A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source

Accelerating imaging research at large-scale scientific facilities through scientific computing

To date, computed tomography experiments, carried-out at synchrotron radiation facilities worldwide, pose a tremendous challenge in terms of the breadth and complexity of the experimental datasets produced. Furthermore, near real-time three-dimensional reconstruction capabilities are becoming a crucial requirement in order to perform high-quality and result-informed synchrotron imaging experiments, where a large amount of data is collected and processed within a short time window. To address these challenges, we have developed and deployed a synchrotron computed tomography framework designed to automatically process online the experimental data from the synchrotron imaging beamlines, while leveraging the high-performance computing cluster capabilities to accelerate the real-time feedback to the users on their experimental results. We have, further, integrated it within a modern unified national authentication and data management framework, which we have developed and deployed, spanning the entire data lifecycle of a large-scale scientific facility. In this study, the overall architecture, functional modules and workflow design of our synchrotron computed tomography framework are presented in detail. Moreover, the successful integration of the imaging beamlines at the Shanghai Synchrotron Radiation Facility into our scientific computing framework is also detailed, which, ultimately, resulted in accelerating and fully automating their entire data processing pipelines. In fact, when compared with the original three-dimensional tomography reconstruction approaches, the implementation of our synchrotron computed tomography framework led to an acceleration in the experimental data processing capabilities, while maintaining a high level of integration with all the beamline processing software and systems.

Mapping of lithium ion concentrations in 3D structures through development of in situ correlative imaging of X-ray Compton scattering-computed tomography

Understanding the correlation between chemical and microstructural properties is critical for unraveling the fundamental relationship between materials chemistry and physical structures that can benefit materials science and engineering. Here, we demonstrate novel in situ correlative imaging of the X-ray Compton scattering computed tomography (XCS-CT) technique for studying this fundamental relationship. XCS-CT can image light elements that do not usually exhibit strong signals using other X-ray characterization techniques. This paper describes the XCS-CT setup and data analysis method for calculating the valence electron momentum density and lithium-ion concentration, and provides two examples of spatially and temporally resolved chemical properties inside batteries in 3D. XCS-CT was applied to study two types of rechargeable lithium batteries in standard coin cell casings: (1) a lithium-ion battery containing a cathode of bespoke microstructure and liquid electrolyte, and (2) a solid-state battery containing a solid-polymer electrolyte. The XCS-CT technique is beneficial to a wide variety of materials and systems to map chemical composition changes in 3D structures.

Single-cell guided prenatal derivation of primary fetal epithelial organoids from human amniotic and tracheal fluids

Isolation of tissue-specific fetal stem cells and derivation of primary organoids is limited to samples obtained from termination of pregnancies, hampering prenatal investigation of fetal development and congenital diseases. Therefore, new patient-specific in vitro models are needed. To this aim, isolation and expansion of fetal stem cells during pregnancy, without the need for tissue samples or reprogramming, would be advantageous. Amniotic fluid (AF) is a source of cells from multiple developing organs. Using single-cell analysis, we characterized the cellular identities present in human AF. We identified and isolated viable epithelial stem/progenitor cells of fetal gastrointestinal, renal and pulmonary origin. Upon culture, these cells formed clonal epithelial organoids, manifesting small intestine, kidney tubule and lung identity. AF organoids exhibit transcriptomic, protein expression and functional features of their tissue of origin. With relevance for prenatal disease modeling, we derived lung organoids from AF and tracheal fluid cells of congenital diaphragmatic hernia fetuses, recapitulating some features of the disease. AF organoids are derived in a timeline compatible with prenatal intervention, potentially allowing investigation of therapeutic tools and regenerative medicine strategies personalized to the fetus at clinically relevant developmental stages.

A well-preserved 'placoderm' (stem-group Gnathostomata) upper jaw from the Early Devonian of Mongolia clarifies jaw evolution

The origin of jaws and teeth remains contentious in vertebrate evolution. 'Placoderms' (Silurian-Devonian armoured jawed fishes) are central to debates on the origins of these anatomical structures. 'Acanthothoracids' are generally considered the most primitive 'placoderms'. However, they are so far known mainly from disarticulated skeletal elements that are typically incomplete. The structure of the jaws-particularly the jaw hinge-is poorly known, leaving open questions about their jaw function and comparison with other placoderms and modern gnathostomes. Here we describe a near-complete 'acanthothoracid' upper jaw, allowing us to reconstruct the likely orientation and angle of the bite and compare its morphology with that of other known 'placoderm' groups. We clarify that the bite position is located on the upper jaw cartilage rather than on the dermal cheek and thus show that there is a highly conserved bite morphology among most groups of 'placoderms', regardless of their overall cranial geometry. Incorporation of the dermal skeleton appears to provide a sound biomechanical basis for jaw origins. It appears that 'acanthothoracid' dentitions were fundamentally similar in location to that of arthrodire 'placoderms', rather than resembling bony fishes. Irrespective of current phylogenetic uncertainty, the new data here resolve the likely general condition for 'placoderms' as a whole, and as such, ancestral morphology of known jawed vertebrates.

Towards routine 3D characterization of intact mesoscale samples by multi-scale and multimodal scanning X-ray tomography

Non-invasive multi-scale and multimodal 3D characterization of heterogeneous or hierarchically structured intact mesoscale samples is of paramount importance in tackling challenging scientific problems. Scanning hard X-ray tomography techniques providing simultaneous complementary 3D information are ideally suited to such studies. However, the implementation of a robust on-site workflow remains the bottleneck for the widespread application of these powerful multimodal tomography methods. In this paper, we describe the development and implementation of such a robust, holistic workflow, including semi-automatic data reconstruction. Due to its flexibility, our approach is especially well suited for on-the-fly tuning of the experiments to study features of interest progressively at different length scales. To demonstrate the performance of the method, we studied, across multiple length scales, the elemental abundances and morphology of two complex biological systems, Arabidopsis plant seeds and mouse renal papilla samples. The proposed approach opens the way towards routine multimodal 3D characterization of intact samples by providing relevant information from pertinent sample regions in a wide range of scientific fields such as biology, geology, and material sciences.

Development and Testing of Copper Filters for Efficient Application in Half-Face Masks

SARS-CoV-2 is the causative agent of severe acute respiratory diseases. Its main transmission pathway is through large and small respiratory droplets, as well as a direct and indirect contact. In this paper, we present the results of the development and research of copper filters produced by powder technology. Four types of copper powders were tested. Technological parameters, a microstructure, an energy dispersive X-ray (EDX) analysis, and fractography of copper (Cu) filters are reported. The pressure losses in the P-Cu-AW315 filter showed a very favorable value for using the filter in half-face masks that meet the requirements of European norms (EN). An X-ray tomography measurement was carried out at the I12-JEEP beamline. A relative volume of grains and pores was estimated (on the basis of the segmentation results) to be approximately 50% to 50% of the investigated filter volume.

On Acquisition Parameters and Processing Techniques for Interparticle Contact Detection in Granular Packings Using Synchrotron Computed Tomography

X-ray computed tomography (XCT) is regularly employed in geomechanics to non-destructively measure the solid and pore fractions of soil and rock from reconstructed 3D images. With the increasing availability of high-resolution XCT imaging systems, researchers now seek to measure microfabric parameters such as the number and area of interparticle contacts, which can then be used to inform soil behaviour modelling techniques. However, recent research has evidenced that conventional image processing methods consistently overestimate the number and area of interparticle contacts, mainly due to acquisition-driven image artefacts. The present study seeks to address this issue by systematically assessing the role of XCT acquisition parameters in the accurate detection of interparticle contacts. To this end, synchrotron XCT has been applied to a hexagonal close-packed arrangement of glass pellets with and without a prescribed separation between lattice layers. Different values for the number of projections, exposure time, and rotation range have been evaluated. Conventional global grey value thresholding and novel U-Net segmentation methods have been assessed, followed by local refinements at the presumptive contacts, as per recently proposed contact detection routines. The effect of the different acquisition set-ups and segmentation techniques on contact detection performance is presented and discussed, and optimised workflows are proposed.

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.

Synchrotron X-Ray Tomography for Rechargeable Battery Research: Fundamentals, Setups and Applications

Understanding the complicated interplay of the continuously evolving electrode materials in their inherent 3D states during the battery operating condition is of great importance for advancing rechargeable battery research. In this regard, the synchrotron X-ray tomography technique, which enables non-destructive, multi-scale, and 3D imaging of a variety of electrode components before/during/after battery operation, becomes an essential tool to deepen this understanding. The past few years have witnessed an increasingly growing interest in applying this technique in battery research. Hence, it is time to not only summarize the already obtained battery-related knowledge by using this technique, but also to present a fundamental elucidation of this technique to boost future studies in battery research. To this end, this review firstly introduces the fundamental principles and experimental setups of the synchrotron X-ray tomography technique. After that, a user guide to its application in battery research and examples of its applications in research of various types of batteries are presented. The current review ends with a discussion of the future opportunities of this technique for next-generation rechargeable batteries research. It is expected that this review can enhance the reader's understanding of the synchrotron X-ray tomography technique and stimulate new ideas and opportunities in battery research.

Core Imaging Library - Part I: a versatile Python framework for tomographic imaging

We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimization framework for prototyping reconstruction methods including sparsity and total variation regularization, as well as tools for loading, preprocessing and visualizing tomographic data. The capabilities of CIL are demonstrated on a synchrotron example dataset and three challenging cases spanning golden-ratio neutron tomography, cone-beam X-ray laminography and positron emission tomography. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Core Imaging Library - Part I: a versatile Python framework for tomographic imaging

We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimization framework for prototyping reconstruction methods including sparsity and total variation regularization, as well as tools for loading, preprocessing and visualizing tomographic data. The capabilities of CIL are demonstrated on a synchrotron example dataset and three challenging cases spanning golden-ratio neutron tomography, cone-beam X-ray laminography and positron emission tomography. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

3D cyclorama for digital unrolling and visualisation of deformed tubes

Colonic crypts are tubular glands that multiply through a symmetric branching process called crypt fission. During the early stages of colorectal cancer, the normal fission process is disturbed, leading to asymmetrical branching or budding. The challenging shapes of the budding crypts make it difficult to prepare paraffin sections for conventional histology, resulting in colonic cross sections with crypts that are only partially visible. To study crypt budding in situ and in three dimensions (3D), we employ X-ray micro-computed tomography to image intact colons, and a new method we developed (3D cyclorama) to digitally unroll them. Here, we present, verify and validate our '3D cyclorama' method that digitally unrolls deformed tubes of non-uniform thickness. It employs principles from electrostatics to reform the tube into a series of onion-like surfaces, which are mapped onto planar panoramic views. This enables the study of features extending over several layers of the tube's depth, demonstrated here by two case studies: (i) microvilli in the human placenta and (ii) 3D-printed adhesive films for drug delivery. Our 3D cyclorama method can provide novel insights into a wide spectrum of applications where digital unrolling or flattening is necessary, including long bones, teeth roots and ancient scrolls.

Data processing methods and data acquisition for samples larger than the field of view in parallel-beam tomography

Parallel-beam tomography systems at synchrotron facilities have limited field of view (FOV) determined by the available beam size and detector system coverage. Scanning the full size of samples bigger than the FOV requires various data acquisition schemes such as grid scan, 360-degree scan with offset center-of-rotation (COR), helical scan, or combinations of these schemes. Though straightforward to implement, these scanning techniques have not often been used due to the lack of software and methods to process such types of data in an easy and automated fashion. The ease of use and automation is critical at synchrotron facilities where using visual inspection in data processing steps such as image stitching, COR determination, or helical data conversion is impractical due to the large size of datasets. Here, we provide methods and their implementations in a Python package, named Algotom, for not only processing such data types but also with the highest quality possible. The efficiency and ease of use of these tools can help to extend applications of parallel-beam tomography systems.

A massively multi-scale approach to characterizing tissue architecture by synchrotron micro-CT applied to the human placenta

Multi-scale structural assessment of biological soft tissue is challenging but essential to gain insight into structure-function relationships of tissue/organ. Using the human placenta as an example, this study brings together sophisticated sample preparation protocols, advanced imaging and robust, validated machine-learning segmentation techniques to provide the first massively multi-scale and multi-domain information that enables detailed morphological and functional analyses of both maternal and fetal placental domains. Finally, we quantify the scale-dependent error in morphological metrics of heterogeneous placental tissue, estimating the minimal tissue scale needed in extracting meaningful biological data. The developed protocol is beneficial for high-throughput investigation of structure-function relationships in both normal and diseased placentas, allowing us to optimize therapeutic approaches for pathological pregnancies. In addition, the methodology presented is applicable in the characterization of tissue architecture and physiological behaviours of other complex organs with similarity to the placenta, where an exchange barrier possesses circulating vascular and avascular fluid spaces.

Progress on In Situ and Operando X-ray Imaging of Solidification Processes

In this review, we present an overview of significant developments in the field of in situ and operando (ISO) X-ray imaging of solidification processes. The objective of this review is to emphasize the key challenges in developing and performing in situ X-ray imaging of solidification processes, as well as to highlight important contributions that have significantly advanced the understanding of various mechanisms pertaining to microstructural evolution, defects, and semi-solid deformation of metallic alloy systems. Likewise, some of the process modifications such as electromagnetic and ultra-sound melt treatments have also been described. Finally, a discussion on the recent breakthroughs in the emerging technology of additive manufacturing, and the challenges thereof, are presented.

Wide-Ranging Multitool Study of Structure and Porosity of PLGA Scaffolds for Tissue Engineering

In this study, the nanoscale transformation of the polylactic-co-glycolic acid (PLGA) internal structure, before and after its supercritical carbon dioxide (sc-CO₂) swelling and plasticization, followed by foaming after a CO₂ pressure drop, was studied by small-angle X-ray scattering (SAXS) for the first time. A comparative analysis of the internal structure data and porosity measurements for PLGA scaffolds, produced by sc-CO₂ processing, on a scale ranging from 0.02 to 1000 μm, was performed by SAXS, helium pycnometry (HP), mercury intrusion porosimetry (MIP) and both “lab-source” and synchrotron X-ray microtomography (micro-CT). This approach opens up possibilities for the wide-scale evaluation, computer modeling, and prediction of the physical and mechanical properties of PLGA scaffolds, as well as their biodegradation behavior in the body. Hence, this study targets optimizing the process parameters of PLGA scaffold fabrication for specific biomedical applications.

Preliminary paleohistological observations of the StW 573 ('Little Foot') skull

Numerous aspects of early hominin biology remain debated or simply unknown. However, recent developments in high-resolution imaging techniques have opened new avenues in the field of paleoanthropology. More specifically, X-ray synchrotron-based analytical imaging techniques have the potential to provide crucial details on the ontogeny, physiology, biomechanics, and biological identity of fossil specimens. Here we present preliminary results of our X-ray synchrotron-based investigation of the skull of the 3.67-million-year-old Australopithecus specimen StW 573 (‘Little Foot’) at the I12 beamline of the Diamond Light Source (United Kingdom). Besides showing fine details of the enamel (i.e., hypoplasias) and cementum (i.e., incremental lines), as well as of the cranial bone microarchitecture (e.g., diploic channels), our synchrotron-based investigation reveals for the first time the 3D spatial organization of the Haversian systems in the mandibular symphysis of an early hominin.

Towards a mechanistic understanding of particle shrinkage during biomass pyrolysis via synchrotron X-ray microtomography and in-situ radiography

Accurate modelling of particle shrinkage during biomass pyrolysis is key to the production of biochars with specific morphologies. Such biochars represent sustainable solutions to a variety of adsorption-dependent environmental remediation challenges. Modelling of particle shrinkage during biomass pyrolysis has heretofore been based solely on theory and ex-situ experimental data. Here we present the first in-situ phase-contrast X-ray imaging study of biomass pyrolysis. A novel reactor was developed to enable operando synchrotron radiography of fixed beds of pyrolysing biomass. Almond shell particles experienced more bulk shrinkage and less change in porosity than did walnut shell particles during pyrolysis, despite their similar composition. Alkaline pretreatment was found to reduce this difference in feedstock behaviour. Ex-situ synchrotron X-ray microtomography was performed to study the effects of pyrolysis on pore morphology. Pyrolysis led to a redistribution of pores away from particle surfaces, meaning newly formed surface area may be less accessible to adsorbates.

Correlating Local Volumetric Tissue Strains with Global Lung Mechanics Measurements

The mechanics of breathing is a fascinating and vital process. The lung has complexities and subtle heterogeneities in structure across length scales that influence mechanics and function. This study establishes an experimental pipeline for capturing alveolar deformations during a respiratory cycle using synchrotron radiation micro-computed tomography (SR-micro-CT). Rodent lungs were mechanically ventilated and imaged at various time points during the respiratory cycle. Pressure-Volume (P-V) characteristics were recorded to capture any changes in overall lung mechanical behaviour during the experiment. A sequence of tomograms was collected from the lungs within the intact thoracic cavity. Digital volume correlation (DVC) was used to compute the three-dimensional strain field at the alveolar level from the time sequence of reconstructed tomograms. Regional differences in ventilation were highlighted during the respiratory cycle, relating the local strains within the lung tissue to the global ventilation measurements. Strains locally reached approximately 150% compared to the averaged regional deformations of approximately 80-100%. Redistribution of air within the lungs was observed during cycling. Regions which were relatively poorly ventilated (low deformations compared to its neighbouring region) were deforming more uniformly at later stages of the experiment (consistent with its neighbouring region). Such heterogenous phenomena are common in everyday breathing. In pathological lungs, some of these non-uniformities in deformation behaviour can become exaggerated, leading to poor function or further damage. The technique presented can help characterize the multiscale biomechanical nature of a given pathology to improve patient management strategies, considering both the local and global lung mechanics.

Structural and compositional characteristics of Fukushima release particulate material from Units 1 and 3 elucidates release mechanisms, accident chronology and future decommissioning strategy

The structural form and elemental distribution of material originating from different Fukushima Daiichi Nuclear Power Plant reactors (Units 1 and 3) is hereby examined to elucidate their contrasting release dynamics and the current in-reactor conditions to influence future decommissioning challenges. Complimentary computed X-ray absorption tomography and X-ray fluorescence data show that the two suites of Si-based material sourced from the different reactor Units have contrasting internal structure and compositional distribution. The known event and condition chronology correlate with the observed internal and external structures of the particulates examined, which suggest that Unit 1 ejecta material sustained a greater degree of melting than that likely derived from reactor Unit 3. In particular, we attribute the near-spherical shape of Unit 1 ejecta and their internal voids to there being sufficient time for surface tension to round these objects before the hot (and so relatively low viscosity) silicate melt cooled to form glass. In contrast, a more complex internal form associated with the sub-mm particulates invoked to originate from Unit 3 suggest a lower peak temperature, over a longer duration. Using volcanic analogues, we consider the structural form of this material and how it relates to its environmental particulate stability and the bulk removal of residual materials from the damaged reactors. We conclude that the brittle and angular Unit 3 particulate are more susceptible to further fragmentation and particulate generation hazard than the round, higher-strength, more homogenous Unit 1 material.

4D In-Situ Microscopy of Aerosol Filtration in a Wall Flow Filter

The transient nature of the internal pore structure of particulate wall flow filters, caused by the continuous deposition of particulate matter, makes studying their flow and filtration characteristics challenging. In this article we present a new methodology and first experimental demonstration of time resolved in-situ synchrotron micro X-ray computed tomography (micro-CT) to study aerosol filtration. We directly imaged in 4D (3D plus time) pore scale deposits of TiO2 nanoparticles (nominal mean primary diameter of 25 nm) with a pixel resolution of 1.6 μm. We obtained 3D tomograms at a rate of ∼1 per minute. The combined spatial and temporal resolution allows us to observe pore blocking and filling phenomena as they occur in the filter’s pore space. We quantified the reduction in filter porosity over time, from an initial porosity of 0.60 to a final porosity of 0.56 after 20 min. Furthermore, the penetration depth of particulate deposits and filtration rate was quantified. This novel image-based method offers valuable and statistically relevant insights into how the pore structure and function evolves during particulate filtration. Our data set will allow validation of simulations of automotive wall flow filters. Evolutions of this experimental design have potential for the study of a wide range of dry aerosol filters and could be directly applied to catalysed automotive wall flow filters.

An Improved Cleaning Protocol for Foraminiferal Calcite from Unconsolidated Core Sediments: HyPerCal—A New Practice for Micropaleontological and Paleoclimatic Proxies

Paleoclimatic and paleoceanographic studies routinely rely on the usage of foraminiferal calcite through faunal, morphometric and physico-chemical proxies. The application of such proxies presupposes the extraction and cleaning of these biomineralized components from ocean sediments in the most efficient way, a process which is often labor intensive and time consuming. In this respect, in this study we performed a systematic experiment for planktonic foraminiferal specimen cleaning using different chemical treatments and evaluated the resulting data of a Late Quaternary gravity core sample from the Aegean Sea. All cleaning procedures adopted here were made on the basis of their minimum potential bias upon foraminiferal proxies, such as the faunal assemblages, degree of fragmentation, stable isotope composition (δ18O and δ13C) and/or Mg/Ca ratios that are frequently used as proxies for surface-ocean climate parameters (e.g., sea surface temperature, sea surface salinity). Six different protocols were tested, involving washing, sieving, and chemical treatment of the samples with hydrogen peroxide and/or sodium hexametaphosphate (Calgon®). Single species foraminifera shell weighing was combined with high-resolution scanning electron microscopy (SEM) and synchrotron X-ray microtomography (SμCT) of the material processed by each of the cleaning protocols, in order to assess the decontamination degree of specimen’s ultrastructure and interior. It appeared that a good compromise between time and cleaning efficiency is the simultaneous treatment of samples with a mixed hydrogen peroxide and Calgon solution, while the most effective way to almost completely decontaminate the calcareous components from undesirable sedimentary material is a two-step treatment—initially with hydrogen peroxide and subsequently with Calgon solutions.

The spatiotemporal spread of cervical spinal cord contusion injury pathology revealed by 3D in-line phase contrast synchrotron X-ray microtomography

Extensive structural changes occur within the spinal cord following traumatic injury. Acute tissue debris and necrotic tissue are broken down, proliferating local glia and infiltrating leukocytes remodel tissue biochemical and biophysical properties, and a chronic cavity surrounded by a scar forms at the injury epicentre. Serial-section 2D histology has traditionally assessed these features in experimental models of spinal cord injury (SCI) to measure the extent of tissue pathology and evaluate efficacy of novel therapies. However, this 2D snapshot approach overlooks slice intervening features, with accurate representation of tissue compromised by mechanical processing artefacts. 3D imaging avoids these caveats and allows full exploration of the injured tissue volume to characterise whole tissue pathology. Amongst 3D imaging modalities, Synchrotron Radiation X-ray microtomography (SRμCT) is advantageous for its speed, ability to cover large tissue volumes at high resolution, and need for minimal sample processing. Here we demonstrate how extended lengths of formalin-fixed, paraffin-embedded (FFPE) rat spinal cord can be completely imaged by SRμCT with micron resolution. Label-free contrast derived from X-ray phase interactions with low-density soft tissues, reveals spinal cord white matter, gray matter, tissue damage and vasculature, with tissue still viable for targeted 2D-histology after 3D imaging. We used SRμCT to quantify tissue pathology after a midline, cervical level (C6), 225 kDyne contusion injury over acute-to-chronic (24 h to 5 weeks) post injury time points. Quantification revealed acute tissue swelling prior to chronic atrophy across the whole imaged region (spanning 2 spinal segments above and below injury), along with rostro-caudal asymmetries in white and gray matter volume loss. 3D volumes revealed satellite damage in tissue far removed from the epicentre, and extensive rostro-caudal spread of damage through the base of the dorsal columns at 24 h post injury. This damage overlapped regions of vasogenic oedema, confirmed with subsequent histology. Tissue damage at later time points in border regions was most prominent in the dorsal columns, where it overlapped sites of damaged venous vasculature. Elaborating rostro-caudal and spatiotemporal asymmetries in reduced traumatic injury models centred on these regions may inform future treatments that seek to limit the spread of tissue pathology to these ‘at-risk’ regions.

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Whole rat spinal cord SRμCT tomograms (up to 20 mm length) with μm resolution

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Pathology of 3 SHAM and 24 acute-to-chronic C6 midline contusion SCIs quantified

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Rostro-caudal asymmetries in gray and white matter pathology progression

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Differences in ascending and descending dorsal column tract pathology

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Delayed rostral-caudal pathology associated with sites of venous vasculature

Novel application of synchrotron x-ray computed tomography for ex-vivo imaging of subcutaneously injected polymeric microsphere suspension formulations

Purpose

Subcutaneously or intramuscularly administered biodegradable microsphere formulations have been successfully exploited in the management of chronic conditions for over two decades, yet mechanistic understanding of the impact of formulation attributes on in vivo absorption rate from such systems is still in its infancy.

Methods

Suspension formulation physicochemical attributes may impact particulate deposition in subcutaneous (s.c.) tissue. Hence, the utility of synchrotron X-ray micro-computed tomography (μCT) for assessment of spatial distribution of suspension formulation components (PLG microspheres and vehicle) was evaluated in a porcine s.c. tissue model. Optical imaging of dyed vehicle and subsequent microscopic assessment of microsphere deposition was performed in parallel to compare the two approaches.

Results

Our findings demonstrate that synchrotron μCT can be applied to the assessment of microsphere and vehicle distribution in s.c. tissue, and that microspheres can also be visualised in the absence of contrast agent using this approach. The technique was deemed superior to optical imaging of macrotomy for the characterisation of microsphere deposition owing to its non-invasive nature and relatively rapid data acquisition time.

Conclusions

The method outlined in this study provides a proof of concept feasibility for μCT application to determining the vehicle and suspended PLG microspheres fate following s.c. injection. A potential application for our findings is understanding the impact of injection, device and formulation variables on initial and temporal depot geometry in pre-clinical or ex-vivo models that can inform product design.

Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans

The compound eyes of insects exhibit striking variation in size, reflecting adaptation to different lifestyles and habitats. However, the genetic and developmental bases of variation in insect eye size is poorly understood, which limits our understanding of how these important morphological differences evolve. To address this, we further explored natural variation in eye size within and between four species of the Drosophila melanogaster species subgroup. We found extensive variation in eye size among these species, and flies with larger eyes generally had a shorter inter-ocular distance and vice versa We then carried out quantitative trait loci (QTL) mapping of intra-specific variation in eye size and inter-ocular distance in both D. melanogaster and D. simulans This revealed that different genomic regions underlie variation in eye size and inter-ocular distance in both species, which we corroborated by introgression mapping in D. simulans This suggests that although there is a trade-off between eye size and inter-ocular distance, variation in these two traits is likely to be caused by different genes and so can be genetically decoupled. Finally, although we detected QTL for intra-specific variation in eye size at similar positions in D. melanogaster and D. simulans, we observed differences in eye fate commitment between strains of these two species. This indicates that different developmental mechanisms and therefore, most likely, different genes contribute to eye size variation in these species. Taken together with the results of previous studies, our findings suggest that the gene regulatory network that specifies eye size has evolved at multiple genetic nodes to give rise to natural variation in this trait within and among species.

Real-time reconstruction and visualisation towards dynamic feedback control during time-resolved tomography experiments at TOMCAT

Tomographic X-ray microscopy beamlines at synchrotron light sources worldwide have pushed the achievable time-resolution for dynamic 3-dimensional structural investigations down to a fraction of a second, allowing the study of quickly evolving systems. The large data rates involved impose heavy demands on computational resources, making it difficult to readily process and interrogate the resulting volumes. The data acquisition is thus performed essentially blindly. Such a sequential process makes it hard to notice problems with the measurement protocol or sample conditions, potentially rendering the acquired data unusable, and it keeps the user from optimizing the experimental parameters of the imaging task at hand. We present an efficient approach to address this issue based on the real-time reconstruction, visualisation and on-the-fly analysis of a small number of arbitrarily oriented slices. This solution, requiring only a single additional computing workstation, has been implemented at the TOMCAT beamline of the Swiss Light Source. The system is able to process multiple sets of slices per second, thus pushing the reconstruction throughput on the same level as the data acquisition. This enables the monitoring of dynamic processes as they occur and represents the next crucial step towards adaptive feedback control of time-resolved in situ tomographic experiments.

Quantification of the Whole Lymph Node Vasculature Based on Tomography of the Vessel Corrosion Casts

Lymph nodes (LN) are crucial for immune function, and comprise an important interface between the blood and lymphatic systems. Blood vessels (BV) in LN are highly specialized, featuring high endothelial venules across which most of the resident lymphocytes crossed. Previous measurements of overall lymph and BV flow rates demonstrated that fluid also crosses BV walls, and that this is important for immune function. However, the spatial distribution of the BV in LN has not been quantified to the degree necessary to analyse the distribution of transmural fluid movement. In this study, we seek to quantify the spatial localization of LNBV, and to predict fluid movement across BV walls. MicroCT imaging of murine popliteal LN showed that capillaries were responsible for approximately 75% of the BV wall surface area, and that this was mostly distributed around the periphery of the node. We then modelled blood flow through the BV to obtain spatially resolved hydrostatic pressures, which were then combined with Starling’s law to predict transmural flow. Much of the total 10 nL/min transmural flow (under normal conditions) was concentrated in the periphery, corresponding closely with surface area distribution. These results provide important insights into the inner workings of LN, and provide a basis for further exploration of the role of LN flow patterns in normal and pathological functions.

Co-electrospraying of tumour cell mimicking hollow polymeric microspheres for diffusion magnetic resonance imaging

Diffusion magnetic resonance imaging (dMRI) is considered as a useful tool to study solid tumours. However, the interpretation of dMRI signal and validation of quantitative measurements of is challenging. One way to address these challenges is by using a standard reference material that can mimic tumour cell microstructure. There is a growing interest in using hollow polymeric microspheres, mainly prepared by multiple steps, as mimics of cells in healthy and diseased tissue. The present work reports on tumour cell-mimicking materials composed of hollow microspheres for application as a standard material in dMRI. These microspheres were prepared via one-step co-electrospraying process. The shell material was poly(d,l-lactic-co-glycolic acid) (PLGA) polymers with different molecule weights and/or ratios of glycolic acid-to-lactic, while the core was polyethylene glycol (PEG) or ethylene glycol. The resultant co-electrosprayed products were characterised by optical microscopy, scanning electron microscopy (SEM) and synchrotron X-ray micro-CT. These products were found to have variable structures and morphologies, e.g. from spherical particles with/without surface hole, through beaded fibres to smooth fibres, which mainly depend on PLGA composition and core materials. Only the shell material of PLGA polymer with ester terminated, Mw 50,000-75,000 g mol-1, and lactide:glycolide 85:15 formed hollow microspheres via the co-electrospraying process using the core material of 8 wt% PEG/chloroform as the core. A water-filled test object (or phantom) was designed and constructed from samples of the material generated from co-electrosprayed PLGA microspheres and tested on a 7 T MRI scanner. The preliminary MRI results provide evidence that hollow PLGA microspheres can restrict/hinder water diffusion as cells do in tumour tissue, implying that the phantom may be suitable for use as a quantitative validation and calibration tool for dMRI.

Synchrotron tomography of intervertebral disc deformation quantified by digital volume correlation reveals microstructural influence on strain patterns

The intervertebral disc (IVD) has a complex and multiscale extracellular matrix structure which provides unique mechanical properties to withstand physiological loading. Low back pain has been linked to degeneration of the disc but reparative treatments are not currently available. Characterising the disc's 3D microstructure and its response in a physiologically relevant loading environment is required to improve understanding of degeneration and to develop new reparative treatments. In this study, techniques for imaging the native IVD, measuring internal deformation and mapping volumetric strain were applied to an in situ compressed ex vivo rat lumbar spine segment. Synchrotron X-ray micro-tomography (synchrotron CT) was used to resolve IVD structures at microscale resolution. These image data enabled 3D quantification of collagen bundle orientation and measurement of local displacement in the annulus fibrosus between sequential scans using digital volume correlation (DVC). The volumetric strain mapped from synchrotron CT provided a detailed insight into the micromechanics of native IVD tissue. The DVC findings showed that there was no slipping at lamella boundaries, and local strain patterns were of a similar distribution to the previously reported elastic network with some heterogeneous areas and maximum strain direction aligned with bundle orientation, suggesting bundle stretching and sliding. This method has the potential to bridge the gap between measures of macro-mechanical properties and the local 3D micro-mechanical environment experienced by cells. This is the first evaluation of strain at the micro scale level in the intact IVD and provides a quantitative framework for future IVD degeneration mechanics studies and testing of tissue engineered IVD replacements. STATEMENT OF SIGNIFICANCE: Synchrotron in-line phase contrast X-ray tomography provided the first visualisation of native intact intervertebral disc microstructural deformation in 3D. For two annulus fibrosus volumes of interest, collagen bundle orientation was quantified and local displacement mapped as strain. Direct evidence of microstructural influence on strain patterns could be seen such as no slipping at lamellae boundaries and maximum strain direction aligned with collagen bundle orientation. Although disc elastic structures were not directly observed, the strain patterns had a similar distribution to the previously reported elastic network. This study presents technical advances and is a basis for future X-ray microscopy, structural quantification and digital volume correlation strain analysis of soft tissue.

Preservation of Bone Tissue Integrity with Temperature Control for In Situ SR-MicroCT Experiments

Digital volume correlation (DVC), combined with in situ synchrotron microcomputed tomography (SR-microCT) mechanics, allows for 3D full-field strain measurement in bone at the tissue level. However, long exposures to SR radiation are known to induce bone damage, and reliable experimental protocols able to preserve tissue properties are still lacking. This study aims to propose a proof-of-concept methodology to retain bone tissue integrity, based on residual strain determination using DVC, by decreasing the environmental temperature during in situ SR-microCT testing. Compact and trabecular bone specimens underwent five consecutive full tomographic data collections either at room temperature or 0 °C. Lowering the temperature seemed to reduce microdamage in trabecular bone but had minimal effect on compact bone. A consistent temperature gradient was measured at each exposure period, and its prolonged effect over time may induce localised collagen denaturation and subsequent damage. DVC provided useful information on irradiation-induced microcrack initiation and propagation. Future work is necessary to apply these findings to in situ SR-microCT mechanical tests, and to establish protocols aiming to minimise the SR irradiation-induced damage of bone.

Synchrotron Big Data Science

The rapid development of synchrotrons has massively increased the speed at which experiments can be performed, while new techniques have increased the amount of raw data collected during each experiment. While this has created enormous new opportunities, it has also created tremendous challenges for national facilities and users. With the huge increase in data volume, the manual analysis of data is no longer possible. As a result, only a fraction of the data collected during the time- and money-expensive synchrotron beam-time is analyzed and used to deliver new science. Additionally, the lack of an appropriate data analysis environment limits the realization of experiments that generate a large amount of data in a very short period of time. The current lack of automated data analysis pipelines prevents the fine-tuning of beam-time experiments, further reducing their potential usage. These effects, collectively known as the "data deluge," affect synchrotrons in several different ways including fast data collection, available local storage, data management systems, and curation of the data. This review highlights the Big Data strategies adopted nowadays at synchrotrons, documenting this novel and promising hybridization between science and technology, which promise a dramatic increase in the number of scientific discoveries.

Effect of SR-microCT radiation on the mechanical integrity of trabecular bone using in situ mechanical testing and digital volume correlation

The use of synchrotron radiation micro-computed tomography (SR-microCT) is becoming increasingly popular for studying the relationship between microstructure and bone mechanics subjected to in situ mechanical testing. However, it is well known that the effect of SR X-ray radiation can considerably alter the mechanical properties of bone tissue. Digital volume correlation (DVC) has been extensively used to compute full-field strain distributions in bone specimens subjected to step-wise mechanical loading, but tissue damage from sequential SR-microCT scans has not been previously addressed. Therefore, the aim of this study is to examine the influence of SR irradiation-induced microdamage on the apparent elastic properties of trabecular bone using DVC applied to in situ SR-microCT tomograms obtained with different exposure times. Results showed how DVC was able to identify high local strain levels (> 10,000 µε) corresponding to visible microcracks at high irradiation doses (~ 230 kGy), despite the apparent elastic properties remained unaltered. Microcracks were not detected and bone plasticity was preserved for low irradiation doses (~ 33 kGy), although image quality and consequently, DVC performance were reduced. DVC results suggested some local deterioration of tissue that might have resulted from mechanical strain concentration further enhanced by some level of local irradiation even for low accumulated dose.

Optimising complementary soft tissue synchrotron X-ray microtomography for reversibly-stained central nervous system samples

Synchrotron radiation microtomography (SRμCT) is a nominally non-destructive 3D imaging technique which can visualise the internal structures of whole soft tissues. As a multi-stage technique, the cumulative benefits of optimising sample preparation, scanning parameters and signal processing can improve SRμCT imaging efficiency, image quality, accuracy and ultimately, data utility. By evaluating different sample preparations (embedding media, tissue stains), imaging (projection number, propagation distance) and reconstruction (artefact correction, phase retrieval) parameters, a novel methodology (combining reversible iodine stain, wax embedding and inline phase contrast) was optimised for fast (~12 minutes), high-resolution (3.2-4.8 μm diameter capillaries resolved) imaging of the full diameter of a 3.5 mm length of rat spinal cord. White-grey matter macro-features and micro-features such as motoneurons and capillary-level vasculature could then be completely segmented from the imaged volume for analysis through the shallow machine learning SuRVoS Workbench. Imaged spinal cord tissue was preserved for subsequent histology, establishing a complementary SRμCT methodology that can be applied to study spinal cord pathologies or other nervous system tissues such as ganglia, nerves and brain. Further, our 'single-scan iterative downsampling' approach and side-by-side comparisons of mounting options, sample stains and phase contrast parameters should inform efficient, effective future soft tissue SRμCT experiment design.

X-ray physico-chemical imaging during activation of cobalt-based Fischer-Tropsch synthesis catalysts

The imaging of catalysts and other functional materials under reaction conditions has advanced significantly in recent years. The combination of the computed tomography (CT) approach with methods such as X-ray diffraction (XRD), X-ray fluorescence (XRF) and X-ray absorption near-edge spectroscopy (XANES) now enables local chemical and physical state information to be extracted from within the interiors of intact materials which are, by accident or design, inhomogeneous. In this work, we follow the phase evolution during the initial reduction step(s) to form Co metal, for Co-containing particles employed as Fischer-Tropsch synthesis (FTS) catalysts; firstly, working at small length scales (approx. micrometre spatial resolution), a combination of sample size and density allows for transmission of comparatively low energy signals enabling the recording of 'multimodal' tomography, i.e. simultaneous XRF-CT, XANES-CT and XRD-CT. Subsequently, we show high-energy XRD-CT can be employed to reveal extent of reduction and uniformity of crystallite size on millimetre-sized TiO₂ trilobes. In both studies, the CoO phase is seen to persist or else evolve under particular operating conditions and we speculate as to why this is observed.This article is part of a discussion meeting issue 'Providing sustainable catalytic solutions for a rapidly changing world'.

Visualising the 3D microstructure of stained and native intervertebral discs using X-ray microtomography

Intervertebral disc degeneration (IVDD) is linked to low back pain. Microstructural changes during degeneration have previously been imaged using 2D sectioning techniques and 3D methods which are limited to small specimens and prone to inducing artefacts from sample preparation. This study explores micro computed X-ray tomography (microCT) methods with the aim of resolving IVD 3D microstructure whilst minimising sample preparation artefacts. Low X-ray absorption contrast in non-mineralised tissue can be enhanced using staining and phase contrast techniques. A step-wise approach, including comparing three stains, was used to develop microCT for bovine tail IVD using laboratory and synchrotron sources. Staining successfully contrasted collagenous structures; however not all regions were stained and the procedure induced macroscopic structural changes. Phase contrast microCT of chemically fixed yet unstained samples resolved the nucleus pulposus, annulus fibrosus and constituent lamellae, and finer structures including collagen bundles and cross-bridges. Using the same imaging methods native tissue scans were of slightly lower contrast but free from sample processing artefacts. In the future these methods may be used to characterise structural remodelling in soft (non-calcified) tissues and to conduct in situ studies of native loaded tissues and constructs to characterise their 3D mechanical properties.

Interpretation and Utility of the Moments of Small-Angle X-Ray Scattering Distributions

Small angle x-ray scattering has been proven to be a valuable method for accessing structural information below the spatial resolution limit implied by direct imaging. Here, we theoretically derive the relation that links the subpixel differential phase signal provided by the sample to the moments of scattering distributions accessible by refraction sensitive x-ray imaging techniques. As an important special case we explain the scatter or dark-field contrast in terms of the sample's phase signal. Further, we establish that, for binary phase objects, the nth moment scales with the difference of the refractive index decrement to the power of n. Finally, we experimentally demonstrate the utility of the moments by quantitatively determining the particle sizes of a range of powders with a laboratory-based setup.

Deformation of the Lamina Cribrosa and Optic Nerve Due to Changes in Cerebrospinal Fluid Pressure

Purpose

Cerebrospinal fluid pressure (CSFp) changes are involved or implicated in various ocular conditions including glaucoma, idiopathic intracranial hypertension, and visual impairment and intracranial pressure syndrome. However, little is known about the effects of CSFp on lamina cribrosa and retrolaminar neural tissue (RLNT) biomechanics, potentially important in these conditions. Our goal was to use an experimental approach to visualize and quantify the deformation of these tissues as CSFp increased.

Methods

The posterior eye and RLNT of porcine eyes (n = 3) were imaged using synchrotron radiation phase-contrast micro-computed tomography (PC μCT) at an intraocular pressure of 15 mm Hg and CSFps of 4, 10, 20, and 30 mm Hg. Scans of each tissue region were acquired at each CSFp step and analyzed using digital volume correlation to determine 3-dimensional tissue deformations.

Results

Elevating CSFp increased the strain in the lamina cribrosa and RLNT of all three specimens, with the largest strains occurring in the RLNT. Relative to the baseline CSFp of 4 mm Hg, at 30 mm Hg, the lamina cribrosa experienced a mean first and third principal strain of 4.4% and −3.5%, respectively. The corresponding values for the RLNT were 9.5% and −9.1%.

Conclusions

CSFp has a significant impact on the strain distributions within the lamina cribrosa and, more prominently, within the RLNT. Elevations in CSFp were positively correlated with increasing deformations in each region and may play a role in ocular pathologies linked to changes in CSFp.

Effects of Peripapillary Scleral Stiffening on the Deformation of the Lamina Cribrosa

Purpose

Scleral stiffening has been proposed as a treatment for glaucoma to protect the lamina cribrosa (LC) from excessive intraocular pressure–induced deformation. Here we experimentally evaluated the effects of moderate stiffening of the peripapillary sclera on the deformation of the LC.

Methods

An annular sponge, saturated with 1.25% glutaraldehyde, was applied to the external surface of the peripapillary sclera for 5 minutes to stiffen the sclera. Tissue deformation was quantified in two groups of porcine eyes, using digital image correlation (DIC) or computed tomography imaging and digital volume correlation (DVC). In group A (n = 14), eyes were subjected to inflation testing before and after scleral stiffening. Digital image correlation was used to measure scleral deformation and quantify the magnitude of scleral stiffening. In group B (n = 5), the optic nerve head region was imaged using synchrotron radiation phase-contrast microcomputed tomography (PC μCT) at an isotropic spatial resolution of 3.2 μm. Digital volume correlation was used to compute the full-field three-dimensional deformation within the LC and evaluate the effects of peripapillary scleral cross-linking on LC biomechanics.

Results

On average, scleral treatment with glutaraldehyde caused a 34 ± 14% stiffening of the peripapillary sclera measured at 17 mm Hg and a 47 ± 12% decrease in the maximum tensile strain in the LC measured at 15 mm Hg. The reduction in LC strains was not due to cross-linking of the LC.

Conclusions

Peripapillary scleral stiffening is effective at reducing the magnitude of biomechanical strains within the LC. Its potential and future utilization in glaucoma axonal neuroprotection requires further investigation.

A convolutional neural network approach to calibrating the rotation axis for X-ray computed tomography

This paper presents an algorithm to calibrate the center-of-rotation for X-ray tomography by using a machine learning approach, the Convolutional Neural Network (CNN). The algorithm shows excellent accuracy from the evaluation of synthetic data with various noise ratios. It is further validated with experimental data of four different shale samples measured at the Advanced Photon Source and at the Swiss Light Source. The results are as good as those determined by visual inspection and show better robustness than conventional methods. CNN has also great potential for reducing or removing other artifacts caused by instrument instability, detector non-linearity, etc. An open-source toolbox, which integrates the CNN methods described in this paper, is freely available through GitHub at tomography/xlearn and can be easily integrated into existing computational pipelines available at various synchrotron facilities. Source code, documentation and information on how to contribute are also provided.

Chemical imaging of Fischer-Tropsch catalysts under operating conditions

Although we often understand empirically what constitutes an active catalyst, there is still much to be understood fundamentally about how catalytic performance is influenced by formulation. Catalysts are often designed to have a microstructure and nanostructure that can influence performance but that is rarely considered when correlating structure with function. Fischer-Tropsch synthesis (FTS) is a well-known and potentially sustainable technology for converting synthetic natural gas ("syngas": CO + H₂) into functional hydrocarbons, such as sulfur- and aromatic-free fuel and high-value wax products. FTS catalysts typically contain Co or Fe nanoparticles, which are often optimized in terms of size/composition for a particular catalytic performance. We use a novel, "multimodal" tomographic approach to studying active Co-based catalysts under operando conditions, revealing how a simple parameter, such as the order of addition of metal precursors and promoters, affects the spatial distribution of the elements as well as their physicochemical properties, that is, crystalline phase and crystallite size during catalyst activation and operation. We show in particular how the order of addition affects the crystallinity of the TiO₂ anatase phase, which in turn leads to the formation of highly intergrown cubic close-packed/hexagonal close-packed Co nanoparticles that are very reactive, exhibiting high CO conversion. This work highlights the importance of operando microtomography to understand the evolution of chemical species and their spatial distribution before any concrete understanding of impact on catalytic performance can be realized.

Towards on-the-fly data post-processing for real-time tomographic imaging at TOMCAT

Sub-second full-field tomographic microscopy at third-generation synchrotron sources is a reality, opening up new possibilities for the study of dynamic systems in different fields. Sustained elevated data rates of multiple GB/s in tomographic experiments will become even more common at diffraction-limited storage rings, coming in operation soon. The computational tools necessary for the post-processing of raw tomographic projections have generally not experienced the same efficiency increase as the experimental facilities, hindering optimal exploitation of this new potential. We present here a fast, flexible, and user-friendly post-processing pipeline overcoming this efficiency mismatch and delivering reconstructed tomographic datasets just few seconds after the data have been acquired, enabling fast parameter and image quality evaluation as well as efficient post-processing of TBs of tomographic data. With this new tool, also able to accept a stream of data directly from a detector, few selected tomographic slices are available in less than half a second, providing advanced previewing capabilities paving the way to new concepts for on-the-fly control of dynamic experiments.

Synchrotron X-ray tomographic quantification of microstructural evolution in ice cream – a multi-phase soft solid

Synchrotron X-ray tomography reveals the evolving internal morphology of a multi-phase soft solid, ice cream, enabling time dependent quantitation.

High-Density Protein Loading on Hierarchically Porous Layered Double Hydroxide Composites with a Rational Mesostructure

Hierarchically porous biocompatible Mg-Al-Cl-type layered double hydroxide (LDH) composites containing aluminum hydroxide (Alhy) have been prepared using a phase-separation process. The sol-gel synthesis allows for the hierarchical pores of the LDH-Alhy composites to be tuned, leading to a high specific solid surface area per unit volume available for high-molecular-weight protein adsorptions. A linear relationship between the effective surface area, SEFF, and loading capacity of a model protein, bovine serum albumin (BSA), is established following successful control of the structure of the LDH-Alhy composite. The threshold of the mean pore diameter, Dpm, above which BSA is effectively adsorbed on the surface of LDH-Alhy composites, is deduced as 20 nm. In particular, LDH-Alhy composite aerogels obtained via supercritical drying exhibit an extremely high capacity for protein loading (996 mg/g) as a result of a large mean mesopore diameter (>30 nm). The protein loading on LDH-Alhy is >14 times that of a reference LDH material (70 mg/g) prepared via a standard procedure. Importantly, BSA molecules pre-adsorbed on porous composites were successfully released on soaking in ionic solutions (HPO4(2-) and Cl(-) aqueous). The superior capability of the biocompatible LDH materials for loading, encapsulation, and releasing large quantities of proteins was clearly demonstrated.

Temporal sparsity exploiting nonlocal regularization for 4D computed tomography reconstruction

X-ray imaging applications in medical and material sciences are frequently limited by the number of tomographic projections collected. The inversion of the limited projection data is an ill-posed problem and needs regularization. Traditional spatial regularization is not well adapted to the dynamic nature of time-lapse tomography since it discards the redundancy of the temporal information. In this paper, we propose a novel iterative reconstruction algorithm with a nonlocal regularization term to account for time-evolving datasets. The aim of the proposed nonlocal penalty is to collect the maximum relevant information in the spatial and temporal domains. With the proposed sparsity seeking approach in the temporal space, the computational complexity of the classical nonlocal regularizer is substantially reduced (at least by one order of magnitude). The presented reconstruction method can be directly applied to various big data 4D (x, y, z+time) tomographic experiments in many fields. We apply the proposed technique to modelled data and to real dynamic X-ray microtomography (XMT) data of high resolution. Compared to the classical spatio-temporal nonlocal regularization approach, the proposed method delivers reconstructed images of improved resolution and higher contrast while remaining significantly less computationally demanding.