Sub-25-nm laboratory x-ray microscopy using a compound Fresnel zone plate

Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection

Herpes simplex virus-1 (HSV-1) is a large, enveloped DNA virus and its assembly in the cell is a complex multi-step process during which viral particles interact with numerous cellular compartments such as the nucleus and organelles of the secretory pathway. Transmission electron microscopy and fluorescence microscopy are commonly used to study HSV-1 infection. However, 2D imaging limits our understanding of the 3D geometric changes to cellular compartments that accompany infection and sample processing can introduce morphological artefacts that complicate interpretation. In this study, we used soft X-ray tomography to observe differences in whole-cell architecture between HSV-1 infected and uninfected cells. To protect the near-native structure of cellular compartments we used a non-disruptive sample preparation technique involving rapid cryopreservation, and a fluorescent reporter virus was used to facilitate correlation of structural changes with the stage of infection in individual cells. We observed viral capsids and assembly intermediates interacting with nuclear and cytoplasmic membranes. Additionally, we observed differences in the morphology of specific organelles between uninfected and infected cells. The local concentration of cytoplasmic vesicles at the juxtanuclear compartment increased and their mean width decreased as infection proceeded, and lipid droplets transiently increased in size. Furthermore, mitochondria in infected cells were elongated and highly branched, suggesting that HSV-1 infection alters the dynamics of mitochondrial fission/fusion. Our results demonstrate that high-resolution 3D images of cellular compartments can be captured in a near-native state using soft X-ray tomography and have revealed that infection causes striking changes to the morphology of intracellular organelles.

Fast and easy fabrication methodology of Fresnel zone plates for the extreme ultraviolet and soft x-ray regions

Zone plate design and efficient methods for the fabrication of zone plates for extreme ultraviolet (EUV) and soft x-ray applications in a newly developed scanning reflection microscope are presented. Based on e-beam lithography, three types of transmission zone plates with focal lengths between 6 and 15 mm are reported: (i) phase-shifting zone plates made by 190 nm thick PMMA rings on Si₃N₄ membranes, (ii) absorbing zone plates made by 75 nm thick Au ring structures on Si₃N₄, and (iii) freestanding Au rings of 50 nm thickness and increased transmission in the EUV range. Experiments at the DELTA synchrotron facility reveal a minimum spot size and resulting spatial resolution of 9±3  μm, which is the theoretical limit resulting from the synchrotron beam parameters at 60 eV photon energy. Images of a Ti/Si chessboard test pattern are recorded exploiting the energy dependence of the element-specific reflectance.

Numerical simulation and design of an apodized diffractive optical element composed of open-ring zones and pinholes

In this paper, we investigate the relationship between open-ring zones of the Fresnel zone plate and the pinhole rings of photon sieves (PSs). Numerical simulations show that the normalized diffraction fields near the focal point of an individual pinhole ring and the circular open-ring zone are the same. It is confirmed that the maximum diffraction efficiency of an open-ring zone is higher than that of the traditional pinhole ring. Meanwhile, pinhole rings have more flexibility for apodization filtering. Based on these key findings, we propose the design theory of an apodized diffractive optical element comprised of open-ring zones and pinholes. To validate the theory, we developed a design example. Compared with traditional apodized PSs, the new apodized diffractive element has a 50.19% higher energy efficiency, and the minimum pinhole size is enlarged by 30.77%.

Nanoparticle Uptake in Plants: Gold Nanomaterial Localized in Roots of Arabidopsis thaliana by X-ray Computed Nanotomography and Hyperspectral Imaging

Terrestrial plants can internalize and translocate nanoparticles (NPs). However, direct evidence for the processes driving the NP uptake and distribution in plants is scarce at the cellular level. Here, NP-root interactions were investigated after 10 days of exposure of Arabidopsis thaliana to 10 mg·L^-1 of negatively or positively charged gold NPs (∼12 nm) in gels. Two complementary imaging tools were used: X-ray computed nanotomography (nano-CT) and enhanced dark-field microscopy combined with hyperspectral imaging (DF-HSI). The use of these emerging techniques improved our ability to detect and visualize NP in plant tissue: by spectral confirmation via DF-HSI, and in three dimensions via nano-CT. The resulting imaging provides direct evidence that detaching border-like cells (i.e., sheets of border cells detaching from the root) and associated mucilage can accumulate and trap NPs irrespective of particle charge. On the contrary, border cells on the root cap behaved in a charge-specific fashion: positively charged NPs induced a higher mucilage production and adsorbed to it, which prevented translocation into the root tissue. Negatively charged NPs did not adsorb to the mucilage and were able to translocate into the apoplast. These observations provide direct mechanistic insight into NP-plant interactions, and reveal the important function of border cells and mucilage in interactions of plants with charged NPs.

Relative intersection of confidence intervals rule for sharper restoration of soft x-ray images

We present a novel method for restoration of images of nanostructures obtained with a soft-ray microscope that uses a 46.9 nm soft x-ray laser microscope for illumination. To suppress the noise and to preserve the image sharpness, we develop a method based on pixel adaptive zero-order modeling of the observed object. Neighboring areas of each pixel are selected using the relative intersection of confidence intervals rule and used for restoration. Due to the non-uniform distribution of noise in the images, we use robust spatial noise modeling. The method provides sharp restored images-sharper than competitive approaches. The sharpness is measured using local phase coherence in the complex wavelet transform domain and shows visible improvement of the novel method.

Differential-interference-contrast digital in-line holography microscopy based on a single-optical-element

Both digital in-line holography (DIH) and zone plate-based microscopy have received considerable interest as powerful imaging tools. However, the former suffers from a twin-image noise problem. The latter suffers from low efficiency and difficulty in fabrication. Here, we present an effective and efficient phase-contrast imaging approach, named differential-interference-contrast digital in-line holography (DIC-DIH), by using a single optical element to split the incident light into a plane wave and a converging spherical wave and generate a two-dimensional (2D) DIC effect simultaneously. Specifically, to improve image contrast, we present a new single optical element, termed 2D DIC compound photon sieves, by combining two overlaid binary gratings and a compound photon sieve through two logical XOR operations. The proof-of-concept experiments demonstrate that the proposed technique can eliminate the twin-image noise problem and improve image contrast with high efficiency. Additionally, we present an example of the phase-contrast imaging nonuniform thick photoresist development process.

Wavefront aberrations of x-ray dynamical diffraction beams

The effects of dynamical diffraction in x-ray diffractive optics with large numerical aperture render the wavefront aberrations difficult to describe using the aberration polynomials, yet knowledge of them plays an important role in a vast variety of scientific problems ranging from optical testing to adaptive optics. Although the diffraction theory of optical aberrations was established decades ago, its application in the area of x-ray dynamical diffraction theory (DDT) is still lacking. Here, we conduct a theoretical study on the aberration properties of x-ray dynamical diffraction beams. By treating the modulus of the complex envelope as the amplitude weight function in the orthogonalization procedure, we generalize the nonrecursive matrix method for the determination of orthonormal aberration polynomials, wherein Zernike DDT and Legendre DDT polynomials are proposed. As an example, we investigate the aberration evolution inside a tilted multilayer Laue lens. The corresponding Legendre DDT polynomials are obtained numerically, which represent balanced aberrations yielding minimum variance of the classical aberrations of an anamorphic optical system. The balancing of classical aberrations and their standard deviations are discussed. We also present the Strehl ratio of the primary and secondary balanced aberrations.

Restoration of soft x-ray laser images of nanostructures

We present advanced techniques for the restoration of images obtained by soft x-ray laser microscopy. We show two methods. One method is based on adaptive thresholding, while the other uses local Wiener filtering in the wavelet domain to achieve high noise gains. These wavelet based denoising techniques are improved using spatial noise modeling. The accurate noise model is built up from two consecutive images of the object and respective background images. To our knowledge, the results of both proposed approaches over-perform competitive methods. The analysis is robust to enable image acquisition with significantly lower exposure times, which is critical in samples that are sensitive to radiation damage as is the case of biological samples imaged by SXR microscopy.

Laboratory cryo soft X-ray microscopy

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.

Laboratory soft-x-ray microscope for cryotomography of biological specimens

Soft-x-ray cryotomography allows quantitative and high-resolution three-dimensional imaging of intact unstained cells. To date, the method relies on synchrotron-radiation sources, which limits accessibility for researchers. Here we present a laboratory water-window microscope for cryotomography. It is based on a λ=2.48 nm liquid-jet laser-plasma source, a normal-incidence multilayer condenser, a 30 nm zone-plate objective, and a cryotilt sample holder. We demonstrate high-resolution imaging, as well as quantitative tomographic imaging, of frozen intact cells. The reconstructed tomogram of the intracellular local absorption coefficient shows details down to ∼100 nm.

Transmission and emission x-ray microscopy: operation modes, contrast mechanisms and applications

Advances in microscopy techniques based on x-rays have opened unprecedented opportunities in terms of spatial resolution, combined with chemical and morphology sensitivity, to analyze solid, soft and liquid matter. The advent of ultrabright third and fourth generation photon sources and the continuous development of x-ray optics and detectors has pushed the limits of imaging and spectroscopic analysis to structures as small as a few tens of nanometers. Specific interactions of x-rays with matter provide elemental and chemical sensitivity that have made x-ray spectromicroscopy techniques a very attractive tool, complementary to other microscopies, for characterization in all actual research fields. The x-ray penetration power meets the demand to examine samples too thick for electron microscopes implementing 3D imaging and recently also 4D imaging which adds time resolution as well. Implementation of a variety of phase contrast techniques enhances the structural sensitivity, especially for the hard x-ray regime. Implementation of lensless or diffraction imaging helps to enhance the lateral resolution of x-ray imaging to the wavelength dependent diffraction limit.

Feasibility study of hard-x-ray nanofocusing above 20 keV using compound photon sieves

Combining the advantages of photon sieves (PSs) and compound Fresnel zone plates (CZPs), we designed compound photon sieves (CPSs) for hard-x-ray nanofocusing. A CPS consists of an inner PS using the first-order diffraction surrounded by an outer zone plate using the third-order diffraction. A robust digital prolate spheroidal window was used as an apodization window for the inner PS, making CPSs more flexible than CZPs. CPSs can provide not only slightly better resolution compared to CZPs, but also it can significantly suppress the sidelobes, leading to a high signal-to-noise ratio. Further improvement of the high-aspect-ratio metal nanostructure process will allow CPSs to be a promising candidate for hard-x-ray nanofocusing in the high-energy region above 20 keV.

Focusing properties of Fresnel zone plates with spiral phase

Focusing properties of Fresnel zone plates with spiral phase with integer and fractional topological charges illuminated by plane wave are studied. Numerical results show that hollow beams can be generated and can also be controlled by the number of the zones and the topological charge, which implies the potential applications of such kind of zone plate in trapping and manipulating particles.