Unveiling Challenging Microbial Fossil Biosignatures from Rio Tinto with Micro-to-Nanoscale Chemical and Ultrastructural Imaging.

Understanding the nature and preservation of microbial traces in extreme environments is crucial for reconstructing Earth's early biosphere and for the search for life on other planets or moons. At Rio Tinto, southwestern Spain, ferric oxide and sulfate deposits similar to those discovered at Meridiani Planum, Mars, entomb a diversity of fossilized organisms, despite chemical conditions commonly thought to be challenging for life and fossil preservation. Investigating this unique fossil microbiota can elucidate ancient extremophile communities and the preservation of biosignatures in acidic environments on Earth and, potentially, Mars. In this study, we use an innovative multiscale approach that combines the state-of-the-art synchrotron X-ray nanoimaging methods of ptychographic X-ray computed laminography and nano-X-ray fluorescence to reveal Rio Tinto's microfossils at subcellular resolution. The unprecedented nanoscale views of several different specimens within their geological and geochemical contexts reveal novel intricacies of preserved microbial communities. Different morphotypes, ecological interactions, and possible taxonomic affinities were inferred based on qualitative and quantitative 3D ultrastructural information, whereas diagenetic processes and metabolic affinities were inferred from complementary chemical information. Our integrated nano-to-microscale analytical approach revealed previously invisible microbial and mineral interactions, which complemented and filled a gap of spatial resolution in conventional methods. Ultimately, this study contributes to the challenge of deciphering the faint chemical and morphological biosignatures that can indicate life's presence on the early Earth and on distant worlds.

Laminography as a tool for imaging large-size samples with high resolution.

Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.

High-energy X-ray micro-laminography to visualize microstructures in dense planar objects.

High-energy X-ray micro-laminography has been developed to observe inner- and near-surface structures in dense planar objects that are not suitable for observation by X-ray micro-tomography. A multilayer-monochromator-based high-intensity X-ray beam with energy of 110 keV was used for high-energy and high-resolution laminographic observations. As a demonstration of high-energy X-ray micro-laminography for observing dense planar objects, a compressed fossil cockroach on a planar matrix surface was analyzed with effective pixel sizes of 12.4 µm and 4.22 µm for wide field of view and high-resolution observations, respectively. In this analysis, the near-surface structure was clearly observed without undesired X-ray refraction-based artifacts from outside of the region of interest, a problem typical in tomographic observations. Another demonstration visualized fossil inclusions in a planar matrix. Micro-scale features of a gastropod shell and micro-fossil inclusions in the surrounding matrix were clearly visualized. When observing local structures in the dense planar object with X-ray micro-laminography, the penetrating path length in the surrounding matrix can be shortened. This is a significant advantage of X-ray micro-laminography where desired signals generated at the region of interest including optimal X-ray refraction effectively contribute to image formation without being disturbed by undesired interactions in the thick and dense surrounding matrix. Therefore, X-ray micro-laminography allows recognition of the local fine structures and slight difference in the image contrast of planar objects undetectable in a tomographic observation.

Geometric parameters sensitivity evaluation based on projection trajectories for X-ray cone-beam computed laminography.

BACKGROUND: X-ray cone-beam computed laminography (CL) is widely used for large flat objects that computed tomography (CT) cannot investigate. The rotation angle of axis tilt makes geometric correction of CL system more complicated and has more uncertain factors. Therefore, it is necessary to evaluate sensitivity of the geometric parameters of CL system in advance. OBJECTIVE: This study aims to objectively and comprehensively evaluate sensitivity of CL geometric parameters based on the projection trajectory. METHODS: This study proposes the Minimum Deviation Unit (MDU) to evaluate sensitivity of CL geometric parameters. First, the projection trajectory formulas are derived according to the spatial relationship of CL system geometric parameters. Next, the MDU of the geometric parameters is obtained based on the projection trajectories and used as the evaluation index to measure the sensitivity of parameters. Then, the influence of the rotation angle of the axis tilt and magnification on the MDU of the parameters is analyzed. RESULTS: At low magnification, three susceptible parameters (η, u0, v0) with MDU less than 1 (° or mm) must be calibrated accurately to avoid geometric artifacts. The sensitivity of CL parameters increases as the magnification increases, and all parameters become highly sensitive when the magnification power is greater than 10. CONCLUSION: The results of this study have important guiding significance for the subsequent further parameter calibration.

Correction of motion artifact in CL based on MAFusNet.

Computed laminography (CL) is one of the best methods for nondestructive testing of plate-like objects. If the object and the detector move continually while the scanning is being done, the data acquisition efficiency of CL will be significantly increased. However, the projection images will contain motion artifact as a result. A multi-angle fusion network (MAFusNet) is presented in order to correct the motion artifact of CL projection images considering the properties of CL projection images. The multi-angle fusion module significantly increases the ability of MAFusNet to deblur by using data from nearby projection images, and the feature fusion module lessens information loss brought on by data flow between the encoders. In contrast to conventional deblurring networks, the MAFusNet network employs synthetic datasets for training and performed well on realistic data, proving the network's outstanding generalization. The multi-angle fusion-based network has a significant improvement in the correction effect of CL motion artifact through ablation study and comparison with existing classical deblurring networks, and the synthetic training dataset can also significantly lower the training cost, which can effectively improve the quality and efficiency of CL imaging in industrial nondestructive testing.

In situ visualization of multicomponents coevolution in a battery pouch cell.

Lithium-ion battery (LIB) is a broadly adopted technology for energy storage. With increasing demands to improve the rate capability, cyclability, energy density, safety, and cost efficiency, it is crucial to establish an in-depth understanding of the detailed structural evolution and cell-degradation mechanisms during battery operation. Here, we present a laboratory-based high-resolution and high-throughput X-ray micro-computed laminography approach, which is capable of in situ visualizing of an industry-relevant lithium-ion (Li-ion) pouch cell with superior detection fidelity, resolution, and reliability. This technique enables imaging of the pouch cell at a spatial resolution of 0.5 µm in a laboratory system and permits the identification of submicron features within cathode and anode electrodes. We also demonstrate direct visualization of the lithium plating in the imaged pouch cell, which is an important phenomenon relevant to battery fast charging and low-temperature cycling. Our development presents an avenue toward a thorough understanding of the correlation among multiscale structures, chemomechanical degradation, and electrochemical behavior of industry-scale battery pouch cells.

Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography.

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.

Three-Dimensional Vortex Gyration Dynamics Unraveled by Time-Resolved Soft X-ray Laminography with Freely Selectable Excitation Frequencies.

The imaging of magneto-dynamical processes has been, so far, mostly a two-dimensional business, also due to the constraints of the available experimental techniques. In this paper, building on the recent developments of soft X-ray magnetic laminography, we present an experimental setup where magneto-dynamical processes can be resolved in all three spatial dimensions and in time at arbitrary frequencies. We employ this setup to investigate two resonant dynamical modes of a CoFeB microstructure, namely, the fundamental vortex gyration mode and a magnetic field-induced domain wall excitation mode. For the former, we observe a large variation of the gyration dynamics across the thickness of the core, coexisting with a breathing mode of the vortex core. For the latter, we observe a uniform displacement of the domain walls across the thickness of the microstructure. The imaging of these two modes establishes the possibility to freely select the excitation frequency for soft X-ray time-resolved laminography, allowing for the investigation of resonant magneto-dynamical processes.

X-ray imaging techniques for inspection of composite pipelines.

The literature has shown that the application of laminography provides advantages as 3D radiographic imaging with depth information for in house and mobile testing. This permits to distinguish between overlapping indications, measure the extension along radiation direction and classify indications as surface open or subsurface ones as required in critical engineering assessment. This work provides a comparative study and measurements of the three techniques Digital Radiography (DR) with Digital Detector Arrays (DDA), Coplanar Translational Laminography (CTL) and Computed Tomography (CT), applied for composite pipeline inspection. It is demonstrated that CTL and CT provide advantages for the evaluation of pipe-to-pipe connections and the evaluation of adhesive applications. They show indications of discontinuities with higher contrast sensitivity than radiography. Beyond it, two specimen, namely Phantom 1 and Phantom 2, were developed and manufactured by additive manufacturing to analyze the preferential detection sensitivity and the direction of features and depth information for laminographic measurements. Another goal was to show the laminographic capabilities to distinguish between overlapping discontinuities. CTL is especially suitable for mobile inspection. Special glass fiber reinforced polymer samples (GRP) were manufactured for further analysis and comparisons between the abovementioned techniques. Finally, Phantoms 1 and 2 show the capability of laminography to detect overlapping indications and also show that discontinuities oriented perpendicular to the scan direction have the highest contrast sensitivity for laminographic measurements.

LamNI - an instrument for X-ray scanning microscopy in laminography geometry.

Across all branches of science, medicine and engineering, high-resolution microscopy is required to understand functionality. Although optical methods have been developed to `defeat' the diffraction limit and produce 3D images, and electrons have proven ever more useful in creating pictures of small objects or thin sections, so far there is no substitute for X-ray microscopy in providing multiscale 3D images of objects with a single instrument and minimal labeling and preparation. A powerful technique proven to continuously access length scales from 10 nm to 10 µm is ptychographic X-ray computed tomography, which, on account of the orthogonality of the tomographic rotation axis to the illuminating beam, still has the limitation of necessitating pillar-shaped samples of small (ca 10 µm) diameter. Large-area planar samples are common in science and engineering, and it is therefore highly desirable to create an X-ray microscope that can examine such samples without the extraction of pillars. Computed laminography, where the axis of rotation is not perpendicular to the illumination direction, solves this problem. This entailed the development of a new instrument, LamNI, dedicated to high-resolution 3D scanning X-ray microscopy via hard X-ray ptychographic laminography. Scanning precision is achieved by a dedicated interferometry scheme and the instrument covers a scan range of 12 mm × 12 mm with a position stability of 2 nm and positioning errors below 5 nm. A new feature of LamNI is a pair of counter-rotating stages carrying the sample and interferometric mirrors, respectively.

From 2D STXM to 3D Imaging: Soft X-ray Laminography of Thin Specimens.

X-ray tomography has become an indispensable tool for studying complex 3D interior structures with high spatial resolution. Three-dimensional imaging using soft X-rays offers powerful contrast mechanisms but has seen limited success with tomography due to the restrictions imposed by the much lower energy of the probe beam. The generalized geometry of laminography, characterized by a tilted axis of rotation, provides nm-scale 3D resolution for the investigation of extended (mm range) but thin (µm to nm) samples that are well suited to soft X-ray studies. This work reports on the implementation of soft X-ray laminography (SoXL) at the scanning transmission X-ray spectromicroscope of the PolLux beamline at the Swiss Light Source, Paul Scherrer Institut, which enables 3D imaging of extended specimens from 270 to 1500 eV. Soft X-ray imaging provides contrast mechanisms for both chemical sensitivity to molecular bonds and oxidation states and magnetic dichroism due to the much stronger attenuation of X-rays in this energy range. The presented examples of applications range from functionalized nanomaterials to biological photonic crystals and sophisticated nanoscaled magnetic domain patterns, thus illustrating the wide fields of research that can benefit from SoXL.

Operando XAFS Imaging of Distribution of Pt Cathode Catalysts in PEFC MEA.

Three-dimensional imaging using X-ray as a probe is state-of-the-art for the characterization of heterogeneous materials. In addition to simple imaging of sample morphology, imaging of elemental distribution and chemical states provides advanced maps of key structural parameters of functional materials. The combination of X-ray absorption fine structure (XAFS) spectroscopy and three-dimensional imaging such as computed tomography (CT) can visualize the three-dimensional distribution of target elements, their valence states, and local structures in a non-destructive manner. In this personal account, our recent results on the three-dimensional XAFS imaging for Pt cathode catalysts in the membrane electrode assembly (MEA) of polymer electrolyte fuel cell (PEFC) are introduced. The distribution and chemical states of Pt cathode catalysts in MEAs remarkably change under PEFC operating conditions, and the 3D XAFS imaging revealed essential events in PEFC MEAs.

Feasibility study of phase-contrast X-ray laminography using X-ray interferometry.

For fine observation of laminar samples, phase-contrast X-ray laminography using X-ray interferometry was developed. An imaging system fitted with a two-crystal X-ray interferometer was used to perform the observations, and the sectional images were calculated by a three-dimensional iterative reconstruction method. Obtained images of an old flat slab of limestone from the Carnic Alps depicted fusulinids in the Carboniferous period with 3 mg cm-3 density resolution, and those of carbon paper used for a fuel-cell battery displayed the inner fibrous structures clearly.

Multi-contrast diffraction enhanced computed laminography at Beijing Synchrotron Radiation Facility.

Synchrotron radiation X-ray computed tomography (CT) enables nondestructive visualization of 3D morphological and chemical changes inside a sample and has become a powerful analysis tool to monitor reactive parts and their chemical states. However, synchrotron radiation CT imaging of specimens with lateral extensions much larger than the acceptance window of detectors is rather problematic due to strong absorption of X-rays in the lateral directions. On the other hand, X-ray computed laminography (CL) permits 3D imaging of flat samples while X-ray diffraction enhanced imaging (DEI) can provide high-quality results with different imaging contrasts such as absorption, phase and dark-field for samples with weak absorptions. Combining CL and DEI together, we have developed a multi-contrast DEI-CL system at the 4W1A beamline of the Beijing Synchrotron Radiation Facility for this kind of sample. Here we reported its design, implementation, and preliminary experimental results of carbon fiber reinforced polymer laminates with three kinds of imaging contrasts. The results have demonstrated the validity of this DEI-CL system. It will be helpful to push the applications of the state-of-the-art synchrotron radiation methods and instruments towards cutting-edge research. Graphical abstract ᅟ.

Spherically symmetric volume elements as basis functions for image reconstructions in computed laminography.

BACKGROUND: Laminography is a tomographic technique that allows three-dimensional imaging of flat and elongated objects that stretch beyond the extent of a reconstruction volume. Laminography images can be reconstructed using iterative algorithms based on the Kaczmarz method. OBJECTIVE: This study aims to develop and demonstrate a new reconstruction algorithm that may provide superior image reconstruction quality for this challenged imaging application. METHODS: The images are initially represented using the coefficients over basis functions, which are typically piecewise constant functions (voxels). By replacing voxels with spherically symmetric volume elements (blobs) based on the generalized Kaiser-Bessel window functions, the images are reconstructed using this new adapted version of the algebraic image reconstruction technique. RESULTS: Band-limiting properties of blob functions are beneficial particular in the case of noisy projections and with only a limited number of available projections. Study showed that using blob basis functions improved full-width-at-half-maximum resolution from 10.2±1.0 to 9.9±0.9 (p < 0.001). Signal-to-noise ratio also improved from 16.1 to 31.0. The increased computational demand per iteration was compensated by using a faster convergence rate, such that the overall performance is approximately identical for blobs and voxels. CONCLUSIONS: Despite the higher complexity, tomographic reconstruction from computed laminography data should be implemented using blob basis functions, especially if noisy data is expected.

X-ray analyzer-based phase-contrast computed laminography.

X-ray analyzer-based phase-contrast imaging is combined with computed laminography for imaging regions of interest in laterally extended flat specimens of weak absorption contrast. The optics discussed here consist of an asymmetrically cut collimator crystal and a symmetrically cut analyzer crystal arranged in a nondispersive (+, -) diffraction geometry. A generalized algorithm is given for calculating multi-contrast (absorption, refraction and phase contrast) images of a sample. Basic formulae are also presented for laminographic reconstruction. The feasibility of the method discussed was verified at the vertical wiggler beamline BL-14B of the Photon Factory. At a wavelength of 0.0733 nm, phase-contrast sectional images of plastic beads were successfully obtained. Owing to strong circular artifacts caused by a sample holder, the field of view was limited to about 6 mm in diameter.

Real-time image-content-based beamline control for smart 4D X-ray imaging.

Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional in situ, in vivo and operando tomography and laminography.

Recent Advances in X-ray Cone-beam Computed Laminography.

X-ray computed tomography is an established volume imaging technique used routinely in medical diagnosis, industrial non-destructive testing, and a wide range of scientific fields. Traditionally, computed tomography uses scanning geometries with a single axis of rotation together with reconstruction algorithms specifically designed for this setup. Recently there has however been increasing interest in more complex scanning geometries. These include so called X-ray computed laminography systems capable of imaging specimens with large lateral dimensions or large aspect ratios, neither of which are well suited to conventional CT scanning procedures. Developments throughout this field have thus been rapid, including the introduction of novel system trajectories, the application and refinement of various reconstruction methods, and the use of recently developed computational hardware and software techniques to accelerate reconstruction times. Here we examine the advances made in the last several years and consider their impact on the state of the art.

Three-dimensional microscale modelling of CO2 transport and light propagation in tomato leaves enlightens photosynthesis.

We present a combined three-dimensional (3-D) model of light propagation, CO2 diffusion and photosynthesis in tomato (Solanum lycopersicum L.) leaves. The model incorporates a geometrical representation of the actual leaf microstructure that we obtained with synchrotron radiation X-ray laminography, and was evaluated using measurements of gas exchange and leaf optical properties. The combination of the 3-D microstructure of leaf tissue and chloroplast movement induced by changes in light intensity affects the simulated CO2 transport within the leaf. The model predicts extensive reassimilation of CO2 produced by respiration and photorespiration. Simulations also suggest that carbonic anhydrase could enhance photosynthesis at low CO2 levels but had little impact on photosynthesis at high CO2 levels. The model confirms that scaling of photosynthetic capacity with absorbed light would improve efficiency of CO2 fixation in the leaf, especially at low light intensity.

Synchrotron radiation computed laminography using an inclined detector.

Synchrotron radiation computed laminography (SR-CL) has been in use in three-dimensional non-destructive imaging of flat objects for several years. A new set-up is proposed based on the traditional SR-CL method but with the detector inclined at the same angle as the sample inclination to collect projections. The results of computer simulations and real-sample experiments demonstrate that reconstructions acquired using an inclined detector are of better quality compared with those acquired using ordinary detecting methods, especially for the situation of few projections and small difference of attenuation ratio of the sample. This method could be applied to obtain high-quality images of weak-contrast samples with short measurement time and mild radiation damage.