PSF correction in soft X-ray tomography

Zooming in and out: Exploring RNA Viral Infections with Multiscale Microscopic Methods

RNA viruses, being submicroscopic organisms, have intriguing biological makeups and substantially impact human health. Microscopic methods have been utilized for studying RNA viruses at a variety of scales. In order of observation scale from large to small, fluorescence microscopy, cryo-soft X-ray tomography (cryo-SXT), serial cryo-focused ion beam/scanning electron microscopy (cryo-FIB/SEM) volume imaging, cryo-electron tomography (cryo-ET), and cryo-electron microscopy (cryo-EM) single-particle analysis (SPA) have been employed, enabling researchers to explore the intricate world of RNA viruses, their ultrastructure, dynamics, and interactions with host cells. These methods evolve to be combined to achieve a wide resolution range from atomic to sub-nano resolutions, making correlative microscopy an emerging trend. The developments in microscopic methods provide multi-fold and spatial information, advancing our understanding of viral infections and providing critical tools for developing novel antiviral strategies and rapid responses to emerging viral threats.

Resolving hidden pixels beyond the resolution limit of projection imaging by square aperture

Projection imaging has been employed widely in many areas, such as x-ray radiography, due to its penetration power and ballistic geometry of their paths. However, its resolution limit remains a major challenge, caused by the conflict of source intensity and source size associated with image blurriness. A simple yet robust scheme has been proposed here to solve the problem. An unconventional square aperture, rather than the usual circular beam, is constructed, which allows for the straightforward deciphering of a blurred spot, to unravel hundreds originally hidden pixels. With numerical verification and experimental demonstration, our proposal is expected to benefit multiple disciplines, not limited to x-ray imaging.

A guide into the world of high-resolution 3D imaging: the case of soft X-ray tomography for the life sciences

In the world of bioimaging, every choice made determines the quality and content of the data collected. The choice of imaging techniques for a study could showcase or dampen expected outcomes. Synchrotron radiation is indispensable for biomedical research, driven by the need to see into biological materials and capture intricate biochemical and biophysical details at controlled environments. The same need drives correlative approaches that enable the capture of heterologous but complementary information when studying any one single target subject. Recently, the applicability of one such synchrotron technique in bioimaging, soft X-ray tomography (SXT), facilitates exploratory and basic research and is actively progressing towards filling medical and industrial needs for the rapid screening of biomaterials, reagents and processes of immediate medical significance. Soft X-ray tomography at cryogenic temperatures (cryoSXT) fills the imaging resolution gap between fluorescence microscopy (in the hundreds of nanometers but relatively accessible) and electron microscopy (few nanometers but requires extensive effort and can be difficult to access). CryoSXT currently is accessible, fully documented, can deliver 3D imaging to 25 nm resolution in a high throughput fashion, does not require laborious sample preparation procedures and can be correlated with other imaging techniques. Here, we present the current state of SXT and outline its place within the bioimaging world alongside a guided matrix that aids decision making with regards to the applicability of any given imaging technique to a particular project. Case studies where cryoSXT has facilitated a better understanding of biological processes are highlighted and future directions are discussed.

Integrative structural modelling and visualisation of a cellular organelle

Models of insulin secretory vesicles from pancreatic beta cells have been created using the cellPACK suite of tools to research, curate, construct and visualise the current state of knowledge. The model integrates experimental information from proteomics, structural biology, cryoelectron microscopy and X-ray tomography, and is used to generate models of mature and immature vesicles. A new method was developed to generate a confidence score that reconciles inconsistencies between three available proteomes using expert annotations of cellular localisation. The models are used to simulate soft X-ray tomograms, allowing quantification of features that are observed in experimental tomograms, and in turn, allowing interpretation of X-ray tomograms at the molecular level.

Foam-like phantoms for comparing tomography algorithms

Tomographic algorithms are often compared by evaluating them on certain benchmark datasets. For fair comparison, these datasets should ideally (i) be challenging to reconstruct, (ii) be representative of typical tomographic experiments, (iii) be flexible to allow for different acquisition modes, and (iv) include enough samples to allow for comparison of data-driven algorithms. Current approaches often satisfy only some of these requirements, but not all. For example, real-world datasets are typically challenging and representative of a category of experimental examples, but are restricted to the acquisition mode that was used in the experiment and are often limited in the number of samples. Mathematical phantoms are often flexible and can sometimes produce enough samples for data-driven approaches, but can be relatively easy to reconstruct and are often not representative of typical scanned objects. In this paper, we present a family of foam-like mathematical phantoms that aims to satisfy all four requirements simultaneously. The phantoms consist of foam-like structures with more than 100000 features, making them challenging to reconstruct and representative of common tomography samples. Because the phantoms are computer-generated, varying acquisition modes and experimental conditions can be simulated. An effectively unlimited number of random variations of the phantoms can be generated, making them suitable for data-driven approaches. We give a formal mathematical definition of the foam-like phantoms, and explain how they can be generated and used in virtual tomographic experiments in a computationally efficient way. In addition, several 4D extensions of the 3D phantoms are given, enabling comparisons of algorithms for dynamic tomography. Finally, example phantoms and tomographic datasets are given, showing that the phantoms can be effectively used to make fair and informative comparisons between tomography algorithms.

Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells

High-resolution and rapid imaging of host cell ultrastructure can generate insights toward viral disease mechanism, for example for a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Here, we employ full-rotation soft X-ray tomography (SXT) to examine organelle remodeling induced by SARS-CoV-2 at the whole-cell level with high spatial resolution and throughput. Most of the current SXT systems suffer from a restricted field of view due to use of flat sample supports and artifacts due to missing data. In this approach using cylindrical sample holders, a full-rotation tomogram of human lung epithelial cells is performed in less than 10 min. We demonstrate the potential of SXT imaging by visualizing aggregates of SARS-CoV-2 virions and virus-induced intracellular alterations. This rapid whole-cell imaging approach allows us to visualize the spatiotemporal changes of cellular organelles upon viral infection in a quantitative manner.

Three-dimensional imaging of mitochondrial cristae complexity using cryo-soft X-ray tomography

Mitochondria are dynamic organelles that change morphology to adapt to cellular energetic demands under both physiological and stress conditions. Cardiomyopathies and neuronal disorders are associated with structure-related dysfunction in mitochondria, but three-dimensional characterizations of the organelles are still lacking. In this study, we combined high-resolution imaging and 3D electron density information provided by cryo-soft X-ray tomography to characterize mitochondria cristae morphology isolated from murine. Using the linear attenuation coefficient, the mitochondria were identified (0.247 ± 0.04 µm-1) presenting average dimensions of 0.90 ± 0.20 µm in length and 0.63 ± 0.12 µm in width. The internal mitochondria structure was successfully identified by reaching up the limit of spatial resolution of 35 nm. The internal mitochondrial membranes invagination (cristae) complexity was calculated by the mitochondrial complexity index (MCI) providing quantitative and morphological information of mitochondria larger than 0.90 mm in length. The segmentation to visualize the cristae invaginations into the mitochondrial matrix was possible in mitochondria with MCI ≥ 7. Altogether, we demonstrated that the MCI is a valuable quantitative morphological parameter to evaluate cristae modelling and can be applied to compare healthy and disease state associated to mitochondria morphology.

Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography

Characterizing relationships between cell structures and functions requires mesoscale mapping of intact cells showing subcellular rearrangements following stimulation; however, current approaches are limited in this regard. Here, we report a unique application of soft x-ray tomography to generate three-dimensional reconstructions of whole pancreatic β cells at different time points following glucose-stimulated insulin secretion. Reconstructions following stimulation showed distinct insulin vesicle distribution patterns reflective of altered vesicle pool sizes as they travel through the secretory pathway. Our results show that glucose stimulation caused rapid changes in biochemical composition and/or density of insulin packing, increased mitochondrial volume, and closer proximity of insulin vesicles to mitochondria. Costimulation with exendin-4 (a glucagon-like peptide-1 receptor agonist) prolonged these effects and increased insulin packaging efficiency and vesicle maturation. This study provides unique perspectives on the coordinated structural reorganization and interactions of organelles that dictate cell responses.

Soft X-ray tomography: virtual sculptures from cell cultures

Cellular complexity is represented best in high-spatial resolution, three-dimensional (3D) reconstructions. Soft X-ray tomography (SXT) generates detailed volumetric reconstructions of cells preserved in a near-to-native, frozen-hydrated state. SXT is broadly applicable and can image specimens ranging from bacteria to large mammalian cells. As a reference, we summarize light and electron microscopic methods. We then present an overview of SXT and discuss its role in cellular imaging. We detail the methods used to image biological specimens and present recent highlights that illustrate the capabilities of the technique. We conclude by discussing correlative imaging, specifically the combination of SXT and fluorescence microscopy performed on the same specimen. This correlated approach combines the structural morphology of a cell with its physiological characteristics to build a deeply informative composite view.

Imaging cell morphology and physiology using X-rays

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.

A method of z-tomography using high-aperture soft X-ray microscopy

Multilayer normal-incidence mirrors allow the numerical aperture (NA=0.3-0.5) of a projection lens to be significantly increased in the spectral ranges of the water (λ = 2.3-4.4 nm) and carbon (λ = 4.4-7 nm) windows, in comparison with the Fresnel zone plates. The low depth of focus of high-aperture optics (tens of nm) makes it possible to use z-tomography to reconstruct the structure of samples in soft X-ray microscopy. The presence of strong absorption prevents the direct use of a powerful deconvolution apparatus developed for fluorescence optical microscopy to improve the clarity of the image. In this article, the "intensity restoration algorithm" is proposed that takes into account the absorption effect before standard deconvolution. For an imagine lens with NA = 0.3 and a working wavelength of 3.37 nm, the results of simulating an image of a protein cell and its deconvolutionary processing are presented, before and after applying the proposed method. After its application, the deconvolution efficiency is significantly increased. A "full-period" resolution of 40 nm was obtained for the image of a simulated protein cell.