The validity of the simulation method was verified by comparing simulated data with experimental data. The simulation method can be used as quantitative method to predict STEM performance or to interpret STEM images of thick specimens.

Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: implications for tomography of thick biological sections

A Monte Carlo electron-trajectory calculation has been implemented to assess the optimal detector configuration for scanning transmission electron microscopy (STEM) tomography of thick biological sections. By modeling specimens containing 2 and 3 at% osmium in a carbon matrix, it was found that for 1-microm-thick samples the bright-field (BF) and annular dark-field (ADF) signals give similar contrast and signal-to-noise ratio provided the ADF inner angle and BF outer angle are chosen optimally. Spatial resolution in STEM imaging of thick sections is compromised by multiple elastic scattering which results in a spread of scattering angles and thus a spread in lateral distances of the electrons leaving the bottom surface. However, the simulations reveal that a large fraction of these multiply scattered electrons are excluded from the BF detector, which results in higher spatial resolution in BF than in high-angle ADF images for objects situated towards the bottom of the sample. The calculations imply that STEM electron tomography of thick sections should be performed using a BF rather than an ADF detector. This advantage was verified by recording simultaneous BF and high-angle ADF STEM tomographic tilt series from a stained 600-nm-thick section of C. elegans. It was found that loss of spatial resolution occurred markedly at the bottom surface of the specimen in the ADF STEM but significantly less in the BF STEM tomographic reconstruction. Our results indicate that it might be feasible to use BF STEM tomography to determine the 3D structure of whole eukaryotic microorganisms prepared by freeze-substitution, embedding, and sectioning.

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

Scanning transmission electron microscopy at 300kV enables the visualization of nucleolar silver-stained structures within thick sections (3-8 microns) of Epon-embedded cells at high tilt angles (-50 degrees; +50 degrees). 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-microns-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-/A2/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-microns-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 microns. 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.

Quantitative energy-filtered electron microscopy of biological molecules in ice

The theoretical and experimental bases for quantitative electron microscopy of frozen-hydrated specimens are described, with special considerations of energy filtration to improve the images. The elastic and inelastic scattering from molecules in vacuum and in ice are calculated, and simple methods to approximate scattering are introduced. Multiple scattering calculations are used to describe the scattering from vitreous ice and to predict the characteristics of images of frozen-hydrated molecules as a function of ice thickness and accelerating voltage. Energy filtration is predicted to improve image contrast and signal-to-noise ratio. Experimental values for the inelastic scattering of ice, the energy spectrum of thick ice, and the contrast of biological specimens are determined. The principles of compensation for the contrast transfer function are presented. Tobacco mosaic virus is used to quantify the accuracy of interpreting image intensities to derive the absolute mass, mass per unit length, and internal mass densities of biological molecules. It is shown that compensation for the contrast transfer function is necessary and sufficient to convert the images into accurate representations of molecular density. At a resolution of 2 nm, the radial density reconstructions of tobacco mosaic virus are in quantitative agreement with the atomic model derived from X-ray results.

Energy filtered STEM imaging of thick biological sections

Energy filtered imaging of thick biological specimens was analysed using a dedicated STEM fitted with an energy loss spectrometer and interfaced with a sophisticated data collection setup. All images were digital, thus permitting a quantitative analysis of the data. We also present a mathematical explanation of the data, which is useful in predicting the quality of thick specimen images formed with energy filtered electrons. It is known that increasing specimen thickness leads to a decrease of the zero energy loss intensity and an increase in higher (multiply scattered) energy loss electrons. We show that contrast decreases gradually with increased energy loss but, most important, the signal to noise ratio is maximal at an energy loss position slightly below the intensity maximum. This is the optimal position for imaging thick specimens. Moreover our studies confirm that the following parameters have similar effects on the energy loss spectra: (1) increased thickness (t); (2) higher average Z number elements (or lower mean free path); and (3) lower primary voltage (V0).

Influence of detector geometry on image properties of the STEM for thick objects

Plural electron scattering within thick objects broadens and smoothes the intensity distribution in the detector plane of a scanning transmission electron microscope. Detector arrangements have been determined which give maximum contrast and optimum S/N when the object details are large compared to the scanning spot. Asymptotic expressions for the optimum detector angles, specimen resolution, and S/N were obtained which are valid for objects thicker than approximately four elastic mean free path lengths. Exact calculations of the changes in contrast and S/N with thickness fluctuations in amorphous carbon foils were performed for atbitrary foil thicknesses. Elastic and inelastic electron scattering was taken into account.

Minimization of dose as a criterion for the selection of imaging modes in electron microscopy of amorphous specimens

A fundamental limitation in electron microscopy of organic specimens is radiation damage by the electron beam. To minimize damage it is necessary to have maximum information collection for a given dose. Various modes of operation of conventional and scanning transmission microscopes are compared with respect to their ability to detect small changes in specimen thickness or density with a given signal to noise ratio. Incoherent imaging is assumed, and this is expected to apply to amorphous specimens under a variety of microscope conditions. For either very thin or very thick specimens, the scanning transmission microscope is found to require nearly 10 times less dose than a conventional microscope for the same signal to noise ratio in the image. For specimens of intermediate thickness, scanning and conventional transmission electron microscopes are roughly equivalent.

Aperture contrast in thick amorphous specimens using scanning transmission electron microscopy

The contrast observed in thick amorphous specimens using a scanning transmission electron microscope (STEM) can be considerably improved by the use of an optimum collector aperture angle. The size of this angle can be calculated by considering the variation of electron current transmitted through the specimen as a function both of the specimen thickness and of the angle of collection subtended at the specimen. Typically these calculations predict optimum angles to be several times the half-width of the elastic scattering distribution, often 10(-1) rad or more. Observations of biological sections of up to 2 micron in thickness using scanning attachments of commercial transmission microscopes have verifie these results at beam voltages of 50, 100 and 200 kV. Wide angle convergent beam diffraction patterns were used to give accurate values of the effective angles represented by the various collector apertures. Once the linearity of the detector-amplifier system had been established, operation in a line modulation mode enabled quantitative measurements to be made of the image contrast. Such measurements also offer a quick effective method of comparing electron beam penetrations.

A method for the improvement of the visibility of transmission electron microscope images

A method is presented of improving the visibility of transmission electron microscope images in any situation in which a high resolution in only one chosen direction is of interest. The technique is based on the use of slot shaped objective apertures. Such apertures are of reduced area relative to a circular aperture giving the same all round resolution. The background intensity due to inelastically scattered electrons is thus reduced. The aperture device developed is described, while the value of the method is demonstrated by its application to the observation of dislocations. Further possible applications are indicated.