Laboratory cryo x-ray microscopy for 3D cell imaging

Laboratory based correlative cryo-soft X-ray tomography and cryo-fluorescence microscopy

Cryo-soft X-ray tomography is the unique technology that can image whole intact cells in 3D under normal and pathological conditions without labelling or fixation, at high throughput and spatial resolution. The sample preparation is relatively straightforward; requiring just fast freezing of the specimen before transfer to the microscope for imaging. It is also possible to image chemically fixed samples where necessary. The technique can be correlated with cryo fluorescence microscopy to localize fluorescent proteins to organelles within the whole cell volume. Cryo-correlated light and soft X-ray tomography is particularly useful for the study of gross morphological changes brought about by disease or drugs. For example, viral fluorescent tags can be co-localized to sites of viral replication in the soft X-ray volume. In general this approach is extremely useful in the study of complex 3D organelle structure, nanoparticle uptake or in the detection of rare events in the context of whole cell structure. The main challenge of soft X-ray tomography is that the soft X-ray illumination required for imaging has heretofore only been available at a small number of synchrotron labs worldwide. Recently, a compact device with a footprint small enough to fit in a standard laboratory setting has been deployed ("the SXT-100") and is routinely imaging cryo prepared samples addressing a variety of disease and drug research applications. The SXT-100 facilitates greater access to this powerful technique and greatly increases the scope and throughput of potential research projects. Furthermore, the availability of cryo-soft X-ray tomography in the laboratory will accelerate the development of novel correlative and multimodal workflows by integration with light and electron microscope based approaches. It also allows for co-location of this powerful imaging modality at BSL3 labs or other facilities where safety or intellectual property considerations are paramount. Here we describe the compact SXT-100 microscope along with its novel integrated cryo-fluorescence imaging capability.

Investigation of structural and reflective characteristics of short-period Mo/B4C multilayer X-ray mirrors

The results of a study of the structural and reflective characteristics of short-period multilayer X-ray mirrors based on Mo/B4C at wavelengths 1.54 Å, 9.89 Å and 17.59 Å are presented. The period of the samples varied in the range 8-35 Å. The average widths of the interfaces were ∼3.5 and 2.2 Å at one and the other boundaries, with a tendency for weak growth with any decrease in the period. The interlayer roughness was ∼1 Å. The research results indicate promising prospects for the use of multilayer Mo/B4C mirrors for synchrotron applications.

Laboratory Liquid-Jet X-ray Microscopy and X-ray Fluorescence Imaging for Biomedical Applications

Diffraction-limited resolution and low penetration depth are fundamental constraints in optical microscopy and in vivo imaging. Recently, liquid-jet X-ray technology has enabled the generation of X-rays with high-power intensities in laboratory settings. By allowing the observation of cellular processes in their natural state, liquid-jet soft X-ray microscopy (SXM) can provide morphological information on living cells without staining. Furthermore, X-ray fluorescence imaging (XFI) permits the tracking of contrast agents in vivo with high elemental specificity, going beyond attenuation contrast. In this study, we established a methodology to investigate nanoparticle (NP) interactions in vitro and in vivo, solely based on X-ray imaging. We employed soft (0.5 keV) and hard (24 keV) X-rays for cellular studies and preclinical evaluations, respectively. Our results demonstrated the possibility of localizing NPs in the intracellular environment via SXM and evaluating their biodistribution with in vivo multiplexed XFI. We envisage that laboratory liquid-jet X-ray technology will significantly contribute to advancing our understanding of biological systems in the field of nanomedical research.

Soft X-ray Microscopy in Cell Biology: Current Status, Contributions and Prospects

The recent advances achieved in microscopy technology have led to a significant breakthrough in biological research. Super-resolution fluorescent microscopy now allows us to visualize subcellular structures down to the pin-pointing of the single molecules in them, while modern electron microscopy has opened new possibilities in the study of protein complexes in their native, intracellular environment at near-atomic resolution. Nonetheless, both fluorescent and electron microscopy have remained beset by their principal shortcomings: the reliance on labeling procedures and severe sample volume limitations, respectively. Soft X-ray microscopy is a candidate method that can compensate for the shortcomings of both technologies by making possible observation of the entirety of the cellular interior without chemical fixation and labeling with an isotropic resolution of 40-70 nm. This will thus bridge the resolution gap between light and electron microscopy (although this gap is being narrowed, it still exists) and resolve the issue of compatibility with the former, and possibly in the near future, the latter methods. This review aims to assess the current state of soft X-ray microscopy and its impact on our understanding of the subcellular organization. It also attempts to look into the future of X-ray microscopy, particularly as relates to its seamless integration into the cell biology toolkit.

Sensing Cells-Peptide Hydrogel Interaction In Situ via Scanning Ion Conductance Microscopy

Peptide-based hydrogels were shown to serve as good matrices for 3D cell culture and to be applied in the field of regenerative medicine. The study of the cell-matrix interaction is important for the understanding of cell attachment, proliferation, and migration, as well as for the improvement of the matrix. Here, we used scanning ion conductance microscopy (SICM) to study the growth of cells on self-assembled peptide-based hydrogels. The hydrogel surface topography, which changes during its formation in an aqueous solution, were studied at nanoscale resolution and compared with fluorescence lifetime imaging microscopy (FLIM). Moreover, SICM demonstrated the ability to map living cells inside the hydrogel. A zwitterionic label-free pH nanoprobe with a sensitivity > 0.01 units was applied for the investigation of pH mapping in the hydrogel to estimate the hydrogel applicability for cell growth. The SICM technique that was applied here to evaluate the cell growth on the peptide-based hydrogel can be used as a tool to study functional living cells.

Fifth-order aberration for soft x-ray and vacuum ultraviolet multi-element optical systems

Based on the recently developed fifth-order intrinsic aberration of a soft x-ray and vacuum ultraviolet single-element optical system, this paper proposes a fifth-order aberration (including intrinsic aberration and extrinsic aberration) calculation method for this kind of optical system with multiple elements. First, the fifth-order intrinsic aberration expressions of soft x-ray and vacuum ultraviolet multi-element optical systems are studied; second, the extrinsic aberration calculation method of this kind of optical system is discussed, and corresponding calculation expressions are derived; third, to improve aberration calculation accuracy, the modification of aberration expressions due to the transfer relationship of aperture-ray coordinates with second-order accuracy on the reference exit wavefront between adjacent optical elements is obtained. Finally, the resultant aberration expressions are applied to calculate the aberration of two design examples of soft x-ray and vacuum ultraviolet double-element optical systems with large apertures, and their images are compared with ray-tracing results using Shadow software to validate the aberration expressions. The study shows that the accuracy of the aberration expressions derived in this paper is satisfactory.

Demonstration of Near Edge X-ray Absorption Fine Structure Spectroscopy of Transition Metals Using Xe/He Double Stream Gas Puff Target Soft X-ray Source

A near 1-keV photons from the Xe/He plasma produced by the interaction of laser beam with a double stream gas puff target were employed for studies of L absorption edges of period 4 transitional metals with atomic number Z from 26 to 30. The dual-channel, compact NEXAFS system was employed for the acquisition of the absorption spectra. L_1-3 absorption edges of the samples were identified in transmission mode using broadband emission from the Xe/He plasma to show the applicability of such source and measurement system to the NEXAFS studies of the transition metals, including magnetic materials.

Intrinsic roughness and interfaces of Cr/Be multilayers

The structures of Cr/Be multilayer mirror interfaces are investigated using X-ray reflectometry, diffuse X-ray scattering and atomic force microscopy. The combination of these methods makes it possible to separate the contributions of roughness and interlayer diffusion/intermixing for each sample. In the range of period thicknesses of 2.26–0.8 nm, it is found that the growth roughness of the Cr/Be multilayer mirrors does not depend on the period thickness and is ∼0.2 nm. The separation of roughness and diffuseness allows estimation of layer material intermixing and the resulting drop in the optical contrast, which is from 0.85 to 0.17 in comparison with an ideally sharp structure.

Projection-based dynamic tomography

Objective. This paper proposes a 4D dynamic tomography framework that allows a moving sample to be imaged in a tomograph as well as the associated space-time kinematics to be measured with nothing more than a single conventional x-ray scan.Approach. The method exploits the consistency of the projection/reconstruction operations through a multi-scale procedure. The procedure is composed of two main parts solved alternatively: a motion-compensated reconstruction algorithm and a projection-based measurement procedure that estimates the displacement field directly on each projection.Main results. The method is applied to two studies: a numerical simulation of breathing from chest computed tomography (4D-CT) and a clinical cone-beam CT of a breathing patient acquired for image guidance of radiotherapy. The reconstructed volume, initially blurred by the motion, is cleaned from motion artifacts.Significance. Applying the proposed approach results in an improved reconstruction quality showing sharper edges and finer details.

Laboratory-size x-ray microscope using Wolter mirror optics and an electron-impact x-ray source

We developed a laboratory-size three-dimensional water-window x-ray microscope using condenser and objective grazing incidence Wolter type I mirrors, an electron-impact-type x-ray source, and a back-illuminated CCD. The imaging system was improved for practical applications in life science research fields. Using a new objective mirror with reduced figure errors, a resolution limit of 3.1 line pairs/μm was achieved for two-dimensional transmission images and sub-micrometer-scale three-dimensional structures were resolved. Incorporating a cryogenic stage into the x-ray microscope, we observed biological samples embedded in ice to evaluate the usefulness of observation in the water-window region and multi-energy observation was demonstrated using an x-ray source with multiple x-ray tubes.

1-keV emission from laser-plasma source based on an Xe/He double stream gas puff target

Characterization of Xe emission in the spectral range between 1 and 1.5 keV is presented in the case when the laser-plasma is generated by nanosecond laser pulse irradiation of a double stream Xe/He gas-puff target. Gas target density was estimated using extreme ultraviolet (EUV) radiography. Emission spectral characteristics in the wavelength range from 0.8 to 5.2 nm were determined by using a flat field SXR spectrometer. Significant emission was recorded in two high-energy bands, the first one at wavelengths 0.8-1.6 nm (photon energy range 0.78-1.5 keV) and the second one at 1.6-2.5 nm (0.5-0.78 keV). Both plasma size and photon yield in each band were measured separately to individually assess radiation and source characteristics. Moreover, a proof-of-principle experiment for near-edge X-ray absorption fine structure spectroscopy of metallic sample near the L_2,3 absorption edge was performed to show one of the applicability areas of such a compact source.

Fifth-order intrinsic aberration calculation method for soft x-ray and vacuum ultraviolet optical systems

In this paper, we propose the fifth-order intrinsic aberration calculation method for soft x-ray and vacuum ultraviolet optical systems. First, the sixth-order intrinsic wave aberrations with the aperture-ray coordinates on the optical surface are derived based on the wave aberration method, and then applying the sixth-order mapping relationship of aperture-ray coordinates between the optical surface and the reference exit wavefront, the expressions with those on the reference exit wavefront can be obtained. Second, we derived the calculation expression for the fifth-order intrinsic aberration on the image plane. Finally, the fifth-order intrinsic aberration calculation expressions of the soft x-ray and vacuum ultraviolet optical system derived in this paper are applied to calculate the aberration distribution on the image plane of two design examples of this kind of optical system, and the calculation results are compared with the ray-tracing ones with Shadow software to validate the aberration expressions. The study shows that the accuracy of the aberration expressions is satisfactory.

Quantitative conversion of biomass in giant DNA virus infection

Bioconversion of organic materials is the foundation of many applications in chemical engineering, microbiology and biochemistry. Herein, we introduce a new methodology to quantitatively determine conversion of biomass in viral infections while simultaneously imaging morphological changes of the host cell. As proof of concept, the viral replication of an unidentified giant DNA virus and the cellular response of an amoebal host are studied using soft X-ray microscopy, titration dilution measurements and thermal gravimetric analysis. We find that virions produced inside the cell are visible from 18 h post infection and their numbers increase gradually to a burst size of 280–660 virions. Due to the large size of the virion and its strong X-ray absorption contrast, we estimate that the burst size corresponds to a conversion of 6–12% of carbonaceous biomass from amoebal host to virus. The occurrence of virion production correlates with the appearance of a possible viral factory and morphological changes in the phagosomes and contractile vacuole complex of the amoeba, whereas the nucleus and nucleolus appear unaffected throughout most of the replication cycle.

Laboratory Soft X-Ray Microscopy with an Integrated Visible-Light Microscope-Correlative Workflow for Faster 3D Cell Imaging

Laboratory transmission soft X-ray microscopy (L-TXM) has emerged as a complementary tool to synchrotron-based TXM and high-resolution biomedical 3D imaging in general in recent years. However, two major operational challenges in L-TXM still need to be addressed: a small field of view and a potentially misaligned rotation stage. As it is not possible to alter the magnification during operation, the field of view in L-TXM is usually limited to a few tens of micrometers. This complicates locating areas and objects of interest in the sample. Additionally, if the rotation axis of the sample stage cannot be adjusted prior to the experiments, an efficient workflow for tomographic imaging cannot be established, as refocusing and sample repositioning will become necessary after each recorded projection. Both these limitations have been overcome with the integration of a visible-light microscope (VLM) into the L-TXM system. Here, we describe the calibration procedure of the goniometer sample stage and the integrated VLM and present the resulting 3D imaging of a test sample. In addition, utilizing this newly integrated VLM, the extracellular matrix of cryofixed THP-1 cells (human acute monocytic leukemia cells) was visualized by L-TXM for the first time in the context of an ongoing biomedical research project.

Third-order aberration of soft X-ray optical systems with orthogonal and coplanar arrangement of the main planes of elements

A third-order aberration analytical analysis method of soft X-ray optical systems with orthogonal and coplanar arrangement of the main planes of elements is proposed. Firstly, the transfer equations of the aperture ray and the principle ray are derived; then, based on the third-order aberration theory with the aperture-ray coordinates on the reference exit wavefront of a plane-symmetric optical system, the aberration expressions contributed by the wave aberration and defocus of this kind of optical system are studied in detail. Finally, the derived aberration calculation expressions are applied to calculate the aberration of two design examples of such types of optical systems; the images are compared with ray-tracing results obtained using the Shadow software to validate the aberration expressions. The study shows that the accuracy of the aberration expressions is satisfactory. The analytical analysis method of aberration is helpful in the design and optimization of the soft X-ray optical systems with orthogonal and coplanar arrangement of the main planes of optical elements.

X-ray tomography of cryopreserved human prostate cancer cells: mitochondrial targeting by an organoiridium photosensitiser

Abstract

The organoiridium complex Ir[(C,N)₂(O,O)] (1) where C, N = 1-phenylisoquinoline and O,O = 2,2,6,6-tetramethyl-3,5-heptanedionate is a promising photosensitiser for Photo-Dynamic Therapy (PDT). 1 is not toxic to cells in the dark. However, irradiation of the compound with one-photon blue or two-photon red light generates high levels of singlet oxygen (¹O₂) (in Zhang et al. Angew Chem Int Ed Engl 56 (47):14898-14902 10.1002/anie.201709082,2017), both within cell monolayers and in tumour models. Moreover, photo-excited 1 oxidises key proteins, causing metabolic alterations in cancer cells with potent antiproliferative activity. Here, the tomograms obtained by cryo-Soft X-ray Tomography (cryo-SXT) of human PC3 prostate cancer cells treated with 1, irradiated with blue light, and cryopreserved to maintain them in their native state, reveal that irradiation causes extensive and specific alterations to mitochondria, but not other cellular components. Such new insights into the effect of ¹O₂ generation during PDT using iridium photosensitisers on cells contribute to a detailed understanding of their cellular mode of action.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-020-01761-8) contains supplementary material, which is available to authorized users.

Stability investigation of a cryo soft x-ray microscope by fiber interferometry

We present a stability investigation of the Stockholm laboratory cryo soft x-ray microscope. The microscope operates at a wavelength of 2.48 nm and can image biological samples at liquid-nitrogen temperatures in order to mitigate radiation damage. We measured the stability of the two most critical components, sample holder and optics holder, in vacuo and at cryo temperatures at both short and long time scales with a fiber interferometer. Results revealed vibrations in the kHz range, originating mainly from a turbo pump, as well as long term drifts in connection with temperature fluctuations. With improvements in the microscope, earlier stability issues vanished and close-to diffraction-limited imaging could be achieved. Moreover, our investigation shows that fiber interferometers are a powerful tool in order to investigate position-sensitive setups at the nanometer level.

Phase-contrast 3D tomography of HeLa cells grown in PLLA polymer electrospun scaffolds using synchrotron X-rays

Advanced imaging is useful for understanding the three-dimensional (3D) growth of cells. X-ray tomography serves as a powerful noninvasive, nondestructive technique that can fulfill these purposes by providing information about cell growth within 3D platforms. There are a limited number of studies taking advantage of synchrotron X-rays, which provides a large field of view and suitable resolution to image cells within specific biomaterials. In this study, X-ray synchrotron radiation microtomography at Diamond Light Source and advanced image processing were used to investigate cellular infiltration of HeLa cells within poly L-lactide (PLLA) scaffolds. This study demonstrates that synchrotron X-rays using phase contrast is a useful method to understand the 3D growth of cells in PLLA electrospun scaffolds. Two different fiber diameter (2 and 4 µm) scaffolds with different pore sizes, grown over 2, 5 and 8 days in vitro, were examined for infiltration and cell connectivity. After performing visualization by segmentation of the cells from the fibers, the results clearly show deeper cell growth and higher cellular interconnectivity in the 4 µm fiber diameter scaffold. This indicates the potential for using such 3D technology to study cell-scaffold interactions for future medical use.

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

BACKGROUND

The visualization of internal 3D-structure of tissues at micron resolutions without staining by contrast reagents is desirable in plant researches, and it can be achieved by an X-ray computed tomography (CT) with a phase-retrieval technique. Recently, a laboratory-based X-ray microscope adopting the phase contrast CT was developed as a powerful tool for the observation of weakly absorbing biological samples. Here we report the observation of unstained pansy seeds using the laboratory-based X-ray phase-contrast CT.

RESULTS

A live pansy seed within 2 mm in size was simply mounted inside a plastic tube and irradiated by in-house X-rays to collect projection images using a laboratory-based X-ray microscope. The phase-retrieval technique was applied to enhance contrasts in the projection images. In addition to a dry seed, wet seeds on germination with the poorer contrasts were tried. The phase-retrieved tomograms from both the dry and the wet seeds revealed a cellular level of spatial resolutions that were enough to resolve cells in the seeds, and provided enough contrasts to delineate the boundary of embryos manually. The manual segmentation allowed a 3D rendering of embryos at three different stages in the germination, which visualized an overall morphological change of the embryo upon germination as well as a spatial arrangement of cells inside the embryo.

CONCLUSIONS

Our results confirmed an availability of the laboratory-based X-ray phase-contrast CT for a 3D-structural study on the development of small seeds. The present method may provide a unique way to observe live plant tissues at micron resolutions without structural perturbations due to the sample preparation.

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.

Perspective: Towards single shot time-resolved microscopy using short wavelength table-top light sources

Time-resolved imaging allows revealing the interaction mechanisms in the microcosm of both inorganic and biological objects. While X-ray microscopy has proven its advantages for resolving objects beyond what can be achieved using optical microscopes, dynamic studies using full-field imaging at the nanometer scale are still in their infancy. In this perspective, we present the current state of the art techniques for full-field imaging in the extreme-ultraviolet- and soft X-ray-regime which are suitable for single exposure applications as they are paramount for studying dynamics in nanoscale systems. We evaluate the performance of currently available table-top sources, with special emphasis on applications, photon flux, and coherence. Examples for applications of single shot imaging in physics, biology, and industrial applications are discussed.

Dynamic Tomographic Reconstruction of Deforming Volumes

The motion of a sample while being scanned in a tomograph prevents its proper volume reconstruction. In the present study, a procedure is proposed that aims at estimating both the kinematics of the sample and its standard 3D imaging from a standard acquisition protocol (no more projection than for a rigid specimen). The proposed procedure is a staggered two-step algorithm where the volume is first reconstructed using a “Dynamic Reconstruction” technique, a variant of Algebraic Reconstruction Technique (ART) compensating for a “frozen” determination of the motion, followed by a Projection-based Digital Volume Correlation (P-DVC) algorithm that estimates the space/time displacement field, with a “frozen” microstructure and shape of the sample. Additionally, this procedure is combined with a multi-scale approach that is essential for a proper separation between motion and microstructure. A proof-of-concept of the validity and performance of this approach is proposed based on two virtual examples. The studied cases involve a small number of projections, large strains, up to 25%, and noise.