Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging

Methods and application of coherent X-ray diffraction imaging of noncrystalline particles

Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. The structure of the particle projected along the direction of the beam is, in principle, retrieved from a finely recorded diffraction pattern alone by using iterative phase-retrieval algorithms. Here, we describe fundamental theory and experimental methods of coherent X-ray diffraction imaging and the recent application in structural studies of noncrystalline specimens by using X-rays available at Super Photon Ring of 8-Gev and SPring-8 Angstrom Compact Free Electron Laser in Japan.

Quantitative ptychographic bio-imaging in the water window

Coherent X-ray ptychography is a tool for highly dose efficient lensless nano-imaging of biological samples. We have used partially coherent soft X-ray synchrotron radiation to obtain a quantitative image of a laterally extended, dried, and unstained fibroblast cell by ptychography. We used data with and without a beam stop that allowed us to measure coherent diffraction with a high-dynamic range of 1.7·10⁶. As a quantitative result, we obtained the refractive index values for two regions of the cell with respect to a reference area. Due to the photon energy in the water window we obtained an extremely high contrast of 53% at 71 nm half-period resolution. The dose applied in our experiment was 9.5·10⁴ Gy and is well below the radiation damage threshold. The concept for dynamic range improvement for low dynamic range detectors with a beam stop opens the path for high resolution nano-imaging of a variety of samples including cryo-preserved, hydrated and unstained biological cells.

Coherent diffractive imaging of graphite nanoparticles using a tabletop EUV source

Structural information of nanostructures plays a key role in synthesis of novel nano-sized materials for promising applications such as high-performance nanoelectronics and nanophotonics. In this study, we apply for the first time the state-of-the-art coherent diffractive imaging method to characterize the structure of graphite nanoparticles. A sample with nanographites on a Si₃N₄ support was exposed to 30 nm radiation from a tabletop laser-driven high-order harmonic generation extreme ultraviolet (EUV) source. From the measured far-field diffraction pattern, we were able to reconstruct the distribution of the graphite nanoparticles with a spatial resolution of ∼330 nm using the standard iterative phase retrieval algorithms. A closer look at the reconstructed images reveals possible absorption effects of graphite nanoparticles. This experiment demonstrates the first step towards wide-field and high-resolution imaging of nuclear materials using the newly established lab-scale EUV source. Having such a source opens the door to performing investigations of nuclear graphite and other radioactive material in the lab, thus avoiding the need to transport samples to external facilities.

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge

Precise localization of nanoparticles within a cell is crucial to the understanding of cell-particle interactions and has broad applications in nanomedicine. Here, we report a proof-of-principle experiment for imaging individual functionalized nanoparticles within a mammalian cell by correlative microscopy. Using a chemically-fixed HeLa cell labeled with fluorescent core-shell nanoparticles as a model system, we implemented a graphene-oxide layer as a substrate to significantly reduce background scattering. We identified cellular features of interest by fluorescence microscopy, followed by scanning transmission X-ray tomography to localize the particles in 3D, and ptychographic coherent diffractive imaging of the fine features in the region at high resolution. By tuning the X-ray energy to the Fe L-edge, we demonstrated sensitive detection of nanoparticles composed of a 22 nm magnetic Fe3O4 core encased by a 25-nm-thick fluorescent silica (SiO2) shell. These fluorescent core-shell nanoparticles act as landmarks and offer clarity in a cellular context. Our correlative microscopy results confirmed a subset of particles to be fully internalized, and high-contrast ptychographic images showed two oxidation states of individual nanoparticles with a resolution of ~16.5 nm. The ability to precisely localize individual fluorescent nanoparticles within mammalian cells will expand our understanding of the structure/function relationships for functionalized nanoparticles.

Three-dimensional single-cell imaging with X-ray waveguides in the holographic regime

X-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.

Microscopic dual-energy CT (microDECT): a flexible tool for multichannel ex vivo 3D imaging of biological specimens

Dual-energy computed tomography (DECT) uses two different x-ray energy spectra in order to differentiate between tissues, materials or elements in a single sample or patient. DECT is becoming increasingly popular in clinical imaging and preclinical in vivo imaging of small animal models, but there have been only very few reports on ex vivo DECT of biological samples at microscopic resolutions. The present study has three main aims. First, we explore the potential of microscopic DECT (microDECT) for delivering isotropic multichannel 3D images of fixed biological samples with standard commercial laboratory-based microCT setups at spatial resolutions reaching below 10 μm. Second, we aim for retaining the maximum image resolution and quality during the material decomposition. Third, we want to test the suitability for microDECT imaging of different contrast agents currently used for ex vivo staining of biological samples. To address these aims, we used microCT scans of four different samples stained with x-ray dense contrast agents. MicroDECT scans were acquired with five different commercial microCT scanners from four companies. We present a detailed description of the microDECT workflow, including sample preparation, image acquisition, image processing and postreconstruction material decomposition, which may serve as practical guide for applying microDECT. The MATLAB script (The Mathworks Inc., Natick, MA, USA) used for material decomposition (including a graphical user interface) is provided as a supplement to this paper (https://github.com/microDECT/DECTDec). In general, the presented microDECT workflow yielded satisfactory results for all tested specimens. Original scan resolutions have been mostly retained in the separate material fractions after basis material decomposition. In addition to decomposition of mineralized tissues (inherent sample contrast) and stained soft tissues, we present a case of double labelling of different soft tissues with subsequent material decomposition. We conclude that, in contrast to in vivo DECT examinations, small ex vivo specimens offer some clear advantages regarding technical parameters of the microCT setup and the use of contrast agents. These include a higher flexibility in source peak voltages and x-ray filters, a lower degree of beam hardening due to small sample size, the lack of restriction to nontoxic contrast agents and the lack of a limit in exposure time and radiation dose. We argue that microDECT, because of its flexibility combined with already established contrast agents and the vast number of currently unexploited stains, will in future represent an important technique for various applications in biological research.

Procedures for cryogenic X-ray ptychographic imaging of biological samples

Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.

Frontier methods in coherent X-ray diffraction for high-resolution structure determination

In 1912, Max von Laue and collaborators first observed diffraction spots from a millimeter-sized crystal of copper sulfate using an X-ray tube. Crystallography was born of this experiment, and since then, diffraction by both X-rays and electrons has revealed a myriad of inorganic and organic structures, including structures of complex protein assemblies. Advancements in X-ray sources have spurred a revolution in structure determination, facilitated by the development of new methods. This review explores some of the frontier methods that are shaping the future of X-ray diffraction, including coherent diffractive imaging, serial femtosecond X-ray crystallography and small-angle X-ray scattering. Collectively, these methods expand the current limits of structure determination in biological systems across multiple length and time scales.