A high-resolution 3D atlas of the spectrum of tuberculous and COVID-19 lung lesions.

Our current understanding of the spectrum of TB and COVID-19 lesions in the human lung is limited by a reliance on low-resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID-19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin-embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID-19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID-19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID-19 lesions within the framework of the entire lung.

Micro-Computed Tomography Analysis of the Human Tuberculous Lung Reveals Remarkable Heterogeneity in Three-dimensional Granuloma Morphology.

Rationale: Our current understanding of tuberculosis (TB) pathophysiology is limited by a reliance on animal models, the paucity of human TB lung tissue, and traditional histopathological analysis, a destructive two-dimensional approach that provides limited spatial insight. Determining the three-dimensional (3D) structure of the necrotic granuloma, a characteristic feature of TB, will more accurately inform preventive TB strategies.Objectives: To ascertain the 3D shape of the human tuberculous granuloma and its spatial relationship with airways and vasculature within large lung tissues.Methods: We characterized the 3D microanatomical environment of human tuberculous lungs by using micro computed tomography, histopathology, and immunohistochemistry. By using 3D segmentation software, we accurately reconstructed TB granulomas, vasculature, and airways in three dimensions and confirmed our findings by using histopathology and immunohistochemistry.Measurements and Main Results: We observed marked heterogeneity in the morphology, volume, and number of TB granulomas in human lung sections. Unlike depictions of granulomas as simple spherical structures, human necrotic granulomas exhibit complex, cylindrical, branched morphologies that are connected to the airways and shaped by the bronchi. The use of 3D imaging of human TB lung sections provides unanticipated insight into the spatial organization of TB granulomas in relation to the airways and vasculature.Conclusions: Our findings highlight the likelihood that a single, structurally complex lesion could be mistakenly viewed as multiple independent lesions when evaluated in two dimensions. In addition, the lack of vascularization within obstructed bronchi establishes a paradigm for antimycobacterial drug tolerance. Lastly, our results suggest that bronchogenic spread of Mycobacterium tuberculosis reseeds the lung.

Data for 3D printing enlarged museum specimens for the visually impaired.

Museums are embracing new technologies and one of these is the use of 3D printing. 3D printing allows for creating physical replicas of items which may, due to great value or significance, not be handled by the public, or which are too small or fragile to be handled or even seen with the naked eye. One such application of new technologies has been welcomed by the National Museum in Bloemfontein, Free State, South Africa. Here, blown-up (enlarged) Museum specimens were 3D printed for various interactive exhibits that are aimed at increasing the accessibility of their permanent displays for visually impaired visitors who rely greatly on touch as a source of observation. A selection of scorpions, pseudoscorpions, mites and archetypal bird skulls were scanned, processed and 3D printed to produce enlarged, highly functional nylon models. This data paper provides the raw micro Computed Tomography (micro-CT) scan data and print ready STL files processed from this data. The STL files may be used in their current format and details of the printing are provided.

Physico-elemental analysis of roasted organic coffee beans from Ethiopia, Colombia, Honduras, and Mexico using X-ray micro-computed tomography and external beam particle induced X-ray emission.

The physico-elemental profiles of commercially attained and roasted organic coffee beans from Ethiopia, Colombia, Honduras, and Mexico were compared using light microscopy, X-ray micro-computed tomography, and external beam particle induced X-ray emission. External beam PIXE analysis detected P, S, Cl, K, Ca, Ti, Mn, Fe, Cu, Zn, Br, Rb, and Sr in samples. Linear discriminant analysis showed that there was no strong association between elemental data and production region, whilst a heatmap combined with hierarchical clustering showed that soil-plant physico-chemical properties may influence regional elemental signatures. Physical trait data showed that Mexican coffee beans weighed significantly more than beans from other regions, whilst Honduras beans had the highest width. X-ray micro-computed tomography qualitative data showed heterogeneous microstructural features within and between beans representing different regions. In conclusion, such multi-dimensional analysis may present a promising tool in assessing the nutritional content and qualitative characteristics of food products such as coffee.

A micro X-ray computed tomography dataset of fossil echinoderms in an ancient obrution bed: a robust method for taphonomic and palaeoecologic analyses.

BACKGROUND: Taphonomic and palaeoecologic studies of obrution beds often employ conventional methods of investigation such as physical removal and extraction of fossils from their host rock (matrix) by mechanical preparation. This often-destructive method is not suitable for studying mold fossils, which are voids left in host rocks due to dissolution of the original organism in post-depositional processes. FINDINGS: Microcomputed tomography (µCT) scan data of 24 fossiliferous rock samples revealed thousands of Paleozoic echinoderms. Digitally "stitching" together individually µCT scanned rock samples within three-dimensional (3D) space allows for quantifiable taphonomic data on a fossil echinoderm-rich obrution deposit from the Devonian (Emsian) of South Africa. Here, we provide a brief step-by-step guide on creating, segmenting, and ultimately combining sections of richly fossiliferous beds to create virtual models suited for the quantitative and qualitative taphonomic analyses of fossil invertebrate assemblages. CONCLUSIONS: Visualizing the internal features of fossiliferous beds in 3D is an invaluable taphonomic tool for analyzing delicate fossils, accounting for all specimens irrespective of their preservation stages and with minimal damage. This technique is particularly useful for analyzing fossiliferous deposits with mold fossils that prove to be difficult to study with traditional methods, because the method relies on the large density contrast between the mold and host rock.

Standard method for microCT-based additive manufacturing quality control 4: Metal powder analysis.

X-ray micro computed tomography (microCT) can be applied to analyse powder feedstock used in additive manufacturing. In this paper, we demonstrate a dedicated workflow for this analysis method, specifically for Ti6Al4V powder typically used in commercial powder bed fusion (PBF) additive manufacturing (AM) systems. The methodology presented includes sample size requirements, scan conditions and settings, reconstruction and image analysis procedures. We envisage this method will support standardization in powder analysis in the additive manufacturing community. This is aimed at ultimately improving the quality of additively manufactured parts, through the identification of impurities and defects in powders. •MicroCT analysis of metal powders for additive manufacturing•Method describes a standard workflow simplifying usage of the technique•Sample requirements and image analysis workflow is described.

Standard method for microCT-based additive manufacturing quality control 3: Surface roughness.

The use of microCT of 10 mm coupon samples produced by AM has the potential to provide useful information of mean density and detailed porosity information of the interior of the samples. In addition, the same scan data can be used to provide surface roughness analysis of the as-built surfaces of the same coupon samples. This can be used to compare process parameters or new materials. While surface roughness is traditionally done using tactile probes or with non-contact interferometric techniques, the complex surfaces in AM are sometimes difficult to access and may be very rough, with undercuts and may be difficult to accurately measure using traditional techniques which are meant for smoother surfaces. This standard workflow demonstrates on a coupon sample how to acquire surface roughness results, and compares the results from roughly the same area of the same sample with tactile probe results. The same principle can be applied to more complex parts, keeping in mind the resolution limit vs sample size of microCT.

Standard method for microCT-based additive manufacturing quality control 2: Density measurement.

MicroCT is best known for its ability to detect and quantify porosity or defects, and to visualize its 3D distribution. However, it is also possible to obtain accurate volumetric measurements from parts - this can be used in combination with the part mass to provide a good measure of its average density. The advantage of this density-measurement method is the ability to combine the density measurement with visualization and other microCT analyses of the same sample. These other analyses may include detailed porosity or void analysis (size and distribution) and roughness assessment, obtainable with the same scan data. Simple imaging of the interior of the sample allows the detection of unconsolidated powder, open porosity to the surface or the presence of inclusions. The CT density method presented here makes use of a 10 mm cube sample and a simple data analysis workflow, facilitating standardization of the method. A laboratory microCT scanner is required at 15 µm voxel size, suitable software to allow sub-voxel precise edge determination of the scanned sample and hence an accurate total volume measurement, and a scale with accuracy to 3 digits. •MicroCT-based mean density measurement method.•Accurate volume measurement and scale mass.•10 mm cube sample allows standardization and automation of workflow.

Standard method for microCT-based additive manufacturing quality control 1: Porosity analysis.

MicroCT is a well-established technique that is used to analyze the interior of objects non-destructively, and it is especially useful for void or porosity analysis. Besides its widespread use, few standards exist and none for additive manufacturing as yet. This is due to the inherent differences in part design, sizes and geometries, which results in different scan resolutions and qualities. This makes direct comparison between different scans of additively manufactured parts almost impossible. In addition, different image analysis methodologies can produce different results. In this method paper, we present a simplified 10 mm cube-shaped coupon sample as a standard size for detailed analysis of porosity using microCT, and a simplified workflow for obtaining porosity information. The aim is to be able to obtain directly comparable porosity information from different samples from the same AM system and even from different AM systems, and to potentially correlate detailed morphologies of the pores or voids with improper process parameters. The method is applied to two examples of different characteristic types of voids in AM: sub-surface lack of fusion due to improper contour scanning, and tree-like pores growing in the build direction. This standardized method demonstrates the capability for microCT to not only quantify porosity, but also identify void types which can be used to improve AM process optimization.

Analyzing nature's protective design: The glyptodont body armor.

Many animal species evolved some form of body armor, such as scales of fish and bony plates or osteoderms of reptiles. Although a protective function is often taken for granted, recent studies show that body armor might comprise multiple functionalities and is shaped by trade-offs among these functionalities. Hence, despite the fact that natural body armor might serve as bio-inspiration for the development of artificial protective materials, focussing on model systems in which body armor serves a solely protective function might be pivotal. In this study, we investigate the osteoderms of Glyptotherium arizonae, an extinct armadillo-like mammal in which body armor evolved as protection against predators and/or tail club blows of conspecifics. By using a combination of micro-computed tomography, reverse-engineering, stress simulations and mechanical testing of 3D printed models, we show that the combination of dense compact layers and porous lattice core might provide an optimized combination of strength and high energy absorption.

Snake fangs: 3D morphological and mechanical analysis by microCT, simulation, and physical compression testing.

This Data Note provides data from an experimental campaign to analyse the detailed internal and external morphology and mechanical properties of venomous snake fangs. The aim of the experimental campaign was to investigate the evolutionary development of 3 fang phenotypes and investigate their mechanical behaviour. The study involved the use of load simulations to compare maximum Von Mises stress values when a load is applied to the tip of the fang. The conclusions of this study have been published elsewhere, but in this data note we extend the analysis, providing morphological comparisons including details such as curvature comparisons, thickness, etc. Physical compression results of individual fangs, though reported in the original paper, were also extended here by calculating the effective elastic modulus of the entire snake fang structure including internal cavities for the first time. This elastic modulus of the entire fang is significantly lower than the locally measured values previously reported from indentation experiments, highlighting the possibility that the elastic modulus is higher on the surface than in the rest of the material. The micro-computed tomography (microCT) data are presented both in image stacks and in the form of STL files, which simplifies the handling of the data and allows its re-use for future morphological studies. These fangs might also serve as bio-inspiration for future hypodermic needles.

Laboratory x-ray micro-computed tomography: a user guideline for biological samples.

Laboratory x-ray micro-computed tomography (micro-CT) is a fast-growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated "how to" guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant setup, scanning, reconstructing, and visualization methods and considerations. Throughout the guide, a Jackson's chameleon specimen, which was scanned at different settings, is used as an interactive example. The ultimate aim of this paper is make new users familiar with the concepts and applications of micro-CT in an attempt to promote its use in future scientific studies.