tomoCAM: fast model-based iterative reconstruction via GPU acceleration and non-uniform fast Fourier transforms.

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM, is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter-based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

Protein Corona-Directed Cellular Recognition and Uptake of Polyethylene Nanoplastics by Macrophages.

The widespread use of plastic products in daily life has raised concerns about the health hazards associated with nanoplastics (NPs). When exposed, NPs are likely to infiltrate the bloodstream, interact with plasma proteins, and trigger macrophage recognition and clearance. In this study, we focused on establishing a correlation between the unique protein coronal signatures of high-density (HDPE) and low-density (LDPE) polyethylene (PE) NPs with their ultimate impact on macrophage recognition and cytotoxicity. We observed that low-density and high-density lipoprotein receptors (LDLR and SR-B1), facilitated by apolipoproteins, played an essential role in PE-NP recognition. Consequently, PE-NPs activated the caspase-3/GSDME pathway and ultimately led to pyroptosis. Advanced imaging techniques, including label-free scattered light confocal imaging and cryo-soft X-ray transmission microscopy with 3D-tomographic reconstruction (nano-CT), provided powerful insights into visualizing NPs-cell interactions. These findings underscore the potential risks of NPs to macrophages and introduce analytical methods for studying the behavior of NPs in biological systems.

Plastic Fruit Stickers in Industrial Composting─Surface and Structural Alterations Revealed by Electron Microscopy and Computed Tomography.

Often large quantities of plastics are found in compost, with price look-up stickers being a major but little-explored component in the contamination path. Stickers glued to fruit or vegetable peels usually remain attached to the organic material despite sorting processes in the composting plant. Here, we investigated the effects of industrial composting on the structural alterations of these stickers. Commercial polypropylene (PP) stickers on banana peels were added to a typical organic material mixture for processing in an industrial composting plant and successfully resampled after a prerotting (11 days) and main rotting step (25 days). Afterward, both composted and original stickers were analyzed for surface and structural changes via scanning electron microscopy, Fourier-transform infrared spectroscopy, and micro- and nano-X-ray computed tomography (CT) combined with deep learning approaches. The composting resulted in substantial surface changes and degradation in the form of microbial colonization, deformation, and occurrence of cracks in all stickers. Their pore volumes increased from 16.7% in the original sticker to 26.3% at the end of the compost process. In a similar way, the carbonyl index of the stickers increased. Micro-CT images additionally revealed structural changes in the form of large adhesions that penetrated the surface of the sticker. These changes were accompanied by delamination after 25 days of composting, thus overall hinting at the degradation of the stickers and the subsequent formation of smaller microplastic pieces.

2D vs. 3D Evaluation of Osteocyte Lacunae - Methodological Approaches, Recommended Parameters, and Challenges: A Narrative Review by the European Calcified Tissue Society (ECTS).

PURPOSE OF REVIEW: Quantification of the morphology of osteocyte lacunae has become a powerful tool to investigate bone metabolism, pathologies and aging. This review will provide a brief overview of 2D and 3D imaging methods for the determination of lacunar shape, orientation, density, and volume. Deviations between 2D-based and 3D-based lacunar volume estimations are often not sufficiently addressed and may give rise to contradictory findings. Thus, the systematic error arising from 2D-based estimations of lacunar volume will be discussed, and an alternative calculation proposed. Further, standardized morphological parameters and best practices for sampling and segmentation are suggested. RECENT FINDINGS: We quantified the errors in reported estimation methods of lacunar volume based on 2D cross-sections, which increase with variations in lacunar orientation and histological cutting plane. The estimations of lacunar volume based on common practice in 2D imaging methods resulted in an underestimation of lacunar volume of up to 85% compared to actual lacunar volume in an artificial dataset. For a representative estimation of lacunar size and morphology based on 2D images, at least 400 lacunae should be assessed per sample.

Comparative evaluation of volumetric changes between two pediatric rotary files (Kedo-S plus, Kedo-SG blue) and manual files (hand K-files) during canal preparation of primary mandibular molars: an in-vitro nano-CT analysis.

Pediatric endodontics has become popular due to advancements in cleaning, shaping and irrigation systems, resulting in faster and effective removal of infected pulp, saving time, and creating a pathogen-free environment. The patented rotary file system, Kedo-S, designed for primary teeth, introduced a single file generation for efficient pulp therapy. However, there are currently no studies assessing canal preparation in primary mandibular molars using nano-CT (computed Tomography). To evaluate the volumetric changes of two recently introduced pediatric rotary file systems in comparison with conventional hand file systems in primary mandibular molar using an ultra-high resolution nano-CT. This in-vitro study was performed in extracted primary mandibular molar based on certain inclusion and exclusion criteria. Samples were prepared and working length was determined before the pre-operative scan using a high resolution nano-CT device (SkyScan 2214, Bruker, Kontich, Belgium). A single well-experienced pediatric dentist prepared the canals using three file systems: Kedo-S plus, Kedo-SG blue and Hand K-files. A post-operative scan was performed similar to pre-operative scan. Image reconstruction was performed with NRecon software for 3D volumetric visualization and analysis of the root canals. Kedo-SG blue file systems had the highest mean difference in the canal volume (8.85%). Hand K-files had the least difference at (1.24%) of canal volume. Kedo-S plus file system had a mean canal volume difference (6.14%) which is closer to hand K-files. Rotary file systems resulted in a significant enlargement of canals compared to hand files.

Laser-based sample preparation for high-resolution X-ray-computed tomography of glasses and glass ceramics.

X-ray-computed tomography with sub-micron resolution (nano-CT) is one of the most useful techniques to examine the 3D microstructure of materials down to voxel sizes 10 nm. However, since size and shape of samples have considerable influence on acquisition time and data quality, adapted and universally applicable workflows are needed. Three novel workflows for sample preparation using ultra-short pulsed lasers are presented which allow for reproducible fabrication, safe extraction and mounting of samples. Their application potential is illustrated via nano-CT measurements of glass ceramics as well as a laser-modified glass. Since the according sample geometries take also the requirements of other analytical techniques such as transmission electron microscopy into account, samples prepared according to the new workflows can be furthermore seen as a starting point for correlative microstructural analyses involving multiple techniques.

Correlated Study of Material Interaction Between Capillary Printed Eutectic Gallium Alloys and Gold Electrodes.

Liquid metals (LMs) play a growing role in flexible electronics and connected applications. Here, LMs come into direct contact with metal electrodes thus allowing for corrosion and additional alloying, potentially compromising device stability. Nevertheless, comprehensive studies on the interfacial interaction of the materials are still sparse. Therefore, a correlated material interaction study of capillary-printed Galinstan (eutetic alloy of Ga/In/Sn) with gold surfaces and electrodes is conducted. Comprehensive application of optical microscopy, vertical scanning interferometry, scanning electron microscopy/spectroscopy, x-ray photon spectroscopy, and atomic force microscopy allow for an in depth characterization of the spreading process of LM lines on gold films, revealing the differential spread of the different LM components and the formation of intermetallic nanostructures on the surface of the surrounding gold film. A model for the growth process based on the penetration of LM along the gold film grain boundaries is proposed based on the obtained time-dependent characterization. The distribution of gold, Galinstan, and intermetallic phases in a gold wire dipped into LM is observed using X-ray nano tomography as a complementary view on the internal nanostructure. Finally, resistance measurements on LM lines connecting gold electrodes over time allow to estimate the influence on the material interaction on electronic applications.

A FIB-SEM Based Correlative Methodology for X-Ray Nanotomography and Secondary Ion Mass Spectrometry: An Application Example in Lithium Batteries Research.

Correlative microscopy approaches are attracting considerable interest in several research fields such as materials and battery research. Recent developments regarding X-ray computer tomography have made this technique available in a compact module for scanning electron microscopes (SEMs). Nano-computed tomography (nanoCT) allows morphological analysis of samples in a nondestructive way and to generate 2D and 3D overviews. However, morphological analysis alone is not sufficient for advanced studies, and to draw conclusions beyond morphology, chemical analysis is needed. While conventional SEM-based chemical analysis techniques such as energy-dispersive X-ray spectroscopy (EDS) are adequate in many cases, they are not well suited for the analysis of trace elements and low-Z elements such as hydrogen or lithium. Furthermore, the large information depth in typical SEM-EDS imaging conditions limits the lateral resolution to micrometer length scales. In contrast, secondary ion mass spectrometry (SIMS) can perform elemental mapping with good surface sensitivity, nanoscale lateral resolution, and the possibility to analyze even low-Z elements and isotopes. In this study, we demonstrate the feasibility and compatibility of a novel FIB-SEM-based correlative nanoCT-SIMS imaging approach to correlate morphological and chemical data of the exact same sample volume, using a cathode material of a commercial lithium battery as an example.

Multiscale Dense U-Net: A Fast Correction Method for Thermal Drift Artifacts in Laboratory NanoCT Scans of Semi-Conductor Chips.

The resolution of 3D structure reconstructed by laboratory nanoCT is often affected by changes in ambient temperature. Although correction methods based on projection alignment have been widely used, they are time-consuming and complex. Especially in piecewise samples (e.g., chips), the existing methods are semi-automatic because the projections lose attenuation information at some rotation angles. Herein, we propose a fast correction method that directly processes the reconstructed slices. Thus, the limitations of the existing methods are addressed. The method is named multiscale dense U-Net (MD-Unet), which is based on MIMO-Unet and achieves state-of-the-art artifacts correction performance in nanoCT. Experiments show that MD-Unet can significantly boost the correction performance (e.g., with three orders of magnitude improvement in correction speed compared with traditional methods), and MD-Unet+ improves 0.92 dB compared with MIMO-Unet in the chip dataset.

Nano-CT imaging of larvae in the ant Pheidole hyatti reveals coordinated growth of a rudimentary organ necessary for soldier development.

The growth of imaginal discs in holometabolous insects is coordinated with larval growth to ensure the symmetrical and proportional development of the adult appendages. In ants, the differential growth of these discs generates distinct castes-the winged male and queen castes and the wingless worker caste. In the hyperdiverse ant genus Pheidole, the worker caste is composed of two morphologically distinct subcastes: small-headed minor workers and larger, big-headed, soldiers. Although these worker subcastes are completely wingless, soldier larvae develop rudimentary forewing discs that function in generating the disproportionate head-to-body scaling and size of soldiers. It remains unclear, however, how rudimentary forewing discs in soldier larvae are coordinated with other imaginal discs. Here we show, using quantitative nano-CT imaging and three-dimensional analyses, that the increase in the volume of the soldier rudimentary forewing discs is coordinated with larval size as well as with the increase in the volume of the leg and eye-antennal (head) discs. However, relative to larval size, we found that when the rudimentary forewing discs appear during the last larval instar, they are relatively smaller but increase in volume faster than that of the head (eye-antennal) and leg discs. These findings show that the rudimentary wing disc in soldier larvae has evolved novel patterns of inter-organ coordination as compared with other insects to generate the big-headed soldier caste in Pheidole. More generally, our study raises the possibility that novel patterns of inter-organ coordination are a general feature of rudimentary organs that acquire novel regulatory functions during development and evolution.

Quantification of the bone lacunocanalicular network from 3D X-ray phase nanotomography images.

There is a growing interest in developing 3D microscopy for the exploration of thick biological tissues. Recently, 3D X-ray nanocomputerised tomography has proven to be a suitable technique for imaging the bone lacunocanalicular network. This interconnected structure is hosting the osteocytes which play a major role in maintaining bone quality through remodelling processes. 3D images have the potential to reveal the architecture of cellular networks, but their quantitative analysis remains a challenge due to the density and complexity of nanometre sized structures and the need to handle and process large datasets, for example, 20483 voxels corresponding to 32 GB per individual image in our case. In this work, we propose an efficient image processing approach for the segmentation of the network and the extraction of characteristic parameters describing the 3D structure. These parameters include the density of lacunae, the porosity of lacunae and canaliculi, and morphological features of lacunae (volume, surface area, lengths, anisotropy etc.). We also introduce additional parameters describing the local environment of each lacuna and its canaliculi. The method is applied to analyse eight human femoral cortical bone samples imaged by magnified X-ray phase nanotomography with a voxel size of 120 nm, which was found to be a good compromise to resolve canaliculi while keeping a sufficiently large field of view of 246 µm in 3D. The analysis was performed on a total of 2077 lacunae showing an average length, width and depth of 17.1 µm × 9.2 µm × 4.4 µm, with an average number of 58.2 canaliculi per lacuna and a total lacuno-canalicular porosity of 1.12%. The reported descriptive parameters provide information on the 3D organisation of the lacuno-canalicular network in human bones.

Laboratory phase-contrast nanotomography of unstained Bombus terrestris compound eyes.

Imaging the visual systems of bumblebees and other pollinating insects may increase understanding of their dependence on specific habitats and how they will be affected by climate change. Current high-resolution imaging methods are either limited to two dimensions (light- and electron microscopy) or have limited access (synchrotron radiation x-ray tomography). For x-ray imaging, heavy metal stains are often used to increase contrast. Here, we present micron-resolution imaging of compound eyes of buff-tailed bumblebees (Bombus terrestris) using a table-top x-ray nanotomography (nano-CT) system. By propagation-based phase-contrast imaging, the use of stains was avoided and the microanatomy could more accurately be reconstructed than in samples stained with phosphotungstic acid or osmium tetroxide. The findings in the nano-CT images of the compound eye were confirmed by comparisons with light- and transmission electron microscopy of the same sample and finally, comparisons to synchrotron radiation tomography as well as to a commercial micro-CT system were done.

Three-dimensional virtual histology enabled through cytoplasm-specific X-ray stain for microscopic and nanoscopic computed tomography.

Many histological methods require staining of the cytoplasm, which provides instrumental details for diagnosis. One major limitation is the production of 2D images obtained by destructive preparation of 3D tissue samples. X-ray absorption micro- and nanocomputed tomography (microCT and nanoCT) allows for a nondestructive investigation of a 3D tissue sample, and thus aids to determine regions of interest for further histological examinations. However, application of microCT and nanoCT to biological samples (e.g., biopsies) is limited by the missing contrast within soft tissue, which is important to visualize morphological details. We describe an eosin-based preparation overcoming the challenges of contrast enhancement and selectivity for certain tissues. The eosin-based staining protocol is suitable for whole-organ staining, which then enables high-resolution microCT imaging of whole organs and nanoCT imaging of smaller tissue pieces retrieved from the original sample. Our results demonstrate suitability of the eosin-based staining method for diagnostic screening of 3D tissue samples without impeding further diagnostics through histological methods.

Contrast-enhanced nano-CT reveals soft dental tissues and cellular layers.

AIM: To introduce a methodology designed to simultaneously visualize dental ultrastructures, including cellular and soft tissue components, by utilizing phosphotungstic acid (PTA) as a contrast-enhancement agent. METHODOLOGY: Sound third molars were collected from healthy human adults and fixed in 4% buffered paraformaldehyde. To evaluate the impact of PTA in concentrations of 0.3%, 0.7% and 1% on dental soft and hard tissues for CT imaging, cementum and dentine-pulp sections were cut, dehydrated and stained with immersion periods of 12, 24 h, 2 days or 5 days. The samples were scanned in a high-resolution nano-CT device using pixel sizes down to 0.5 µm to examine both the cementum and pulpal regions. RESULTS: Dental cementum and periodontium as well as odontoblasts and predentine were made visible through PTA staining in high-resolution three-dimensional nano-CT scans. Different segments of the tooth required different staining protocols. The thickness of the cementum could be computed over the length of the tooth once it was made visible by the PTA-enhanced contrast, and the attached soft tissue components of the interior of the tooth could be shown on the dentine-pulp interface in greater detail. Three-dimensional illustrations allowed a histology-like visualization of the sections in all orientations with a single scan and easy sample preparation. The segmentation of the sigmoidal dentinal tubules and the surrounding dentine allowed a three-dimensional investigation and quantitative of the dentine composition, such as the tubular lumen or the ratio of the tubular lumen area to the dentinal surface. CONCLUSION: The staining protocol made it possible to visualize hard tissues along with cellular layers and soft tissues in teeth using a laboratory-based nano-CT technique. The protocol depended on both tissue type and size. This methodology offers enhanced possibilities for the concomitant visualization of soft and hard dental tissues.

Thermal Drift Correction for Laboratory Nano Computed Tomography via Outlier Elimination and Feature Point Adjustment.

Thermal drift of nano-computed tomography (CT) adversely affects the accurate reconstruction of objects. However, feature-based reference scan correction methods are sometimes unstable for images with similar texture and low contrast. In this study, based on the geometric position of features and the structural similarity (SSIM) of projections, a rough-to-refined rigid alignment method is proposed to align the projection. Using the proposed method, the thermal drift artifacts in reconstructed slices are reduced. Firstly, the initial features are obtained by speeded up robust features (SURF). Then, the outliers are roughly eliminated by the geometric position of global features. The features are refined by the SSIM between the main and reference projections. Subsequently, the SSIM between the neighborhood images of features are used to relocate the features. Finally, the new features are used to align the projections. The two-dimensional (2D) transmission imaging experiments reveal that the proposed method provides more accurate and robust results than the random sample consensus (RANSAC) and locality preserving matching (LPM) methods. For three-dimensional (3D) imaging correction, the proposed method is compared with the commonly used enhanced correlation coefficient (ECC) method and single-step discrete Fourier transform (DFT) algorithm. The results reveal that proposed method can retain the details more faithfully.

In situ observation of void evolution in 1,3,5-triamino-2,4,6-trinitrobenzene under compression by synchrotron radiation X-ray nano-computed tomography.

The formation and development of voids in 1,3,5-triamino-2,4,6-trinitrobenzene crystals under compression were characterized in situ by X-ray nano-computed tomography. Benefiting from high spatial resolution (30 nm) and excellent imaging contrast, the X-ray nano-computed tomography images revealed the presence of a small fraction of inhomogeneous structures in the original crystal (volume ratio ∼1.2%). Such an inhomogeneity acts as a nucleation of voids and produces stress concentration during compression, which leads to continuous growth of the voids under loading. Meanwhile, the results further reveal that the developing voids are not isotropic: voids with higher surface roughness and irregular structures are easier to break and form new micro-voids. These new voids with higher irregular structures are weaker and easier to break into smaller ones compared with the originals, leading to the development of voids along these weak zones. Finally large voids form. The experiments allow direct investigation of void formation and development, which helps in studying the mechanisms of void development and energetic materials deterioration during manufacturing and transporting.

Myoanatomy of the velvet worm leg revealed by laboratory-based nanofocus X-ray source tomography.

X-ray computed tomography (CT) is a powerful noninvasive technique for investigating the inner structure of objects and organisms. However, the resolution of laboratory CT systems is typically limited to the micrometer range. In this paper, we present a table-top nanoCT system in conjunction with standard processing tools that is able to routinely reach resolutions down to 100 nm without using X-ray optics. We demonstrate its potential for biological investigations by imaging a walking appendage of Euperipatoides rowelli, a representative of Onychophora-an invertebrate group pivotal for understanding animal evolution. Comparative analyses proved that the nanoCT can depict the external morphology of the limb with an image quality similar to scanning electron microscopy, while simultaneously visualizing internal muscular structures at higher resolutions than confocal laser scanning microscopy. The obtained nanoCT data revealed hitherto unknown aspects of the onychophoran limb musculature, enabling the 3D reconstruction of individual muscle fibers, which was previously impossible using any laboratory-based imaging technique.

New Insights into the Three-Dimensional Anatomy of the Facial Mimetic Muscles Related to the Nasolabial Fold: An Iodine Staining Technique Based on Nano-computed Tomography.

PURPOSE: This study aimed to introduce a novel approach to study the facial mimetic muscles (FMMs) in relation to the nasolabial fold (NLF) and realize the visualization of complex three-dimensional (3D) structures and spatial relationships of the FMMs. MATERIALS AND METHODS: Nano-computed tomography (nano-CT) and iodine staining techniques were used to obtain the two-dimensional (2D) radiographs of the FMMs. Materialise Mimics software was then used to reconstruct the 3D model of the FMMs. RESULTS: The zygomaticus major muscle (ZMM) was divided into trunk fibers and branch fibers. The trunk fibers of the ZMM were subdivided into branch fibers layer-by-layer. Adipose tissue in the cheek was not a mass of unorganized fat. It was separated and fixed by branch fibers. Moreover, the trunk fibers of the ZMM were directly connected to the levator anguli oris (LAO), not the skin. On the contrary, the ZMM was connected to the skin by its subdivided branch fibers indirectly. The muscle fibers in the modiolus were organized, rather than disorganized. In other words, the terminal of the trunk fibers of the ZMM was located in the LAO. Moreover, the terminal of the trunk fibers of the LAO was located at the terminal of the trunk fibers of the musculus depressor anguli oris at the corner of the mouth. Furthermore, the levator labii superioris alaeque nasi was not directly connected to the orbicularis oris muscle. It was connected to the combination of the LLS and the rhinaeus. CONCLUSIONS: Although nano-CT has many disadvantages, it enabled the 3D anatomical study of the FMMs in relation to the NLF when combined with iodine staining. We imported the 2D images obtained by nano-CT scanning into the Mimics software, successfully reconstructed the FMMs, and finally obtained images of complex 3D structures of the FMMs. The shapes, positions, and 3D spatial relationships of the FMMs were clearly visualized. The novel insights into the 3D anatomy of the FMMs may help understand the formation of the NLF. Finally, the results of this study may help improve the rejuvenation surgery of the NLF soon. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

Scalable Double Regularization for 3D Nano-CT Reconstruction.

Nano-CT (computerized tomography) has emerged as a non-destructive high-resolution cross-sectional imaging technique to effectively study the sub-µm pore structure of shale, which is of fundamental importance to the evaluation and development of shale oil and gas. Nano-CT poses unique challenges to the inverse problem of reconstructing the 3D structure due to the lower signal-to-noise ratio (than Micro-CT) at the nano-scale, increased sensitivity to the misaligned geometry caused by the movement of object manipulator, limited sample size, and a larger volume of data at higher resolution. We propose a scalable double regularization (SDR) method to utilize the entire dataset for simultaneous 3D structural reconstruction across slices through total variation regularization within slices and L 1 regularization between adjacent slices. SDR allows information borrowing both within and between slices, contrasting with the traditional methods that usually build on slice by slice reconstruction. We develop a scalable and memory-efficient algorithm by exploiting the systematic sparsity and consistent geometry induced by such Nano-CT data. We illustrate the proposed method using synthetic data and two Nano-CT imaging datasets of Jiulaodong (JLD) shale and Longmaxi (LMX) shale acquired in the Sichuan Basin. These numerical experiments show that the proposed method substantially outperforms selected alternatives both visually and quantitatively.

External cervical resorption-part 1: histopathology, distribution and presentation.

External cervical resorption (ECR) is the loss of dental hard tissue as a result of odontoclastic action. It is a dynamic process that involves periodontal, dental and in later stages pulpal tissues. Over the last two decades, ECR has attracted increased interest; this is in part due to novel micro-CT and histopathological techniques for its assessment and also improved radiographic detection using CBCT. This literature review will cover the aetiology, potential predisposing factors, histopathology and diagnosis of ECR. Part 2 will cover the management of ECR.