Development of phase plates for electron microscopes and their biological application

Ultrafast Transverse Modulation of Free Electrons by Interaction with Shaped Optical Fields

Spatiotemporal electron-beam shaping is a bold frontier of electron microscopy. Over the past decade, shaping methods evolved from static phase plates to low-speed electrostatic and magnetostatic displays. Recently, a swift change of paradigm utilizing light to control free electrons has emerged. Here, we experimentally demonstrate arbitrary transverse modulation of electron beams without complicated electron-optics elements or material nanostructures, but rather using shaped light beams. On-demand spatial modulation of electron wavepackets is obtained via inelastic interaction with transversely shaped ultrafast light fields controlled by an external spatial light modulator. We illustrate this method for the cases of Hermite-Gaussian and Laguerre-Gaussian modulation and discuss their use in enhancing microscope sensitivity. Our approach dramatically widens the range of patterns that can be imprinted on the electron profile and greatly facilitates tailored electron-beam shaping.

Phase plates in the transmission electron microscope: operating principles and applications

In this paper, we review the current state of phase plate imaging in a transmission electron microscope. We focus especially on the hole-free phase plate design, also referred to as the Volta phase plate. We discuss the implementation, operating principles and applications of phase plate imaging. We provide an imaging theory that accounts for inelastic scattering in both the sample and in the hole-free phase plate.

Effect of Carbon Nanotube Diameter and Stiffness on Their Phase Behavior in Crowded Solutions

The unique carbon nanotube (CNT) properties are mainly determined by their geometry, e.g., their aspect ratio, diameter, and number of walls. So far, chlorosulfonic acid is the only practical true solvent for carbon nanotubes, forming thermodynamically stable molecular solutions. Above a critical concentration the system forms an ordered, nematic liquid-crystalline phase. That phase behavior is the basis for liquid-phase processing and the optimal translation of the carbon nanotube molecular properties to the macroscopic scale. The final material properties depend on the phase behavior of the "dope" from which it is prepared, which depends on the CNT parameters themselves. Earlier work determined that CNT aspect ratio controls the phase behavior, in accordance with classical rigid-rod theories. Here we use cryogenic transmission electron microscopy and Raman spectroscopy to understand the relation between the geometry of the CNTs, the chemical interaction with chlorosulfonic acid, and the phase behavior of crowded solutions. We show that the CNT diameter and number of walls also play an independent role in the phase transition and phase morphology of the system because of their effect on the CNT bending stiffness.

Surfactant-assisted individualization and dispersion of boron nitride nanotubes

Boron nitride nanotubes (BNNTs) belong to a novel class of material with useful thermal, electronic and optical properties. However, the study and the development of applications of this material requires the formation of stable dispersions of individual BNNTs in water. Here we address the dispersion of BNNT material in water using surfactants with varying properties. The surfactants were compared based on the quantity of BNNTs dispersed and the quality of the dispersions, as visualized by AFM and cryo-TEM. All surfactants produce dispersions of individualized or small bundles of BNNTs. Of the surfactants tested, high molecular weight, nonionic surfactants suspend the most BNNTs, while ionic surfactants remove the most h-BN impurities. The surfactant dispersions were further characterized by ensemble measurements, such as UV absorption and photoluminescence, dynamic light scattering (DLS), and zeta potential to investigate dispersion stability and quality. These techniques provide a facile strategy for testing future BNNT dispersions. The results of this study reveal that BNNT dispersions in aqueous solution can be tuned to fit a specific application through surfactant selection.

Axicon Lens for Electrons Using a Magnetic Vortex: The Efficient Generation of a Bessel Beam

We demonstrate experimentally an efficient electron axicon lens using a magnetic vortex. We show that naturally occurring magnetic vortices with circular magnetic moment distributions in a soft-magnetic thin film create conical phase shifts for fast electrons. Such radially symmetric linear phase ramps are equivalent to ideal light optical axicons. We apply this lens to generate efficient nondiffracting electron Bessel beams, which we observe experimentally in through-focus Lorentz images as well as in propagated off-axis electron holograms. This highlights the potential for using magnetic nanostructures as highly efficient and flexible phase plates for crafting desired electron beam shapes.

In-focus electrostatic Zach phase plate imaging for transmission electron microscopy with tunable phase contrast of frozen hydrated biological samples

Transmission electron microscopy (TEM) images of beam sensitive weak-phase objects such as biological cryo samples usually show a very low signal-to-noise ratio. These samples have almost no amplitude contrast and instead structural information is mainly encoded in the phase contrast. To increase the sample contrast in the image, especially for low spatial frequencies, the use of phase plates for close to focus phase contrast enhancement in TEM has long been discussed. Electrostatic phase plates are favorable in particular, as their tunable potential will allow an optimal phase shift adjustment and higher resolution than film phase plates as they avoid additional scattering events in matter. Here we show the first realization of close to focus phase contrast images of actin filament cryo samples acquired using an electrostatic Zach phase plate. Both positive and negative phase contrast is shown, which is obtained by applying appropriate potentials to the phase plate. The dependence of phase contrast improvement on sample orientation with respect to the phase plate is demonstrated and single-sideband artifacts are discussed. Additionally, possibilities to reduce contamination and charging effects of the phase plate are shown.

Biological applications of phase-contrast electron microscopy

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

Invited review article: Methods for imaging weak-phase objects in electron microscopy

Contrast has traditionally been produced in electron-microscopy of weak phase objects by simply defocusing the objective lens. There now is renewed interest, however, in using devices that apply a uniform quarter-wave phase shift to the scattered electrons relative to the unscattered beam, or that generate in-focus image contrast in some other way. Renewed activity in making an electron-optical equivalent of the familiar "phase-contrast" light microscope is based in part on the improved possibilities that are now available for device microfabrication. There is also a better understanding that it is important to take full advantage of contrast that can be had at low spatial frequency when imaging large, macromolecular objects. In addition, a number of conceptually new phase-plate designs have been proposed, thus increasing the number of options that are available for development. The advantages, disadvantages, and current status of each of these options is now compared and contrasted. Experimental results that are, indeed, superior to what can be accomplished with defocus-based phase contrast have been obtained recently with two different designs of phase-contrast aperture. Nevertheless, extensive work also has shown that fabrication of such devices is inconsistent, and that their working lifetime is short. The main limitation, in fact, appears to be electrostatic charging of any device that is placed into the electron diffraction pattern. The challenge in fabricating phase plates that are practical to use for routine work in electron microscopy thus may be more in the area of materials science than in the area of electron optics.

Vortex beam production and contrast enhancement from a magnetic spiral phase plate

Electron vortex beam probes offer the possibility of mapping magnetic moments with atomic resolution. In this work we consider using the stray magnetic field produced from a narrow ferromagnetic rod magnetised along its long axis to produce a vortex beam probe, as an alternative to the currently used holographic apertures or gratings. We show through numerical modelling, electron holography observations and direct imaging of the electron probe, that a long narrow ferromagnetic rod induces a phase shift in the wave-function of passing electrons that approximately describes a helix in the regions near its ends. Directing this rod towards the optical axis of a charged-particle beam probe forming system at a limiting aperture position, with the free-end sufficiently close to the axis, is shown to offer a point spread function composed of vortex modes, with evidence of this appearing in observations of the electron probe formed from inserting a micro-fabricated CoFe rod into the beam path of a 300 keV transmission electron microscope (TEM). If the rod is arranged to contain the magnetic flux of h/e, thus producing a maximum phase shift of 2π, it produces a simple spiral-like phase contrast transfer function for weak phase objects. In this arrangement the ferromagnetic rod can be used as a phase plate, positioned at the objective aperture position of a TEM, yielding enhanced image contrast which is simulated to be intermediate between comparable Zernike and Hilbert phase plates. Though this aspect of the phase plate performance is not demonstrated here, agreement between our observations and models for the probe formed from an example rod containing a magnetic flux of ~2.35h/e, indicate this phase plate arrangement could be a simple means of enhancing contrast and gaining additional information from TEM imaged weak phase samples, while also offering the capability to produce vortex beam probes. However, steps still need to be taken to either remove or improve the support membrane for the rod in our experiments to reduce any effects from charging in the phase plate.

Future developments in instrumentation for electron crystallography

Advances in instrumentation have proceeded at an impressive rate since the invention of the electron microscope. These advances have produced a continuous expansion of the capabilities and range of application of electron microscopy. In order to provide some insights on how continuing advances may enhance cryo-electron microscopy and electron crystallography, we review some of the active areas of instrumentation development. There is strong momentum in areas including detectors, phase contrast devices, and aberration correctors that may have substantial impact on the productivity and expectations of electron crystallographers.

Novel vortex generator and mode converter for electron beams

A mode converter for electron vortex beams is described. Numerical simulations, confirmed by experiment, show that the converter transforms a vortex beam with a topological charge m=±1 into beams closely resembling Hermite-Gaussian HG(10) and HG(01) modes. The converter can be used as a mode discriminator or filter for electron vortex beams. Combining the converter with a phase plate turns a plane wave into modes with topological charge m=±1. This combination serves as a generator of electron vortex beams of high brilliance.

Characterisation of ferromagnetic rings for Zernike phase plates using the Aharonov-Bohm effect

Holographic measurements on magnetised thin-film cobalt rings have demonstrated both onion and vortex states of magnetisation. For a ring in the vortex state, the difference between phases of electron paths that pass through the ring and those that travel outside it was found to agree very well with Aharonov-Bohm theory within measurement error. Thus the magnetic flux in thin-film rings of ferromagnetic material can provide the phase shift required for phase plates in transmission electron microscopy. When a ring of this type is used as a phase plate, scattered electrons will be intercepted over a radial range similar to the ring width. A cobalt ring of thickness 20 nm can produce a phase difference of π/2 from a width of just under 30 nm, suggesting that the range of radial interception for this type of phase plate can be correspondingly small.

Design of a hybrid double-sideband/single-sideband (schlieren) objective aperture suitable for electron microscopy

A novel design is described for an aperture that blocks a half-plane of the electron diffraction pattern out to a desired scattering angle, and then--except for a narrow support beam--transmits all of the scattered electrons beyond that angle. Our proposed tulip-shaped design is thus a hybrid between the single-sideband (ssb) aperture, which blocks a full half-plane of the diffraction pattern, and the conventional (i.e. fully open) double-sideband (dsb) aperture. The benefits of this hybrid design include the fact that such an aperture allows one to obtain high-contrast images of weak-phase objects with the objective lens set to Scherzer defocus. We further demonstrate that such apertures can be fabricated from thin-foil materials by milling with a focused ion beam (FIB), and that such apertures are fully compatible with the requirements of imaging out to a resolution of at least 0.34nm. As is known from earlier work with single-sideband apertures, however, the edge of such an aperture can introduce unwanted, electrostatic phase shifts due to charging. The principal requirement for using such an aperture in a routine data-collection mode is thus to discover appropriate materials, protocols for fabrication and processing and conditions of use such that the hybrid aperture remains free of charging over long periods of time.

Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects

Although cryo-electron microscopy (cryo-EM) of biological macromolecules has made important advances in the past few years, the level of current technical performance is still well below what the physics of electron scattering would allow. It should be possible, for example, to use cryo-EM to solve protein structures at atomic resolution for particle sizes well below 80 kDa, but currently this has been achieved only for particles at least 10 times larger than that. In this review, we first examine some of the reasons for this large gap in performance. We then give an overview of work that is currently in progress to 1), improve the signal/noise ratio for area detectors; 2), improve the signal transfer between the scattered electrons and the corresponding images; and 3), reduce the extent to which beam-induced movement causes a steep fall-off of signal at high resolution. In each case, there is substantial reason to think that cryo-EM can indeed be made to approach the estimated physical limits.

The surface of evaporated carbon films is an insulating, high-bandgap material

The electrical conductance and the optical density of evaporated carbon films are measured as a function of the thickness of the films. The resulting data show that up to a thickness of approximately 4 nm, carbon films are optically transparent and electrically insulating. The same data also suggest that this insulating character persists near to the surface when the overall thickness is further increased. Since a support film with poor surface conductivity is undesirable for many applications in electron microscopy, we suggest that the usefulness of evaporated carbon films in electron microscopy might be further improved by doping or by other methods that improve the electrical conductivity near the surface.

Another 60 years in electron microscopy: development of phase-plate electron microscopy and biological applications

It has been six decades since the concept of phase-plate electron microscopy was first reported by Boersch, but an experimental report on a phase plate with a theoretically rational performance has only recently been released by a group including the present author. Currently, many laboratories around the world are attempting to develop a wide range of phase plates to enhance the capabilities of transmission electron microscopy. They are reporting not only advantages of their own developments but also a fundamental problem inherent to electron beam devices, namely charging, i.e. the accumulation of electrostatic charge. In this report, we review the 60-year history of phase-plate development, with a particular focus on the fundamental issue of phase-plate charging. Next, we review biological applications of qualified phase plates, which have been successful in avoiding charging to some extent. Finally, we compare and discuss electron microscopic images, taken with or without phase plates, of biological targets such as proteins (GroEL and TRPV4), protein complexes (flagellar motor), viruses (T4 phage, ε-15 phage and herpes simplex virus), bacterial (cyanobacteria) and mammalian (PtK2) cells.

Phase Contrast Enhancement with Phase Plates in Biological Electron Microscopy

Theoretically, transmission electron microscopy (TEM) is compatible with three different types of phase plate: thin-film, electrostatic, and magnetic. However, designing functional phase plates has been an arduous process that has suffered from unavoidable technical obstacles such as phase-plate charging and difficulties associated with micro-fabrication of electrostatic and magnetic phase plates. This review discusses phase-contrast schemes that allow visualization of transparent objects with high contrast. Next it deals with recent studies on biological applications ranging from proteins and viruses to whole cells. Finally, future prospects for overcoming the problem of phase-plate charging and for designing the next generation of phase-plates to solve the problem of electron loss inherent in thin-film phase plates are discussed.

Phase plates for transmission electron microscopy

Phase plates are a new technique in the field of cryo-electron microscopy. They provide improved contrast and signal-to-noise ratio in images of radiation sensitive specimens. Thin film phase plates are being tested in biological applications and have demonstrated benefits for single particle analysis and cryo-tomography. There are still unsolved problems, such as reliability of manufacturing and deterioration of performance with time. Several other types of phase plates are currently under development and may become available for cryo-microscopy in near future. Presented is a short overview of the current state of the field as well as ideas for the future directions. Also included is a detailed description of the instrumentation requirements and the experimental procedures for phase plate application.

Phase TEM for biological imaging utilizing a Boersch electrostatic phase plate: theory and practice

A Boersch electrostatic phase plate (BEPP) used in a transmission electron microscope (TEM) system can provide tuneable phase shifts and overcome the low contrast problem for biological imaging. Theoretically, a pure phase image with a high phase contrast can be obtained using a BEPP. However, a currently available TEM system utilizing a BEPP cannot achieve sufficiently high phase efficiency for biological imaging, owing to the practical conditions. The low phase efficiency is a result of the blocking of partial unscattered electrons by BEPP, and the contribution of absorption contrast. The fraction of blocked unscattered beam is related to BEPP dimensions and to divergence of the illumination system of the TEM. These practical issues are discussed in this paper. Phase images of biological samples (negatively stained ferritin) obtained by utilizing a BEPP are reported, and the phase contrast was found to be enhanced by a factor of approximately 1.5, based on the calculation using the Rose contrast criterion. The low gain in phase contrast is consistent with the expectation from the current TEM/BEPP system. A new generation of phase TEM utilizing BEPP and designed for biological imaging with a high phase efficiency is proposed.

High-contrast imaging of plastic-embedded tissues by phase contrast electron microscopy

Phase contrast electron microscopy utilizing phase plates has been considered suitable for high-contrast observation of weak phase objects. This novel technique was newly applied to histochemically stained strong phase objects of osmificated biological specimens. Sections of various thicknesses, specifically stained for the Golgi apparatus by the ZIO technique using the heavy metals Zn and Os, were observed with a phase contrast electron microscope in Zernike and Hilbert imaging modes. Quantitative analysis of image contrast in real space and the power spectrum in Fourier space showed a high-contrast gain even for strong phase objects. This result clearly indicates that phase contrast electron microscopy can be effectively used not only for weak phase objects but also for strong phase objects in biology.

Practical factors affecting the performance of a thin-film phase plate for transmission electron microscopy

A number of practical issues must be addressed when using thin carbon films as quarter-wave plates for Zernike phase-contrast electron microscopy. We describe, for example, how we meet the more stringent requirements that must be satisfied for beam alignment in this imaging mode. In addition we address the concern that one might have regarding the loss of some of the scattered electrons as they pass through such a phase plate. We show that two easily measured parameters, (1) the low-resolution image contrast produced in cryo-EM images of tobacco mosaic virus particles and (2) the fall-off of the envelope function at high resolution, can be used to quantitatively compare the data quality for Zernike phase-contrast images and for defocused bright-field images. We describe how we prepare carbon-film phase plates that are initially free of charging or other effects that degrade image quality. We emphasize, however, that even though the buildup of hydrocarbon contamination can be avoided by heating the phase plates during use, their performance nevertheless deteriorates over the time scale of days to weeks, thus requiring their frequent replacement in order to maintain optimal performance.

Phase-plate electron microscopy: a novel imaging tool to reveal close-to-life nano-structures

After slow progress in the efforts to develop phase plates for electron microscopes, functional phase plate using thin carbon film has been reported recently. It permits collecting high-contrast images of close-to-life biological structures with cryo-fixation and without staining. This report reviews the state of the art for phase plates and what is innovated with them in biological electron microscopy. The extension of thin-film phase plates to the material-less type using electrostatic field or magnetic field is also addressed.

Restoration of weak phase-contrast images recorded with a high degree of defocus: the "twin image" problem associated with CTF correction

Relatively large values of objective-lens defocus must normally be used to produce detectable levels of image contrast for unstained biological specimens, which are generally weak phase objects. As a result, a subsequent restoration operation must be used to correct for oscillations in the contrast transfer function (CTF) at higher resolution. Currently used methods of CTF correction assume the ideal case in which Friedel mates in the scattered wave have contributed pairs of Fourier components that overlap with one another in the image plane. This "ideal" situation may be only poorly satisfied, or not satisfied at all, as the particle size gets smaller, the defocus value gets larger, and the resolution gets higher. We have therefore investigated whether currently used methods of CTF correction are also effective in restoring the single-sideband image information that becomes displaced (delocalized) by half (or more) the diameter of a particle of finite size. Computer simulations are used to show that restoration either by "phase flipping" or by multiplying by the CTF recovers only about half of the delocalized information. The other half of the delocalized information goes into a doubly defocused "twin" image of the type produced during optical reconstruction of an in-line hologram. Restoration with a Wiener filter is effective in recovering the delocalized information only when the signal-to-noise ratio (S/N) is orders of magnitude higher than that which exists in low-dose images of biological specimens, in which case the Wiener filter approaches division by the CTF (i.e. the formal inverse). For realistic values of the S/N, however, the "twin image" problem seen with a Wiener filter is very similar to that seen when either phase flipping or multiplying by the CTF is used for restoration. The results of these simulations suggest that CTF correction is a poor alternative to using a Zernike-type phase plate when imaging biological specimens, in which case the images can be recorded in a close-to-focus condition, and delocalization of high-resolution information is thus minimized.