Following recent advances in bioimaging, high-resolution 3D models of biological structures are now generated rapidly and at low-cost. To use this data to address evolutionary and ecological ...questions, an array of tools has been developed to conduct shape analysis and quantify topographic complexity. Here we focus particularly on shape techniques applied to irregular-shaped objects lacking clear homologous landmarks, and propose a new 'alpha-shapes' method for quantifying 3D shape complexity.
We apply alpha-shapes to quantify shape complexity in the mammalian baculum as an example of a morphologically disparate structure. Micro- computed-tomography (μCT) scans of bacula were conducted. Bacula were binarised and converted into point clouds. Following application of a scaling factor to account for absolute size differences, a suite of alpha-shapes was fitted per specimen. An alpha shape is formed from a subcomplex of the Delaunay triangulation of a given set of points, and ranges in refinement from a very coarse mesh (approximating convex hulls) to a very fine fit. 'Optimal' alpha was defined as the refinement necessary in order for alpha-shape volume to equal CT voxel volume, and was taken as a metric of overall 'complexity'.
Our results show that alpha-shapes can be used to quantify interspecific variation in shape 'complexity' within biological structures of disparate geometry. The 'stepped' nature of alpha curves is informative with regards to the contribution of specific morphological features to overall 'complexity'. Alpha-shapes agrees with other measures of complexity (dissection index, Dirichlet normal energy) in identifying ursid bacula as having low shape complexity. However, alpha-shapes estimates mustelid bacula as being most complex, contrasting with other shape metrics. 3D fractal dimension is identified as an inappropriate metric of complexity when applied to bacula.
Alpha-shapes is used to calculate 'optimal' alpha refinement as a proxy for shape 'complexity' without identifying landmarks. The implementation of alpha-shapes is straightforward, and is automated to process large datasets quickly. We interpret alpha-shapes as being particularly sensitive to concavities in surface topology, potentially distinguishing it from other shape complexity metrics. Beyond genital shape, the alpha-shapes technique holds considerable promise for new applications across evolutionary, ecological and palaeoecological disciplines.
Phyllosilicates are common constituents of upper crustal faults and subduction forearcs. We studied the effect of mineralogy and controlled effective normal stress (between 5 MPa and 100 MPa) on ...frictional strength. Although the effect of mineralogy on frictional strength of single-phase phyllosilicate gouges has been previously studied, the influence of effective normal stress has not. We conducted water-saturated and vacuum-dry frictional tests on single-phase phyllosilicate gouges using a triaxial apparatus. Minerals included talc, pyrophyllite, kaolinite, lizardite, illite, montmorillonite, chlorite, muscovite, phlogopite, and biotite (particle size <30 μm). Results show friction coefficients between 0.22 – 0.44 (dry) and 0.12–0.38 (wet). Wet strength is always lower than dry strength for the same phyllosilicate, and those with hydrophilic surfaces are especially weakened by water. Tri-octahedral minerals are weaker than di-octahedral minerals with otherwise similar structures. The dependence of friction on interlayer bond strength is less clear than previously suggested. At effective normal stresses > 20 MPa dry friction coefficients are constant, and wet friction coefficients show a small increase. This is attributed to loss of water and increased contact area. The results indicate that frictional strength of clay-rich faults increases at depths less than ≈1 km under hydrostatic pore fluid pressures.
► Measured frictional strength of 10 phyllosilicates for range of effective normal stress. ► Frictional weakness of phyllosilicates depends on mineral structure. ► Dry friction coefficients are constant for normal stress between 20 MPa and 100 Mpa. ► Wet friction coefficients increase between 20 MPa and 100 MPa effective normal stress. ► Hydrophobicity of mineral surfaces influences wet frictional strength.
Particle size and morphology analysis is a problem common to a wide range of applications, including additive manufacturing, geological and agricultural materials' characterisation, food ...manufacturing and pharmaceuticals. Here, we review the use of microfocus X-ray computed tomography (X-ray CT) for particle analysis. We give an overview of different sample preparation methods, image processing protocols, the morphology parameters that can be determined, and types of materials that are suitable for analysis of particle sizes using X-ray CT. The main conclusion is that size and shape parameters can be determined for particles larger than approximately 2 to 3 μm, given adequate resolution of the X-ray CT setup. Particles composed of high atomic number materials (Z > 40) require careful sample preparation to ensure X-ray transmission. Problems occur when particles with a broad range of sizes are closely packed together, or when particles are fused (sintered or cemented). The use of X-ray CT for particle size analysis promises to become increasingly widespread, offering measurements of size, shape, and porosity of large numbers of particles within one X-ray CT scan.
•X-ray CT and SEM was used to reconstruct the high-fidelity, eye-specific, 3D microstructure of the TM/JCT/SC complex FE models.•The TM and JCT in the glaucoma eyes are 1.32-fold and 1.13-fold larger ...beam thickness compared to the healthy eyes.•Excessive ECM formation in the glaucoma JCT region may play a major role in outflow resistance rather than the trabecular beam thickness.
Intraocular pressure (IOP) is maintained via a dynamic balance between the production of aqueous humor and its drainage through the trabecular meshwork (TM), juxtacanalicular connective tissue (JCT), and Schlemm's canal (SC) endothelium of the conventional outflow pathway. Primary open angle glaucoma (POAG) is often associated with IOP elevation that occurs due to an abnormally high outflow resistance across the outflow pathway. Outflow tissues are viscoelastic and actively interact with aqueous humor dynamics through a two-way fluid-structure interaction coupling. While glaucoma affects the morphology and stiffness of the outflow tissues, their biomechanics and hydrodynamics in glaucoma eyes remain largely unknown. This research aims to develop an image-to-model method allowing the biomechanics and hydrodynamics of the conventional aqueous outflow pathway to be studied.
We used a combination of X-ray computed tomography and scanning electron microscopy to reconstruct high-fidelity, eye-specific, 3D microstructural finite element models of the healthy and glaucoma outflow tissues in cellularized and decellularized conditions. The viscoelastic TM/JCT/SC complex finite element models with embedded viscoelastic beam elements were subjected to a physiological IOP load boundary; the stresses/strains and the flow state were calculated using fluid-structure interaction and computational fluid dynamics.
Based on the resultant hydrodynamics parameters across the outflow pathway, the primary site of outflow resistance in healthy eyes was in the JCT and immediate vicinity of the SC inner wall, while the majority of the outflow resistance in the glaucoma eyes occurred in the TM. The TM and JCT in the glaucoma eyes showed 1.32-fold and 1.13-fold larger beam thickness and smaller trabecular space size (2.24-fold and 1.50-fold) compared to the healthy eyes.
Characterizing the accurate morphology of the outflow tissues may significantly contribute to constructing more accurate, robust, and reliable models, that can eventually help to better understand the dynamic IOP regulation, hydrodynamics of the aqueous humor, and outflow resistance dynamic in the human eyes. This model demonstrates proof of concept for determining changes to outflow resistance in healthy and glaucomatous tissues and thus may be utilized in larger cohorts of donor tissues where disease specificity, race, age, and gender of the eye donors may be accounted for.
Vascular calcification describes the formation of mineralized tissue within the blood vessel wall, and it is highly associated with increased cardiovascular morbidity and mortality in patients with ...chronic kidney disease, diabetes, and atherosclerosis. In this article, we briefly review different rodent models used to study vascular calcification in vivo, and critically assess the strengths and weaknesses of the current techniques used to analyze and quantify calcification in these models, namely 2-D histology and the
-cresolphthalein assay. In light of this, we examine X-ray micro-computed tomography (µCT) as an emerging complementary tool for the analysis of vascular calcification in animal models. We demonstrate that this non-destructive technique allows us to simultaneously quantify and localize calcification in an intact vessel in 3-D, and we consider recent advances in µCT sample preparation techniques. This review also discusses the potential to combine 3-D µCT analyses with subsequent 2-D histological, immunohistochemical, and proteomic approaches in correlative microscopy workflows to obtain rich, multifaceted information on calcification volume, calcification load, and signaling mechanisms from within the same arterial segment. In conclusion we briefly discuss the potential use of µCT to visualize and measure vascular calcification in vivo in real-time.
Human trabecular meshwork is a sieve-like tissue with large pores, which plays a vital role in aqueous humor outflow. Dysfunction of this tissue can occur, which leads to glaucoma and permanent ...vision loss. Replacement of trabecular meshwork with a tissue-engineered device is the ultimate objective. This study aimed to create a biomimetic structure of trabecular meshwork using electrospinning. Conventional electrospinning was compared to cryogenic electrospinning, the latter being an adaptation of conventional electrospinning whereby dry ice is incorporated in the fiber collector system. The dry ice causes ice crystals to form in-between the fibers, increasing the inter-fiber spacing, which is retained following sublimation. Structural characterization demonstrated cryo-scaffolds to have closer recapitulation of the trabecular meshwork, in terms of pore size, porosity, and thickness. The attachment of a healthy, human trabecular meshwork cell line (NTM5) to the scaffold was not influenced by the fabrication method. The main objective was to assess cell infiltration. Cryo-scaffolds supported cell penetration deep within their structure after seven days, whereas cells remained on the outer surface for conventional scaffolds. This study demonstrates the suitability of cryogenic electrospinning for the close recapitulation of trabecular meshwork and its potential as a 3D in vitro model and, in time, a tissue-engineered device.
Glaucoma is linked to raised intraocular pressure (IOP). The trabecular meshwork (TM) plays a major role in regulating IOP by enabling outflow of aqueous humor from the eye through its complex 3D ...structure. A lack of therapies targeting the dysfunctional TM highlights the need to develop biomimetic scaffolds that provide 3D in vitro models for glaucoma research or as implantable devices to regenerate TM tissue. To artificially mimic the TM's structure, we assessed methods for its decellularization and outline an optimized protocol for cell removal and structural retention. Using bovine TM, we trialed 2 lysing agents-Trypsin (0.05%
) and Ammonium Hydroxide (NH
OH; 2%
). Twenty-four hours in Trypsin caused significant structural changes. Shorter exposure (2 h) reduced this disruption whilst decellularizing the tissue (dsDNA 26 ± 14 ng/mL (control 1970 ± 146 ng/mL)). In contrast, NH
OH lysed all cells (dsDNA 25 ± 21 ng/mL), and the TM structure remained intact. For human TM, 2%
NH
OH similarly removed cells (dsDNA 52 ± 4 ng/mL (control 1965 ± 233 ng/mL)), and light microscopy and SEM presented no structural damage. X-ray computed tomography enabled a novel 3D reconstruction of decellularized human TM and observation of the tissue's intricate architecture. This study provides a new, validated method using NH
OH to decellularize delicate human TM without compromising tissue structure.
Solenopora jurassica is a fossil calcareous alga that functioned as an important reef-building organism during the Palaeozoic. It is of significant palaeobiological interest due to its distinctive ...but poorly understood pink and white banding. Though widely accepted as an alga there is still debate over its taxonomic affinity, with recent work arguing that it should be reclassified as a chaetetid sponge. The banding is thought to be seasonal, but there is no conclusive evidence for this. Other recent work has, however demonstrated the presence of a unique organic boron-containing pink/red pigment in the pink bands of S. jurassica. We present new geochemical evidence concerning the seasonality and pigmentation of S. jurassica. Seasonal growth cycles are demonstrated by X-ray radiography, which shows differences in calcite density, and by varying δ13C composition of the bands. Temperature variation in the bands is difficult to constrain accurately due to conflicting patterns arising from Mg/Ca molar ratios and δ18O data. Fluctuating chlorine levels indicate increased salinity in the white bands, when combined with the isotope data this suggests more suggestive of marine conditions during formation of the white band and a greater freshwater component (lower chlorinity) during pink band precipitation (δ18O). Increased photosynthesis is inferred within the pink bands in comparison to the white, based on δ13C. Pyrolysis Gas Chromatography Mass Spectrometry (Py-GCMS) and Fourier Transform Infrared Spectroscopy (FTIR) show the presence of tetramethyl pyrrole, protein moieties and carboxylic acid groups, suggestive of the presence of the red algal pigment phycoerythrin. This is consistent with the pink colour of S. jurassica. As phycoerythrin is only known to occur in algae and cyanobacteria, and no biomarker evidence of bacteria or sponges was detected we conclude S. jurassica is most likely an alga. Pigment analysis may be a reliable classification method for fossil algae.
We carried out a residual stress distribution analysis in a APS TBC throughout the depth of the coatings. The samples were heat treated at 1150°C for 190h and the data analysis used image based ...modelling based on the real 3D images measured by Computed Tomography (CT). The stress distribution in several 2D slices from the 3D model is included in this paper as well as the stress distribution along several paths shown on the slices. Our analysis can explain the occurrence of the “jump” features near the interface between the top coat and the bond coat. These features in the residual stress distribution trend were measured (as a function of depth) by high-energy synchrotron XRD (as shown in our related research article entitled ‘Understanding the Residual Stress Distribution through the Thickness of Atmosphere Plasma Sprayed (APS) Thermal Barrier Coatings (TBCs) by high energy Synchrotron XRD; Digital Image Correlation (DIC) and Image Based Modelling’) (Li et al., 2017) 1.
Understanding the role of power quality in aging of HVDC cable systems is critical to the reliable connection of offshore renewable energy sources, and hence global ambitions to reduce carbon ...emissions. This work investigates electrical treeing with a needle-plane geometry in low density polyethylene under a high negative DC voltage superimposed with AC ripples (-60 kV DC ± 7 kV AC). Tree initiation showed behavior similar to that widely reported under pure power frequencies. Subsequent tree growth, however, was observed to be confined in a smaller area with limited length and width than seen under pure AC voltages, even after long periods of voltage application. Traditional 2D imaging showed overlapped tree channels which developed to cover the whole area within the tree outline. A distinguishing tree shape resulted, which we have named a 'slim bouquet' shape. The volume rendering from XCT showed the structure had a 3D fractal dimension greater than 2, considerably larger than its 2D representation. PD signals during the growth had wing-like PRPD clusters and signal phase concentrations between 10-45° appeared after hours of growth. There was comb-like appearance in maximum PD magnitude variation, which is typical in pure high negative DC fields. Consideration is given to both space charge distribution controlled by high DC fields and continuous degradation by AC fields to explain the slim bouquet tree formation.
PDF
