X-ray Phase-contrast Microtomography Research Articles

Unveiling tumor invasiveness: enhancing cancer diagnosis with phase-contrast microtomography for 3D virtual histology

Malignant diseases are characterized by a critical trait known as invasiveness, where tumor cells tend to spread from the primary tissue layer into surrounding healthy tissues and distant organs. Presently, histopathology offers essential insights for diagnosing, classifying, predicting outcomes, and guiding patient-specific treatments. However, histology offers two-dimensional data from chosen cutting planes. Although 3D histological volumes can be generated through serial sectioning or whole slide imaging, this method is laborious, may introduce processing artefacts, and lacks isotropic spatial resolution. These limitations pose a considerable challenge to accurate diagnoses, particularly when dealing with micro-infiltrating carcinomas. These lesions, characterized by minute infiltrations, demand a three-dimensional representation for comprehensive visualization, essential for precise identification and assessment. Emerging X-ray-based virtual histology technology offers three-dimensional visualization of soft-tissue specimens, enabling virtual slicing in any direction or at any point. This approach can assist in guiding tissue sectioning for optimal representation of tumor cross sections during histological analysis. Micro-infiltrating carcinomas from the breast, cervix, and thyroid were imaged using X-ray phase-contrast microtomography (PhC-μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mu$$\\end{document}CT) at the Elettra synchrotron facility in Trieste, Italy. Comparative assessment of histological and CT slices by pathologists revealed that PhC-μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mu$$\\end{document}CT aids in classifying lesions by highlighting distinct tissue components and, notably, identifying tissue invasion. Reviewing a volume image allows pathologists to trace the entire lesion, identifying invasion sites that might be overlooked in individual or serial histological sections. Consequently, this proposed method could complement pathologists’ tools, potentially enhancing diagnoses by minimizing under-staging and reducing false negative results.

The human middle ear in motion: 3D visualization and quantification using dynamic synchrotron-based X-ray imaging

The characterization of the vibrations of the middle ear ossicles during sound transmission is a focal point in clinical research. However, the small size of the structures, their micrometer-scale movement, and the deep-seated position of the middle ear within the temporal bone make these types of measurements extremely challenging. In this work, dynamic synchrotron-based X-ray phase-contrast microtomography is used on acoustically stimulated intact human ears, allowing for the three-dimensional visualization of entire human eardrums and ossicular chains in motion. A post-gating algorithm is used to temporally resolve the fast micromotions at 128 Hz, coupled with a high-throughput pipeline to process the large tomographic datasets. Seven ex-vivo fresh-frozen human temporal bones in healthy conditions are studied, and the rigid body motions of the ossicles are quantitatively delineated. Clinically relevant regions of the ossicular chain are tracked in 3D, and the amplitudes of their displacement are computed for two acoustic stimuli.

Quantitative phase contrast X-ray tomography of aluminium metal matrix composite

The quantitative assessment of micro-structure and load-induced damages in Al–SiC metal matrix composites (MMC) is important for its design optimization, performance evaluation and structure-property correlation. X-ray Phase contrast micro-tomography is potentially used for evaluation of its 3 dimensional micro-structure manifested in the form of voids, cracks, embedded particles, and load-induced damages. However, the contrast between Al matrix and SiC particles is insufficient for their clear morphological identification and quantitative assessment. In the present study, we have proposed and applied single image-based phase retrieval as a pre-processing step to micro-tomography reconstruction for improved assessment of micro-structure and cohesion-induced damages in Al–SiC MMC. The advantages of applying different phase retrieval techniques in the enhancement of image quality and morphological quantification of SiC particles, pores and cohesion damages are discussed. It is observed that the Paganin method offers the best improvement in contrast to noise ratio for the measurement of SiC particles embedded in the Al matrix.

Terabyte-scale supervised 3D training and benchmarking dataset of the mouse kidney

The performance of machine learning algorithms, when used for segmenting 3D biomedical images, does not reach the level expected based on results achieved with 2D photos. This may be explained by the comparative lack of high-volume, high-quality training datasets, which require state-of-the-art imaging facilities, domain experts for annotation and large computational and personal resources. The HR-Kidney dataset presented in this work bridges this gap by providing 1.7 TB of artefact-corrected synchrotron radiation-based X-ray phase-contrast microtomography images of whole mouse kidneys and validated segmentations of 33 729 glomeruli, which corresponds to a one to two orders of magnitude increase over currently available biomedical datasets. The image sets also contain the underlying raw data, threshold- and morphology-based semi-automatic segmentations of renal vasculature and uriniferous tubules, as well as true 3D manual annotations. We therewith provide a broad basis for the scientific community to build upon and expand in the fields of image processing, data augmentation and machine learning, in particular unsupervised and semi-supervised learning investigations, as well as transfer learning and generative adversarial networks.

X-ray phase-contrast microtomography of soft tissues using a compact laboratory system with two-directional sensitivity.

X-ray microtomography is a nondestructive, three-dimensional inspection technique applied across a vast range of fields and disciplines, ranging from research to industrial, encompassing engineering, biology, and medical research. Phase-contrast imaging extends the domain of application of x-ray microtomography to classes of samples that exhibit weak attenuation, thus appearing with poor contrast in standard x-ray imaging. Notable examples are low-atomic-number materials, like carbon-fiber composites, soft matter, and biological soft tissues. We report on a compact and cost-effective system for x-ray phase-contrast microtomography. The system features high sensitivity to phase gradients and high resolution, requires a low-power sealed x-ray tube, a single optical element, and fits in a small footprint. It is compatible with standard x-ray detector technologies: in our experiments, we have observed that single-photon counting offered higher angular sensitivity, whereas flat panels provided a larger field of view. The system is benchmarked against known-material phantoms, and its potential for soft-tissue three-dimensional imaging is demonstrated on small-animal organs: a piglet esophagus and a rat heart. We believe that the simplicity of the setup we are proposing, combined with its robustness and sensitivity, will facilitate accessing quantitative x-ray phase-contrast microtomography as a research tool across disciplines, including tissue engineering, materials science, and nondestructive testing in general.

New Cretaceous empidoids and the Mesozoic dance fly revolution (Diptera: Empidoidea).

Dance flies and relatives (Empidoidea) are a diverse and ecologically important group of Diptera in nearly all modern terrestrial ecosystems. Their fossil record, despite being scattered, attests to a long evolutionary history dating back to the early Mesozoic. Here, we describe seven new species of Empidoidea from Cretaceous Kachin amber inclusions, assigning them to the new genus Electrochoreutes gen.n. (type species: Electrochoreutes trisetigerus sp.n.) based on unique apomorphies among known Diptera. Like many extant dance flies, the males of Electrochoreutes are characterized by species-specific sexually dimorphic traits, which are likely to have played a role in courtship. The fine anatomy of the fossils was investigated through high-resolution X-ray phase-contrast microtomography to reconstruct their phylogenetic affinities within the empidoid clade, using cladistic reasoning. Morphology-based phylogenetic analyses including a selection of all extant family- and subfamily-ranked empidoid clades along with representatives of all extinct Mesozoic genera, were performed using a broad range of analytical methods (maximum parsimony, maximum-likelihood and Bayesian inference). These analyses converged in reconstructing Electrochoreutes as a stem-group representative of the Dolichopodidae, suggesting that complex mating rituals evolved in this lineage during the Cretaceous.

Reduced volume of diabetic pancreatic islets in rodents detected by synchrotron X-ray phase-contrast microtomography and deep learning network

The pancreatic islet is a highly structured micro-organ that produces insulin in response to rising blood glucose. Here we develop a label-free and automatic imaging approach to visualize the islets in situ in diabetic rodents by the synchrotron radiation X-ray phase-contrast microtomography (SRμCT) at the ID17 station of the European Synchrotron Radiation Facility. The large-size images (3.2mm×15.97mm) were acquired in the pancreas in STZ-treated mice and diabetic GK rats. Each pancreas was dissected by 3000 reconstructed images. The image datasets were further analysed by a self-developed deep learning method, AA-Net. All islets in the pancreas were segmented and visualized by the three-dimension (3D) reconstruction. After quantifying the volumes of the islets, we found that the number of larger islets (=>1500 μm3) was reduced by 2-fold (wt 1004±94 vs GK 419±122, P<0.001) in chronically developed diabetic GK rat, while in STZ-treated diabetic mouse the large islets were decreased by half (189±33 vs 90±29, P<0.001) compared to the untreated mice. Our study provides a label-free tool for detecting and quantifying pancreatic islets in situ. It implies the possibility of monitoring the state of pancreatic islets in vivo diabetes without labelling.

Anatomical study of the red flour beetle using synchrotron radiation X-ray phase-contrast micro-tomography.

Synchrotron X-ray phase-contrast microtomography (SR-PhC micro-CT) is well established, fast and non-destructive imaging technique for data acquisition that is currently being used to obtain new insights into insect anatomy and function in physiological, morphological and phylogenetic studies. In this study, we described in situ the internal organs of the red flour beetle Tribolium castaneum Herbst 1797, a widespread pest of cereals and stored food causing serious damage to the human economy. Two-dimensional virtual sections and volumetric reconstructions of the nervous, alimentary and reproductive systems were carried out in both sexes. The results provided a comprehensive overview of the morphological characteristics of this species, such as the different maturation stages of ovarioles and the realistic location, size and shape of internal organs. Given the great interest in this model species in experimental biology and forensic entomology, complete knowledge of the general anatomy is required for future functional applications in pest control and experimental studies. In addition, this study confirms SR-PhC micro-CT as a powerful and innovative tool in entomology, particularly suitable for small species and chitinized structures that are difficult to analyse using conventional dissection and histological methods.

Structural and spectral morphometry and diagnosis of lung tumors

Visualization of multi-dimensional (3D) pathological information of lung specimens can provide better understanding for the diagnosis of lung cancers. Phase-sensitive computed tomography has been employed to investigate non-destructive 3D histology and morphometry of soft tissues in the last decade. However, it’s insufficient to make an accurate diagnosis by only using the microstructural morphology of tumor specimens linked to clinical data. Synchrotron-based micro-structural and infrared spectroscopic techniques was employed to improve the level of diagnosing lung tumor (LT) with combination of traditional medical examination. The synchrotron X-ray phase-contrast microtomography can provide the elucidation of correlated cross-scale morphometry of LT, including biological boundary, 3D histologic features, and quantitative volumetric lesion statistics. Compared to conventional histopathological sections, it facilitated the time-efficient scouting for regions of interest related to LT. The Fourier transform infrared micro-spectroscopy successfully revealed the IR spectral correlations and differences between normal and tumor tissues, partially confirmed by conventional biochemical examinations. Especially, lacking the peak of 1733 cm−1 could be considered as an important indicator for malignant LT. The dual-modality imaging fusion of LT samples was capable of better explanation of LT biomolecular and microenvironmental evolution. We demonstrated the multi-dimensional imaging protocol for LT-related diagnosis has a good potential in early lung cancer screening and clinical assessment.

Exploring Compound Eyes in Adults of Four Coleopteran Species Using Synchrotron X-ray Phase-Contrast Microtomography (SR-PhC Micro-CT).

Compound eyes in insects are primary visual receptors of surrounding environments. They show considerable design variations, from the apposition vision of most day-active species to the superposition vision of nocturnal insects, that sacrifice resolution to increase sensitivity and are able to overcome the challenges of vision during lightless hours or in dim habitats. In this study, Synchrotron radiation X-ray phase-contrast microtomography was used to describe the eye structure of four coleopteran species, showing species-specific habitat demands and different feeding habits, namely the saproxylic Clinidium canaliculatum (Costa, 1839) (Rhysodidae), the omnivorous Tenebrio molitor (Linnaeus, 1758) and Tribolium castaneum (Herbest, 1797) (Tenebrionidae), and the generalist predator Pterostichus melas italicus (Dejean, 1828) (Carabidae). Virtual sections and 3D volume renderings of the heads were performed to evaluate the application and limitations of this technique for studying the internal dioptrical and sensorial parts of eyes, and to avoid time-consuming methods such as ultrastructural analyses and classic histology. Morphological parameters such as the area of the corneal facet lens and cornea, interocular distance, facet density and corneal lens thickness were measured, and differences among the studied species were discussed concerning the differences in lifestyle and habitat preferences making different demands on the visual system. Our imaging results provide, for the first time, morphological descriptions of the compound eyes in these species, supplementing their ecological and behavioural traits.

Elucidating the formation of structural defects in flax fibres through synchrotron X-ray phase-contrast microtomography

The creation and ultrastructure of kink-bands in flax fibres are key issues for developing more and more performing biobased composite materials. Nevertheless, despite many hypotheses and structural characterisation, the exact origin of kink-bands and the moment they appear remain unexplained. Here, by using cutting-edge techniques such as microtomography, a range of flax stems and fibres, from the green stem to stretched fibres, were morphologically explored. The study shows that all the extracted fibres, whether scutched, combed or stretched, contain significant amounts of kink-bands, which can be identified by the large pores they contain. On the other hand, at the scale of the green or retted stems, tomographic analysis does not reveal any kink-bands. These original observations suggest that the stress undergone by the plants during their growth is not sufficient, without major growth or lodging accidents, to generate these structural defects; the latter are only revealed after mechanical extraction of the fibres. Hypotheses regarding the kink-band appearance deformation levels are also given to complete the observations.

Virtual sections and 3D reconstructions of female reproductive system in a carabid beetle using synchrotron X-ray phase-contrast microtomography

Morphological analyses of the internal anatomy are a milestone in different fields of animal biology, such as physiology, development and reproduction, and systematic studies. Synchrotron radiation X-ray phase-contrast microtomography (SR-PhC micro-CT) has become a valuable imaging tool used for non-invasive analyses of the insect internal anatomy. The ground beetle Pterostichus melas italicus Dejean, 1828 (Coleoptera, Carabidae, Harpalinae) is an important predator of the trophic web in cropland involved in pest biological control. The anatomy of the reproductive system was first described in mature females scanning the samples at the SYRMEP beamline of the Elettra synchrotron facility in Trieste (Italy). The female reproductive tract consists of paired ovaries each containing six polytrophic ovarioles, a common oviduct and a spermatheca. Oocytes at different stages of differentiation were identified to be associated with nurse cells in the follicle. Virtual dissections and 3D rendering allowed to describe in situ the morphology of each structure. This investigation adds to the scarce information on internal genitalia of carabid females and provides a basis for further research on the reproductive strategies of P. melas. High quality images and the supplementary video from SR-PhC micro-CT analyses represent a significant advance in data collection to study insect morphology and function.

Measurement of local orientation of cardiomyocyte aggregates in human left ventricle free wall samples using X-ray phase-contrast microtomography.

Most cardiomyocytes in the left ventricle wall are grouped in aggregates of four to five units that are quasi-parallel to each other. When one or more "cardiomyocyte aggregates" are delimited by two cleavage planes, this defines a "sheetlet" that can be considered as a "work unit" that contributes to the thickening of the wall during the cardiac cycle. In this paper, we introduce the skeleton method to measure the local three-dimensional (3D) orientation of cardiomyocyte aggregates in the sheetlets in three steps: data segmentation; extraction of the skeleton of the sheetlets; and calculation of the local orientation of the cardiomyocyte aggregates inside the sheetlets. These data include a series of virtual tissue volumes and five transmural human left ventricle free wall samples, imaged with 3D synchrotron radiation phase-contrast microtomography, and reconstructed with a 3.5×3.5×3.5μm3voxel size. We computed the local orientation of the cardiomyocyte aggregates inside the sheetlets with a working window of 112×112×112μm3 in size. These data demonstrate that the skeleton method can provide accurate 3D measurements and reliable screening of the 3D evolution of the orientation of cardiomyocyte aggregates within the sheetlets. We showed that in regions that contain one population of quasi-parallel sheetlets, the orientation of the cardiomyocyte aggregates undergo "oscillations" along the perpendicular direction of the sheetlets. In regions that contain two populations of sheetlets with a different angular range, we demonstrate some discontinuity of the helix angle of the cardiomyocyte aggregates at the interface between the two populations.

3D ring artifacts removal algorithm combined low-rank tensor decomposition with spatial-sequential total variation regularization and its application in phase-contrast microtomography.

High-resolution synchrotron radiation X-ray phase contrast microtomography (PC-μCT) images often suffer from severe ring artifacts, which are mainly caused by undesirable responses of detector elements. In the medical imaging field, the existence of ring artifacts can lead to degraded visual quality and can directly affect diagnosis accuracy. Thus, removing or at least effectively reducing ring artifacts is indispensable. The existing ring artifacts removal algorithms mainly focus on two-dimensional (matrix-based) priors, and these algorithms fail to consider correlations hidden in sequential computed tomography (CT) images. This paper proposed a novel three-dimensional (tensor-based) ring artifacts removal algorithm for synchrotron radiation X-ray PC-μCT images. In the sinogram domain, ring artifacts manifest as vertical stripe artifacts. From an image decomposition perspective, a degraded sinogram can be decomposed into a stripe artifacts component and an underlying clean sinogram component. The proposed algorithm is designed to detect and remove stripe artifacts from a degraded sinogram by fully identifying the characteristics of the two components. Specifically, for the stripe artifacts component, tensor Tucker decomposition is used to describe its low-rank character. For the underlying clean sinogram component, spatial-sequential total variation regularization is adopted to enhance the piecewise smoothness. Moreover, the Frobenius norm term is further used to model Gaussian noise. An efficient augmented Lagrange multiplier method is designed to solve the proposed optimization model. The proposed method is evaluated utilizing both simulations and real data containing different ring artifacts patterns. In the simulations, the human chest CT images are used for evaluating the proposed method. We compare the peak signal-to-noise ratio (PSNR), structural similarity (SSIM), and mean absolute error (MAE) results of our algorithm with the Naghia's method, the RRRTV method, the wavelet-FFT method, and the SDRSD-GIF method. The proposed method was also evaluated on real data from rat liver samples and rat tooth samples. Our proposed method outperforms the competing methods in terms of both qualitative and quantitative evaluation results. Additionally, the 3D visualization results were presented to make the ring artifacts removal effect more intuitive. The experimental results on simulations and real data clearly demonstrated that the proposed algorithm can significantly improve the quality of PC-μCT images compared with the existing popular algorithms, and it has great potential to promote the application of high-resolution imaging for visualizing biological tissues.

The Symmetric 3D Organization of Connective Tissue around Implant Abutment: A Key-Issue to Prevent Bone Resorption

Symmetric and well-organized connective tissues around the longitudinal implant axis were hypothesized to decrease early bone resorption by reducing inflammatory cell infiltration. Previous studies that referred to the connective tissue around implant and abutments were based on two-dimensional investigations; however, only advanced three-dimensional characterizations could evidence the organization of connective tissue microarchitecture in the attempt of finding new strategies to reduce inflammatory cell infiltration. We retrieved three implants with a cone morse implant–abutment connection from patients; they were investigated by high-resolution X-ray phase-contrast microtomography, cross-linking the obtained information with histologic results. We observed transverse and longitudinal orientated collagen bundles intertwining with each other. In the longitudinal planes, it was observed that the closer the fiber bundles were to the implant, the more symmetric and regular their course was. The transverse bundles of collagen fibers were observed as semicircular, intersecting in the lamina propria of the mucosa and ending in the oral epithelium. No collagen fibers were found radial to the implant surface. This intertwining three-dimensional pattern seems to favor the stabilization of the soft tissues around the implants, preventing inflammatory cell apical migration and, consequently, preventing bone resorption and implant failure. This fact, according to the authors’ best knowledge, has never been reported in the literature and might be due to the physical forces acting on fibroblasts and on the collagen produced by the fibroblasts themselves, in areas close to the implant and to the symmetric geometry of the implant itself.

Discovery of Lebambromyia in Myanmar Cretaceous Amber: Phylogenetic and Biogeographic Implications (Insecta, Diptera, Phoroidea).

Simple SummaryPhoroid flies are an ancient lineage of Diptera, which includes megadiverse, widespread groups like the scuttle flies, as well as species-poor, sometimes relict, groups like flat-footed and ironic flies. The earliest fossils of phoroid flies are from Early Cretaceous. In this paper we describe a second species of the enigmatic phoroid fly genus Lebambromyia. The genus was erected to accommodate an extinct species, L. acrai Grimaldi and Cumming, from Lebanese amber deposit, dated at ca. 120 Mya. A new species, L. sacculifera sp. nov., is described here based on a single female specimen embedded in Myanmar “mid-Cretaceous” amber, which is over 20 Ma younger than the Lebanese outcrop, implying that this genus had a wide geographic and temporal distribution. The state of preservation of the new specimen and its study with phase contrast X-ray microtomography show that this ancient fly was characterized by a mix of ancient and modern features, such as specialized sensory areas in the antenna. Phylogenetic analyses support that Lebambromyia was related to flat-footed and ironic flies, but a clear phylogenetic position remains elusive.Lebambromyia sacculifera sp. nov. is described from Late Cretaceous amber from Myanmar, integrating traditional observation techniques and X-ray phase contrast microtomography. Lebambromyia sacculifera is the second species of Lebambromyia after L. acrai Grimaldi and Cumming, described from Lebanese amber (Early Cretaceous), and the first record of this taxon from Myanmar amber, considerably extending the temporal and geographic range of this genus. The new specimen bears a previously undetected set of phylogenetically relevant characters such as a postpedicel sacculus and a prominent clypeus, which are shared with Ironomyiidae and Eumuscomorpha. Our cladistic analyses confirmed that Lebambromyia represented a distinct monophyletic lineage related to Platypezidae and Ironomyiidae, though its affinities are strongly influenced by the interpretation and coding of the enigmatic set of features characterizing these fossil flies.

Characterization of the microstructures of specialty optical fibers for electric-field sensing by propagation-based x-ray phase-contrast microtomography

In this work, we present a quantitative (statistical) 3D morphological characterization of optical fibers used in electric-field sensing. The characterization technique employs propagation-based x-ray phase-contrast microcomputed tomography (micro-CT). In particular, we investigate specialty optical fibers that contain microstructured holes that are electro-optically modified by thermal poling to induce second-order nonlinear effects (SONE). The efficiency of the SONE is reflected in the characterization parameter, Vπ , which is highly dependent on the dimensions of the fiber. The fiber microstructures must be uniform to support the fabrication of reproducible devices. The results obtained using the micro-CT technique show that uncertainty of ±1.7% arises in the determination of the expected value of the voltage that causes a change in the phase of the electromagnetic wave equal to π rad (Vπ ), demonstrating a great advantage, compared with other techniques e.g. SEM, which would need at least 1000 images of the cross-section of an optical fiber, taken at different points, making the process more expensive and time-consuming.

Double-exposure method for speckle-tracking x-ray phase-contrast microtomography

X-ray phase-contrast microtomography based on speckle tracking is an attractive method for non-destructive three-dimensional imaging owing to its simple setup and ability to yield absorption, refractive, and scattering images simultaneously. However, the edge-enhancement effect usually results in image artifacts or inaccurate phase retrieval, limiting the extensive application of this method in biomedical research and for low-Z materials. In this paper, a double-exposure method is introduced to solve this problem efficiently and accurately. Pure phase samples with various microstructures and densities and a biological sample with a distinct edge-enhancement effect were used to verify the effectiveness of the developed method. In an experiment performed using a polymer phantom with an evenly distributed density, 17 irregularly shaped particles with diameters ranging from 15 to 25 μm were successfully reconstructed with the effective elimination of the edge-enhancement effect. The results obtained for a sample composed of different polymer materials demonstrated that, in contrast with the traditional speckle-tracking method, the present method is able to discriminate materials with similar x-ray attenuations. Finally, experiments were performed using a dehydrated fish, which entail typical edge enhancement and a complex microstructure; notably, it was verified that the fine structure of the fish, including its fins and intestines, was reconstructed completely using the proposed method, whereas the standard speckle-tracking method was ineffective. In conclusion, the developed double-exposure method can serve as an efficient and accurate technique for the x-ray phase-contrast microtomography of samples comprising low-Z materials and complicated microstructures.

Efficient three-dimensional characterization of C/C composite reinforced with densely distributed fibers via X-ray phase-contrast microtomography

Carbon fiber (CF)/pyrolytic graphite (PG) composites are promising structural materials for molten salt reactors because of their superior performance. Due to the minor density difference between CF and PG, existing methods are impractical for efficient three-dimensional characterization of CF/PG composites. Therefore, in this study, a method based on in-line phase-contrast X-ray microtomography was developed to solve the aforementioned problem. Experimental results demonstrate that the method is suitable for comprehensive characterization of CF/PG composites. The relationship between the microporous defects and fiber orientations of such composites was also elucidated. The findings can be useful for improving the manufacturing process of CF/PG composites.

Steerable3D: An ImageJ plugin for neurovascular enhancement in 3-D segmentation

Abstract Purpose Image processing plays a fundamental role in the study of central nervous system, for example in the analysis of the vascular network in neurodegenerative diseases. Synchrotron X-ray Phase-contrast micro-Tomography (SXPCT) is a very attractive method to study weakly absorbing samples and features, such as the vascular network in the spinal cord (SC). However, the identification and segmentation of vascular structures in SXPCT images is seriously hampered by the presence of image noise and strong contrast inhomogeneities, due to the sensitivity of the technique to small electronic density variations. In order to help with these tasks, we implemented a user-friendly ImageJ plugin based on a 3D Gaussian steerable filter, tuned up for the enhancement of tubular structures in SXPCT images. Methods The developed 3D Gaussian steerable filter plugin for ImageJ is based on the steerability properties of Gaussian derivatives. We applied it to SXPCT images of ex-vivo mouse SCs acquired at different experimental conditions. Results The filter response shows a strong amplification of the source image contrast-to-background ratio (CBR), independently of structures orientation. We found that after the filter application, the CBR ratio increases by a factor ranging from ~6 to ~60. In addition, we also observed an increase of 35% of the contrast to noise ratio in the case of injured mouse SC. Conclusion The developed tool can generally facilitate the detection/segmentation of capillaries, veins and arteries that were not clearly observable in non-filtered SXPCT images. Its systematic application could allow obtaining quantitative information from pre-clinical and clinical images.