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

Investigating Bubble Formation and Evolution in Vanadium Redox Flow Batteries via Synchrotron X-Ray Imaging

The parasitic hydrogen evolution reaction (HER) hinders electrolyte transport. It reduces the effective electrochemical surface area in the negative half-cell of vanadium redox flow batteries (VRFBs), resulting in substantial efficiency losses. This study investigates the formation and evolution of hydrogen bubbles within VRFB electrodes through comprehensive experimental characterization and a detailed analysis of the resolved bubbles. The electrode is imaged using synchrotron X-ray tomography, and gas bubbles in the images are identified and characterized using a deep learning model combined with a morphological analysis tool. The HER intensity increases at more negative working electrode potentials, causing residual bubbles to grow and fuse in the electrode central region. In contrast, independent bubbles predominantly form at the electrode edges. Furthermore, bubble growth leads to the gradual development of irregular shapes. These observations provide insights into bubble formation and evolution rules, contributing to a better understanding of the system.

Structure and variability in the female genital atrium of Uropodina (Acari: Parasitiformes)

Primary and secondary sexual characters of Mesostigmata are often used in species descriptions and phylogenetic analyses. The use of these characters has been focused almost exclusively on external structures. Digital 3D reconstruction based on synchrotron X-ray microtomography (SR-μCT) data allowed a comparative investigation of the structure of an internal system, the female genital atrium, in the mite lineage Uropodina (Parasitiformes: Mesostigmata). Despite substantial variability in observed structures, a general model for the endogynium, vagina, and muscle structure has been generated using a combination of SR-μCT and light microscopy. Most of the variations are hypothesized as related to species recognition and/or manipulation of the endospermatophore. The recorded variability may have substantial phylogenetic value, as a previously unreported modification of the vagina appears to diagnose a substantial lineage of "higher" Uropodina. This set of observations also support the hypothesis that the large family Urodinychidae is polyphyletic. Overall, SR-μCT and 3D reconstruction turned out to be very helpful for studies on internal organ systems in these very small organisms, lessening the need for laborious dissections or extensive Transmission electron microscopy-based investigations.

The cranial gland system of Nasonia spp.: a link between chemical ecology, evo-devo, and descriptive taxonomy (Hymenoptera: Chalcidoidea)

Nasonia is an emerging model system for investigating the evolution of complex species-specific behavioral and morphological phenotypes. For example, the male head shape differs considerably between Nasonia Ashmead (Hymenoptera: Chalcidoidea) species. In addition, differences in courtship behaviors, and possibly influences of a male-specific aphrodisiac pheromone, contribute to interspecific prezygotic isolation. However, the possible relationships between courtship, pheromone signaling, and male head shape are unknown. Using multimodal imaging techniques, we conducted a comprehensive examination of the skeletomuscular and exocrine gland systems of the lower head region of all 4 Nasonia species and their sister genus Trichomalopsis Crawford (Hymenoptera: Chalcidoidea). This analysis reveals the presence of 3 undescribed exocrine glands in the lower head region and a unique mandibular modification, the basal mandibular carina, that might be involved in pheromone spread. We performed morphometric and volumetric analyses using 3D datasets from synchrotron X-ray microtomography and found that the size of the genomandibular gland and the corresponding basal mandibular carina correlates with both interspecific courtship length and head shape differences, indicating that this gland is a likely source of the oral aphrodisiac pheromone. These differences correlate with the prevalence of within-host mating rather than phylogenetic relatedness in Nasonia species, with increased within-host mating occurring in species with larger genomandibular glands. Our findings create an opportunity to better understand the complex gene regulatory networks underlying superficially unrelated traits and serve as a link between behavior, chemical ecology, evo-devo, and descriptive taxonomy.

Multi-stage deep learning artifact reduction for parallel-beam computed tomography

Computed tomography (CT) using synchrotron radiation is a powerful technique that, compared with laboratory CT techniques, boosts high spatial and temporal resolution while also providing access to a range of contrast-formation mechanisms. The acquired projection data are typically processed by a computational pipeline composed of multiple stages. Artifacts introduced during data acquisition can propagate through the pipeline and degrade image quality in the reconstructed images. Recently, deep learning has shown significant promise in enhancing image quality for images representing scientific data. This success has driven increasing adoption of deep learning techniques in CT imaging. Various approaches have been proposed to incorporate deep learning into computational pipelines, but each has limitations in addressing artifacts effectively and efficiently in synchrotron CT, either in properly addressing the specific artifacts or in computational efficiency. Recognizing these challenges, we introduce a novel method that incorporates separate deep learning models at each stage of the tomography pipeline - projection, sinogram and reconstruction - to address specific artifacts locally in a data-driven way. Our approach includes bypass connections that feed both the outputs from previous stages and raw data to subsequent stages, minimizing the risk of error propagation. Extensive evaluations on both simulated and real-world datasets illustrate that our approach effectively reduces artifacts and outperforms comparison methods.

Characterization of hydrogel-scaffold mechanical properties and microstructure by using synchrotron propagation-based imaging

Hydrogel-based scaffolds have been widely used in soft tissue regeneration due to their biocompatible and tissue-like environment for maintaining cellular functions and tissue regeneration. Understanding the mechanical properties and internal microstructure of hydrogel-based scaffold, once implanted, is imperative in tissue engineering applications and longitudinal studies. Notably, this has been challenging to date as various conventional characterization methods by, for example, mechanical testing (for mechanical properties) and microscope (for internal microstructure) are destructive as they require removing scaffolds from the implantation site and processing samples for characterization. Synchrotron radiation propagation-based imaging-computed tomography (SR-PBI-CT) is feasible and promising for non-destructive visualizing of hydrogel scaffolds. As inspired, this study aimed to perform a study on the characterization of mechanical properties and microstructure of hydrogel scaffolds based on the SR-PBI-CT. In this study, hydrogel biomaterial inks composed of 3% w/v alginate and 1% w/v gelatin were printed to form scaffolds, with some scaffolds being degraded over 3 days. Both degraded and undegraded scaffolds underwent compressive testing, with the strains being controlled at the preset values; meanwhile stresses within scaffolds were measuring, resulting the stress-strain curves. Concurrently, the scaffolds were also imaged and examined by SR-PBI-CT at Canadian Light Source (CLS). During the imaging process, the scaffolds were mechanically loaded, respectively, with the strains same as the ones in the aforementioned compressive testing, and at each strain, the scaffold was scanned with a pixel size of 13 μm. From the stress-strain curves obtained in the compression testing, the Young's modulus was evaluated to characterize the elastic behavior of scaffolds: with the range between around 5-25 kPa. From the images captured by SR-PBI-CT, the scaffolds microstructures were examined in terms of the strand cross-section area, pore size, and hydrogel volume. Further, from the SR-PBI-CT images, the stress within hydrogel of scaffolds were evaluated, showing the agreement with those obtained from compression testing. These results have illustrated that the mechanical properties and microstructures of scaffolds, ether being degraded or not, can be examined and characterized by the SR-PBI-CT imaging, in a non-destructive manner. This would represent a significant advance for facilitating longitudinal studies on the scaffolds once implanted in-vivo.

Applications of synchrotron light in seed research: an array of x-ray and infrared imaging methodologies

Synchrotron radiation (SR) provides a wide spectrum of bright light that can be tailored to test myriad research questions. SR provides avenues to illuminate structure and composition across scales, making it ideally suited to the study of plants and seeds. Here, we present an array of methodologies and the data outputs available at a light source facility. Datasets feature seed and grain from a range of crop species including Citrullus sp. (watermelon), Brassica sp. (canola), Pisum sativum (pea), and Triticum durum (wheat), to demonstrate the power of SR for advancing plant science. The application of SR micro-computed tomography (SR-µCT) imaging revealed internal seed microstructures and their three-dimensional morphologies in exquisite detail, without the need for destructive sectioning. Spectroscopy in the infrared spectrum probed sample biochemistry, detailing the spatial distribution of seed macronutrients such as lipid, protein and carbohydrate in the embryo, endosperm and seed coat. Methods using synchrotron X-rays, including X-ray absorption spectroscopy (XAS) and X-ray fluorescence (XRF) imaging revealed elemental distributions, to spatially map micronutrients in seed subcompartments and to determine their speciation. Synchrotron spectromicroscopy (SM) allowed chemical composition to be resolved at the nano-scale level. Diverse crop seed datasets showcase the range of structural and chemical insights provided by five beamlines at the Canadian Light Source, and the potential for synchrotron imaging for informing plant and agricultural research.

Plant tissue-based scaffolds filled with oil function as adipose tissue mimetics

Cellulosic scaffolds filled with oil were designed to replicate animal adipose tissues. Many plants are structured as polysaccharide-based cellular solids. They maintain their integrity after drying, can serve as a scaffold for incorporating fat, and do not lose integrity upon heating, thus resembling native adipose tissue. Carrots, broccoli, and asparagus were freeze-dried and subsequently filled with peanut oil, its glycerolysis product (GP), and the oleogel of this GP. Oleogel-filled scaffolds displayed high oil binding capacity (≥95%), and an oil loss resembling that of adipose tissue. In addition, the texture of oleogel-filled asparagus and broccoli tissue closely resembled that of beef and pork adipose tissues, respectively. Plant scaffolds closely emulated the temperature-dependent rheological behavior of adipose tissue. These new materials could significantly improve the quality of plant-based meat analogues, such as burgers and sausages, by preventing the thermal softening of the material upon cooking and excessive oil loss.

Development of a low-dose strategy for propagation-based imaging helical computed tomography (PBI-HCT): high image quality and reduced radiation dose

Background. Propagation-based imaging computed tomography (PBI-CT) has been recently emerging for visualizing low-density materials due to its excellent image contrast and high resolution. Based on this, PBI-CT with a helical acquisition mode (PBI-HCT) offers superior imaging quality (e.g., fewer ring artifacts) and dose uniformity, making it ideal for biomedical imaging applications. However, the excessive radiation dose associated with high-resolution PBI-HCT may potentially harm objects or hosts being imaged, especially in live animal imaging, raising a great need to reduce radiation dose.Methods. In this study, we strategically integrated Sparse2Noise (a deep learning approach) with PBI-HCT imaging to reduce radiation dose without compromising image quality. Sparse2Noise uses paired low-dose noisy images with different photon fluxes and projection numbers for high-quality reconstruction via a convolutional neural network (CNN). Then, we examined the imaging quality and radiation dose of PBI-HCT imaging using Sparse2Noise, as compared to when Sparse2Noise was used in low-dose PBI-CT imaging (circular scanning mode). Furthermore, we conducted a comparison study on the use of Sparse2Noise versus two other state-of-the-art low-dose imaging algorithms (i.e., Noise2Noise and Noise2Inverse) for imaging low-density materials using PBI-HCT at equivalent dose levels.Results. Sparse2Noise allowed for a 90% dose reduction in PBI-HCT imaging while maintaining high image quality. As compared to PBI-CT imaging, the use of Sparse2Noise in PBI-HCT imaging shows more effective by reducing additional radiation dose (30%-36%). Furthermore, helical scanning mode also enhances the performance of existing low-dose algorithms (Noise2Noise and Noise2Inverse); nevertheless, Sparse2Noise shows significantly higher signal-to-noise ratio (SNR) value compared to Noise2Noise and Noise2Inverse at the same radiation dose level.Conclusions and significance. Our proposed low-dose imaging strategy Sparse2Noise can be effectively applied to PBI-HCT imaging technique and requires lower dose for acceptable quality imaging. This would represent a significant advance imaging for low-density materials imaging and for future live animals imaging applications.

Experimental investigation of dynamic drying in single pharmaceutical granules containing acetaminophen or carbamazepine using synchrotron X-ray micro computed tomography

Drying time, velocity, and temperature are important aspects of the drying process for pharmaceutical granules observed during tablet manufacturing. However, the drying mechanism of single granules is often limited to modelling and simulation, with the internal and physical changes difficult to quantify at an experimental level. In this study, in-situ synchrotron-based X-ray imaging techniques were used for the first time to investigate the dynamic drying of single pharmaceutical granules, quantifying internal changes occurring over the drying time. Two commonly used excipients (lactose monohydrate (LMH) and microcrystalline cellulose (MCC)) were used as pure components and binary mixtures with one of either two active pharmaceutical ingredients of differing hydrophilicity/hydrophobicity (acetaminophen (APAP) and carbamazepine (CBZ)). Water was used as a liquid binder to generate single granules of 25 % to 30 % moisture content. Results showed that for most samples, the drying time and composition significantly influences the pore volume evolution and the moisture ratio, with the velocity and temperature of the drying air possessing mixed significance on increasing the rate of pore connectivity and moisture removal depending on the sample composition. Effects of active ingredient loading resulted in minimal influence on the drying of CBZ and generated binary mixtures, with APAP and its respective mixtures' drying behaviour dominated by the material's hydrophilic nature.

First fossil mountain midges (Diptera, Deuterophlebiidae) and their evolutionary and ecological implication

We present here the first-ever fossil flies from the family Deuterophlebiidae. The recent adults have an exceptionally brief lifespan, with males surviving only two hours. Their distinctive features include a complete reduction of mouthparts, and wing venation characterized by a dense net of false veins replacing most of true veins. Due to this distinctive venation the phylogenetic position of Deuterophlebiidae was unclear, compounded by the absence of fossils that could shed light on the early development of these characters. Two new genera and species are described from Burmese amber, Protodeuterophlebia oosterbroeki Krzemiński, Krzemińska & Soszyńska, gen. et sp. nov. and Cretodeuterophlebia courtneyi, Krzemiński, Skibińska & Kopeć, gen. et sp. nov. They date back the age of the family to the mid-Cretaceous. Notably, the fossils reveal first false veins and reduced mouthparts, suggesting a short lifespan in these Cretaceous mountain midges. A comparative analysis of wing venation indicated the Hennigmatidae as a plausible ancestral group to the Deuterophlebiidae. A syninclusion of mayfly indicates the coexistence of these short-lived insects during the same flight period. This synchrony extends to their brief time in flight aligning with the flow of fluid resin. The occurrence of these simultaneous events is extremely low, emphasizing the significance of these findings.

Phase retrieval in propagation-based X-ray imaging beyond the limits of transport of intensity and contrast transfer function approaches

We derive a phase retrieval formula for propagation-based phase contrast X-ray imaging that does not require weakly attenuating objects or short propagation distances. It is directly applicable to both single- and multiple-distance scenarios. We show the validity conditions and study the error of the underlying mutual intensity approximation, which uses the common assumptions of weak phase shift variations and phase-attenuation duality. The approximation generalizes those behind the transport of intensity (TIE) and contrast transfer function (CTF) models, and it approaches them when their respective additional assumptions are satisfied. When they are not, it clearly outperforms them, which we show both theoretically and practically on synthetic and measured data.

Hard X-ray imaging and tomography at the Biomedical Imaging and Therapy beamlines of Canadian Light Source

The Biomedical Imaging and Therapy facility of the Canadian Light Source comprises two beamlines, which together cover a wide X-ray energy range from 13 keV up to 140 keV. The beamlines were designed with a focus on synchrotron applications in preclinical imaging and veterinary science as well as microbeam radiation therapy. While these remain a major part of the activities of both beamlines, a number of recent upgrades have enhanced the versatility and performance of the beamlines, particularly for high-resolution microtomography experiments. As a result, the user community has been quickly expanding to include researchers in advanced materials, batteries, fuel cells, agriculture, and environmental studies. This article summarizes the beam properties, describes the endstations together with the detector pool, and presents several application cases of the various X-ray imaging techniques available to users.

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.

Male genitalia, hierarchical homology, and the anatomy of the bullet ant (Paraponera clavata; Hymenoptera, Formicidae)

The male genitalia of insects are among the most variable, complex, and informative character systems for evolutionary analysis and taxonomic purposes. Because of these general properties, many generations of systematists have struggled to develop a theory of homology and alignment of parts. This struggle continues to the present day, where fundamentally different models and nomenclatures for the male genitalia of Hymenoptera, for example, are applied. Here, we take a multimodal approach to digitalize and comprehensively document the genital skeletomuscular anatomy of the bullet ant (Paraponera clavata; Hymenoptera: Formicidae), including hand dissection, synchrotron radiation microcomputed tomography, microphotography, scanning electron microscopy, confocal laser scanning microscopy, and 3D-printing. Through this work, we generate several new concepts for the structure and form of the male genitalia of Hymenoptera, such as for the endophallic sclerite (=fibula ducti), which we were able to evaluate in detail for the first time for any species. Based on this phenomic anatomical study and comparison with other Holometabola and Hexapoda, we reconsider the homologies of insect genitalia more broadly, and propose a series of clarifications in support of the penis-gonopod theory of male genital identity. Specifically, we use the male genitalia of Paraponera and insects more broadly as an empirical case for hierarchical homology by applying and refining the 5-category classification of serial homologs from DiFrisco et al. (2023) (DLW23) to all of our formalized concepts. Through this, we find that: (1) geometry is a critical attribute to account for in ontology, especially as all individually identifiable attributes are positionally indexed hence can be recognized as homomorphic; (2) the definition of "structure" proposed by DLW23 is difficult to apply, and likely heterogeneous; and (3) formative elements, or spatially defined foldings or in- or evaginations of the epidermis and cuticle, are an important yet overlooked class of homomorphs. We propose a morphogenetic model for male and female insect genitalia, and a model analogous to gene-tree species-tree mappings for the hierarchical homology of male genitalia specifically. For all of the structures evaluated in the present study, we provide 3D-printable models - with and without musculature, and in various states of digital dissection - to facilitate the development of a tactile understanding. Our treatment of the male genitalia of P. clavata serves as a basic template for future phenomic studies of male insect genitalia, which will be substantially improved with the development of automation and collections-based data processing pipelines, that is, collectomics. The Hymenoptera Anatomy Ontology will be a critical resource to include in this effort, and in best practice concepts should be linked.

Microarchitecture of the penis bone (baculum) of a seal: A 3D morphometric examination using synchrotron and laboratory micro-computed tomography

We examined the ultrastructure of the mammalian os penis at the high-resolution synchrotron level. Previously, bacular microanatomy had only been investigated histologically. We studied the baculum of the harp seal (Pagophilus groenlandicus), in which the baculum varies more in size and shape than does a mechanically constrained bone (humerus). We (1) investigated the microarchitecture of bacula and humeri from the same seal specimens, and (2) described changes in bone micro- and macro-morphology associated with age (n = 15, age range = 1-35 years) and bone type. We analyzed cross-sectional geometry non-destructively through laboratory micro-computed tomography. We suggest that the midshaft may resist axial compression while the proximal region may resist torsion, based on measurements of cross-sectional and cortical areas, perimeter, ratio of maximum and minimum moments of inertia, and polar moment of inertia. In addition, midshaft bacula may be less mechanosensitive than humeri, based on microstructural variables (e.g., volume, surface area, diameter associated with lacunae and cortical porosity) analyzed across age groupings. Our findings related to the microarchitecture of the pinniped baculum provide a basis for further studies on development, mechanical properties, functions, and adaptations in this and other pinniped species. Our use of a multi-modal imaging approach was minimally destructive for reproducible and accurate comparison of three-dimensional bone ultrastructure. Such methods, coupled with multidisciplinary analyses, enable diverse studies of bone biology, life history, and evolution using museum collections.

Bee morphology: A skeletomuscular anatomy of Thyreus (Hymenoptera: Apidae)

Although the knowledge of the skeletal morphology of bees has progressed enormously, a corresponding advance has not happened for the muscular system. Most of the knowledge about bee musculature was generated over 50 years ago, well before the digital revolution for anatomical imaging, including the application of microcomputed tomography. This technique, in particular, has made it possible to dissect small insects digitally, document anatomy efficiently and in detail, and visualize these data three dimensionally. In this study, we document the skeletomuscular system of a cuckoo bee, Thyreus albomaculatus and, with that, we provide a 3D atlas of bee skeletomuscular anatomy. The results obtained for Thyreus are compared with representatives of two other bee families (Andrenidae and Halictidae), to evaluate the generality of our morphological conclusions. Besides documenting 199 specific muscles in terms of origin, insertion, and structure, we update the interpretation of complex homologies in the maxillolabial complex of bee mouthparts. We also clarify the complicated 3D structure of the cephalic endoskeleton, identifying the tentorial, hypostomal, and postgenal structures and their connecting regions. We describe the anatomy of the medial elevator muscles of the head, precisely identifying their origins and insertions as well as their homologs in other groups of Hymenoptera. We reject the hypothesis that the synapomorphic propodeal triangle of Apoidea is homologous with the metapostnotum, and instead recognize that this is a modification of the third phragma. We recognize two previously undocumented metasomal muscle groups in bees, clarifying the serial skeletomusculature of the metasoma and revealing shortcomings of Snodgrass' "internal-external" terminological system for the abdomen. Finally, we elucidate the muscular structure of the sting apparatus, resolving previously unclear interpretations. The work conducted herein not only provides new insights into bee morphology but also represents a source for future phenomic research on Hymenoptera.

Visualization and Quantitative Evaluation of Functional Structures of Soybean Root Nodules via Synchrotron X-ray Imaging

The efficiency of N2-fixation in legume-rhizobia symbiosis is a function of root nodule activity. Nodules consist of 2 functionally important tissues: (a) a central infected zone (CIZ), colonized by rhizobia bacteria, which serves as the site of N2-fixation, and (b) vascular bundles (VBs), serving as conduits for the transport of water, nutrients, and fixed nitrogen compounds between the nodules and plant. A quantitative evaluation of these tissues is essential to unravel their functional importance in N2-fixation. Employing synchrotron-based x-ray microcomputed tomography (SR-μCT) at submicron resolutions, we obtained high-quality tomograms of fresh soybean root nodules in a non-invasive manner. A semi-automated segmentation algorithm was employed to generate 3-dimensional (3D) models of the internal root nodule structure of the CIZ and VBs, and their volumes were quantified based on the reconstructed 3D structures. Furthermore, synchrotron x-ray fluorescence imaging revealed a distinctive localization of Fe within CIZ tissue and Zn within VBs, allowing for their visualization in 2 dimensions. This study represents a pioneer application of the SR-μCT technique for volumetric quantification of CIZ and VB tissues in fresh, intact soybean root nodules. The proposed methods enable the exploitation of root nodule's anatomical features as novel traits in breeding, aiming to enhance N2-fixation through improved root nodule activity.

The hidden diversity of vascular patterns in flower heads

Vascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flower heads. We imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism. The vascular system in the head of the model plant Gerbera hybrida is qualitatively different from those of Bellis perennis and Helianthus annuus, characterized previously. Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, and Tanacetum vulgare represent variants of the Bellis and Helianthus systems. In each species, the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values. In spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature.

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.

TomoPyUI: a user-friendly tool for rapid tomography alignment and reconstruction

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

Utilizing Synchrotron-Based X-ray Micro-Computed Tomography to Visualize the Microscopic Structure of Starch Hydrogels In Situ

This study aimed to visualize the microstructures of starch hydrogels using synchrotron-based X-ray micro-computed tomography (μCT). Waxy maize starch (WMS, 3.3% amylose, db), pea starch (PS, 40.3% amylose), and high-amylose maize starch (HMS, 63.6% amylose) were cooked at 95 and 140 °C to prepare starch hydrogels. WMS and HMS failed to form a gel after 95 °C cooking and storage, while PS developed a firm gel. At 140 °C cooking, HMS of a high amylose nature was fully gelatinized and generated a rigid gel with the highest strength. Both scanning electron microscopy (SEM) and μCT revealed the unique structural features of various starch hydrogels/pastes prepared at different temperatures, which were greatly affected by the degree of swelling and dispersity of the starches. As a nondestructive method, μCT showed certain advantages over SEM, including minimal shrinkage of the hydrogels, relatively simple sample preparation, and allowing for three-dimensional reconstruction of the hydrogel microstructure. This study indicated that synchrotron-based μCT could be a useful technique in visualizing biopolymer-based hydrogels.

Alrecon: computed tomography reconstruction web application based on Solara

Synchrotron X-ray computed tomography is a non-destructive 3D imaging technique that offers the possibility to study the internal microstructure of samples with high spatial and temporal resolution. Given its unmatched image quality and acquisition speed, and the possibility to preserve the specimens, there is an increasing demand for this technique, from scientific users from innumerable disciplines. Computed tomography reconstruction is the computational process by which experimental radiographs are converted to a meaningful 3-dimensional image after the scan. The procedure involves pre-processing steps for image background and artifact correction on raw data, a reconstruction step approximating the inverse Radon-transform, and writing of the reconstructed volume image to disk. Several open-source Python packages exist to help scientists in the process of tomography reconstruction, by offering efficient implementations of reconstruction algorithms exploiting central or graphics processing unit (CPU and GPU, respectively), and by automating significant portions of the data processing pipeline. A further increase in productivity is attained by scheduling and parallelizing demanding reconstructions on high performance computing (HPC) clusters. Nevertheless, visual inspection and interactive selection of optimal reconstruction parameters remain crucial steps that are often performed in close interaction with the end-user of the data. As a result, the reconstruction task involves more than one software. Graphical user interfaces are provided to the user for fast inspection and optimization of reconstructions, while HPC resources are often accessed through scripts and command line interface. We propose Alrecon, a pure Python web application for tomographic reconstruction built using Solara. Alrecon offers users an intuitive and reactive environment for exploring data and customizing reconstruction pipelines. By leveraging upon popular 3D image visualization tools, and by providing a user-friendly interface for reconstruction scheduling on HPC resources, Alrecon guarantees productivity and efficient use of resources for any type of beamline user.

New Canadian amber deposit fills gap in fossil record near end-Cretaceous mass extinction

Amber preserves an exceptional record of tiny, soft-bodied organisms and chemical environmental signatures, elucidating the evolution of arthropod lineages and the diversity, ecology, and biogeochemistry of ancient ecosystems. However, globally, fossiliferous amber deposits are rare in the latest Cretaceous and surrounding the Cretaceous-Paleogene (K-Pg) mass extinction.1,2,3,4,5 This faunal gap limits our understanding of arthropod diversity and survival across the extinction boundary.2,6 Contrasting hypotheses propose that arthropods were either relatively unaffected by the K-Pg extinction or experienced a steady decline in diversity before the extinction event followed by rapid diversification in the Cenozoic.2,6 These hypotheses are primarily based on arthropod feeding traces on fossil leaves and time-calibrated molecular phylogenies, not direct observation of the fossil record.2,7 Here, we report a diverse amber assemblage from the Late Cretaceous (67.04 ± 0.16 Ma) of the Big Muddy Badlands, Canada. The new deposit fills a critical 16-million-year gap in the arthropod fossil record spanning the K-Pg mass extinction. Seven arthropod orders and at least 11 insect families have been recovered, making the Big Muddy amber deposit the most diverse arthropod assemblage near the K-Pg extinction. Amber chemistry and stable isotopes suggest the amber was produced by coniferous (Cupressaceae) trees in a subtropical swamp near remnants of the Western Interior Seaway. The unexpected abundance of ants from extant families and the virtual absence of arthropods from common, exclusively Cretaceous families suggests that Big Muddy amber may represent a yet unsampled Late Cretaceous environment and provides evidence of a faunal transition before the end of the Cretaceous.

A multi-technique and multiscale comparative study on the efficiency of conservation methods for the stabilisation of waterlogged archaeological pine

Archaeological wood can be preserved in waterlogged conditions. Due to their degradation in the ground, these archaeological remains are endangered after their discovery, since they decay irretrievably during drying. Conservation measures are used to preserve waterlogged archaeological objects, maintaining their shape and character as much as possible. However, different methods have been developed leading to varying results. This study compares their effectiveness in order to clarify their mode of action. The methods including alcohol-ether resin, lactitol/trehalose, melamine formaldehyde, polyethylene glycol impregnation prior to freeze-drying, saccharose and silicone oil were assessed by analysing mass changes and volume stability using structured-light 3D scanning. The state of the conserved wood samples including the spatial distribution of the conservation agent was examined using synchrotron micro-computed tomography. Raman spectroscopy was used to observe the agent´s spatial distribution within the cells. The findings demonstrated that melamine formaldehyde stabilises the degraded cell walls. The lumens are void, as in the case with alcohol-ether resin, while polyethylene glycol, silicone oil, saccharose and lactitol/trehalose also occupy the lumens. It is assumed that the drying method has an effect on the distribution of the solidifying agent. The knowledge gained affords insights into the mechanism of conservation methods, which in turn accounts for the varied outcomes. It also allows conclusions to be drawn about the condition and stability of conserved museum objects and serves as a starting point for the further development of conservation methods.

Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.

Defensive glands in Stylotermitidae (Blattodea, Isoptera)

The large abundance of termites is partially achieved by their defensive abilities. Stylotermitidae represented by a single extant genus, Stylotermes, is a member of a termite group Neoisoptera that encompasses 83% of termite species and 94% of termite genera and is characterized by the presence of the frontal gland. Within Neoisoptera, Stylotermitidae represents a species-poor sister lineage of all other groups. We studied the structure of the frontal, labral and labial glands in soldiers and workers of Stylotermes faveolus, and the composition of the frontal gland secretion in S. faveolus and Stylotermes halumicus. We show that the frontal gland is a small active secretory organ in soldiers and workers. It produces a cocktail of monoterpenes in soldiers, and some of these monoterpenes and unidentified proteins in workers. The labral and labial glands are developed similarly to other termite species and contribute to defensive activities (labral in both castes, labial in soldiers) or to the production of digestive enzymes (labial in workers). Our results support the importance of the frontal gland in the evolution of Neoisoptera. Toxic, irritating and detectable monoterpenes play defensive and pheromonal functions and are likely critical novelties contributing to the ecological success of these termites.

Pelvic Pseudotumor Associated With a Ceramic Bearing Total Hip

Pseudotumors have been well documented to occur most frequently in metal-metal bearing total hip arthroplasties and less frequently in metal-polyethylene bearings. There are few cases in the literature of pseudotumors occurring in ceramic-ceramic articulations. We report a case of a large pelvic pseudotumor in a patient with a ceramic-ceramic bearing articulation in a 67-year-old man. In addition to the usual investigations, we did a detailed wear analysis of the ceramic implants and an examination of the soft tissues for particulate debris. The detailed wear analysis did show evidence of stripe wear; however, the volumetric wear was within the expected range. Synchrotron imaging identified strontium and zirconium debris arising from the ceramic surfaces. Although association does not mean causation, no other cause for the large pseudotumor could be identified and presumably represents an idiosyncratic reaction to ceramic debris.

Study of Microstructural, Nutritional, and Biochemical Changes in Hulled and Hulless Barley during Storage Using X-ray and Infrared Techniques

Four varieties of barley (Esma, AC Metacalf, Tradition, and AB Cattlelac), representing four Canadian barley classes, were stored at 17% moisture content (mc) for 8 week. Stored barely was characterized using synchrotron X-ray phase contrast microcomputed tomography, synchrotron X-ray fluorescence imaging, and mid-infrared spectroscopy at the Canadian Light Source, Saskatoon. The deterioration was observed in all the selected varieties of barley at the end of 8 week of storage. Changes due to spoilage over time were observed in the grain microstructure and its nutrient distribution and composition. This study underscores the critical importance of the initial condition of barley grain microstructure in determining its storage life, particularly under unfavorable conditions. The hulled barley varieties showed more deterioration in microstructure than the hulless varieties of barley, where a direct correlation between microstructural changes and alterations in nutritional content was found. All selected barley classes showed changes in the distribution of nutrients (Ca, Fe, K, Mn, Cu, and Zn), but the two-row AC Metcalf variety exhibited more substantial variations in their nutrient distribution (Zn and Mn) than the other three varieties during storage. The two-row class barley varieties showed more changes in biochemical components (protein, lipids, and carbohydrates) than the six-row class varieties.

Sparse2Noise: Low-dose synchrotron X-ray tomography without high-quality reference data

BACKGROUND

Synchrotron radiation computed tomography (SR-CT) holds promise for high-resolution in vivo imaging. Notably, the reconstruction of SR-CT images necessitates a large set of data to be captured with sufficient photons from multiple angles, resulting in high radiation dose received by the object. Reducing the number of projections and/or photon flux is a straightforward means to lessen the radiation dose, however, compromises data completeness, thus introducing noises and artifacts. Deep learning (DL)-based supervised methods effectively denoise and remove artifacts, but they heavily depend on high-quality paired data acquired at high doses. Although algorithms exist for training without high-quality references, they struggle to effectively eliminate persistent artifacts present in real-world data.

METHODS

This work presents a novel low-dose imaging strategy namely Sparse2Noise, which combines the reconstruction data from paired sparse-view CT scan (normal-flux) and full-view CT scan (low-flux) using a convolutional neural network (CNN). Sparse2Noise does not require high-quality reconstructed data as references and allows for fresh training on data with very small size. Sparse2Noise was evaluated by both simulated and experimental data.

RESULTS

Sparse2Noise effectively reduces noise and ring artifacts while maintaining high image quality, outperforming state-of-the-art image denoising methods at same dose levels. Furthermore, Sparse2Noise produces impressive high image quality for ex vivo rat hindlimb imaging with the acceptable low radiation dose (i.e., 0.5 Gy with the isotropic voxel size of 26 μm).

CONCLUSIONS

This work represents a significant advance towards in vivo SR-CT imaging. It is noteworthy that Sparse2Noise can also be used for denoising in conventional CT and/or phase-contrast CT.

Drought-induced fiber water release and xylem embolism susceptibility of intact balsam poplar saplings

Balsam poplar (Populus balsamifera L.) is a widespread tree species in North America with significant ecological and economic value. However, little is known about the susceptibility of saplings to drought-induced embolism and its link to water release from surrounding xylem fibers. Questions remain regarding localized mechanisms that contribute to the survival of saplings in vivo of this species under drought. Using X-ray micro-computed tomography on intact saplings of genotypes Gillam-5 and Carnduff-9, we found that functional vessels are embedded in a matrix of water-filled fibers under well-watered conditions in both genotypes. However, water-depleted fibers started to appear under moderate drought stress while vessels remained water-filled in both genotypes. Drought-induced xylem embolism susceptibility was comparable between genotypes, and a greater frequency of smaller diameter vessels in GIL-5 did not increase embolism resistance in this genotype. Despite having smaller vessels and a total vessel number that was comparable to CAR-9, stomatal conductance was generally higher in GIL-5 compared to CAR-9. In conclusion, our in vivo data on intact saplings indicate that differences in embolism susceptibility are negligible between GIL-5 and CAR-9, and that fiber water release should be considered as a mechanism that contributes to the maintenance of vessel functional status in saplings of balsam poplar experiencing their first drought event.

Characterization of Pharmaceutical Tablets by X-ray Tomography

Solid dosage forms such as tablets are extensively used in drug administration for their simplicity and large-scale manufacturing capabilities. High-resolution X-ray tomography is one of the most valuable non-destructive techniques to investigate the internal structure of the tablets for drug product development as well as for a cost effective production process. In this work, we review the recent developments in high-resolution X-ray microtomography and its application towards different tablet characterizations. The increased availability of powerful laboratory instrumentation, as well as the advent of high brilliance and coherent 3rd generation synchrotron light sources, combined with advanced data processing techniques, are driving the application of X-ray microtomography forward as an indispensable tool in the pharmaceutical industry.

In situ wet pharmaceutical granulation captured using synchrotron radiation based dynamic micro-CT

Synchrotron radiation based dynamic micro-computed tomography (micro-CT) is a powerful technique available at synchrotron light sources for investigating evolving microstructures. Wet granulation is the most widely used method of producing pharmaceutical granules, precursors to products like capsules and tablets. Granule microstructures are known to influence product performance, so this is an area for potential application of dynamic CT. Here, lactose monohydrate (LMH) was used as a representative powder to demonstrate dynamic CT capabilities. Wet granulation of LMH has been observed to occur on the order of several seconds, which is too fast for lab-based CT scanners to capture the changing internal structures. The superior X-ray photon flux from synchrotron light sources makes sub-second data acquisition possible and well suited for analysis of the wet-granulation process. Moreover, synchrotron radiation based imaging is non-destructive, does not require altering the sample in any way, and can enhance image contrast with phase-retrieval algorithms. Dynamic CT can bring insights to wet granulation, an area of research previously only studied via 2D and/or ex situ techniques. Through efficient data-processing strategies, dynamic CT can provide quantitative analysis of how the internal microstructure of an LMH granule evolves during the earliest moments of wet granulation. Here, the results revealed granule consolidation, the evolving porosity, and the influence of aggregates on granule porosity.

A multimodal 3D imaging approach of pore networks in the human femur to assess age-associated vascular expansion and Lacuno-Canalicular reduction

Cellular communication in the mechanosensory osteocyte Lacuno-Canalicular Network (LCN) regulates bone tissue remodeling throughout life. Age-associated declines in LCN size and connectivity dysregulate mechanosensitivity to localized remodeling needs of aging or damaged tissue, compromising bone quality. Synchrotron radiation-based micro-Computed Tomography (SRμCT) and Confocal Laser Scanning Microscopy (CLSM) were employed to visualize LCN and vascular canal morphometry in an age series of the anterior femur (males n = 14, females n = 11, age range = 19-101, mean age = 55). Age-associated increases in vascular porosity were driven by pore coalescence, including a significant expansion in pore diameter and a significant decline in pore density. In contrast, the LCN showed significant age-associated reductions in lacunar volume fraction, mean diameter, and density, and in canalicular volume fraction and connectivity density. Lacunar density was significantly lower in females across the lifespan, exacerbating their age-associated decline. Canalicular connectivity density was also significantly lower in females but approached comparable declining male values in older age. Our data illuminate the trajectory and potential morphometric sources of age-associated bone loss. Increased vascular porosity contributes to bone fragility with aging, while an increasingly reduced and disconnected LCN undermines the mechanosensitivity required to repair and reinforce bone. Understanding why and how this degradation occurs is essential for improving the diagnosis and treatment of age-related changes in bone quality and fragility.

Hierarchically guided in situ nanolaminography for the visualisation of damage nucleation in alloy sheets

Hierarchical guidance is developed for three-dimensional (3D) nanoscale X-ray imaging, enabling identification, refinement, and tracking of regions of interest (ROIs) within specimens considerably exceeding the field of view. This opens up new possibilities for in situ investigations. Experimentally, the approach takes advantage of rapid multiscale measurements based on magnified projection microscopy featuring continuous zoom capabilities. Immediate and continuous feedback on the subsequent experimental progress is enabled by suitable on-the-fly data processing. For this, by theoretical justification and experimental validation, so-called quasi-particle phase-retrieval is generalised to conical-beam conditions, being key for sufficiently fast computation without significant loss of imaging quality and resolution compared to common approaches for holographic microscopy. Exploiting 3D laminography, particularly suited for imaging of ROIs in laterally extended plate-like samples, the potential of hierarchical guidance is demonstrated by the in situ investigation of damage nucleation inside alloy sheets under engineering-relevant boundary conditions, providing novel insight into the nanoscale morphological development of void and particle clusters under mechanical load. Combined with digital volume correlation, we study deformation kinematics with unprecedented spatial resolution. Correlation of mesoscale (i.e. strain fields) and nanoscale (i.e. particle cracking) evolution opens new routes for the understanding of damage nucleation within sheet materials with application-relevant dimensions.

4D study of liquid binder penetration dynamics in pharmaceutical powders using synchrotron X-ray micro computed tomography

The properties of pharmaceutical powders, and the liquid binder, directly influence the penetration behavior in the wet granulation process of the pharmaceutical industry. Conventional methods encounter challenges in understanding this fast process. In this work, an emerging synchrotron-based X-ray imaging technique (having fast imaging capability) was employed to investigate the internal process from 2D and 3D to real-time (in-situ with ms time intervals) 3D (also considered 4D) perspectives. Two commonly used excipients (lactose monohydrate (LMH) and microcrystalline cellulose (MCC)) were used to make binary mixtures with acetaminophen (APAP) as the active pharmaceutical ingredient (API). Isopropanol and water were employed as liquid binders in the single droplet impact method. Results showed that for most of the mixtures, the porosity increased at higher fractions of APAP. MCC mixtures experienced less agglomeration and more uniform pore distribution than LMH ones, resulting in a faster droplet penetration with isopropanol. Moreover, the imbibition-spreading studies showed that isopropanol penetration in MCC powders followed more unidirectional vertical movement than horizontal spreading. Our results also demonstrated that simultaneous granulation of LMH with water resulted in much slower penetration. This study revealed that synchrotron X-ray imaging can investigate 3D internal pore structures and how they affect the quantitively real-time internal penetration dynamics.

A new pan-kinosternid, Leiochelys tokaryki, gen. et sp. nov., from the late Maastrichtian Frenchman formation, Saskatchewan Canada

Previously, only a single member of Pan-Kinosternidae (Yelmochelys rosarioae) had been documented from the Late Cretaceous epoch. In this report we describe a new pan-kinosternid genus and species, herein named Leiochelys tokaryki, based on a nearly complete, articulated skeleton from the Late Cretaceous (Maastrichtian) Frenchman Formation of Saskatchewan, Canada. L. tokaryki differs most notably from the previously described Y. rosarioae in having triangular plastral lobes, and in that the suture between the hyo- and hypoplastron is in line with the suture between the fifth and sixth peripherals. A maximum parsimony analysis suggests that L. tokaryki is intermediate between Y. rosarioae and crown-group kinosternids. Kinosternid features present in L. tokaryki include the presence of a reduced plastral bridge that extends from the posterior tip of peripheral 4 to the anterior tip of peripheral 7, two inframarginals that contact one another, a smooth triturating surface, and participation of the palatine in the triturating surface. An unexpected feature of the skull is the presence of a large stapedial canal, suggesting that the decrease in size of the stapedial canal and increase in the canalis caroticus cerebralis occurred independently in Dermatemydidae and Kinosternidae. The character-states of the skull and skeleton of L. tokaryki indicate that morphological changes occurring during the diversification of Kinosternoidea were more complex than expected based on data from derived members of the group.