Insight into 3D micro‐CT data: exploring segmentation algorithms through performance metrics

Three‐dimensional (3D) micro‐tomography (µ‐CT) has proven to be an important imaging modality in industry and scientific domains. Understanding the properties of material structure and behavior has produced many scientific advances. An important component of the 3D µ‐CT pipeline is image partitioning (or image segmentation), a step that is used to separate various phases or components in an image. Image partitioning schemes require specific rules for different scientific fields, but a common strategy consists of devising metrics to quantify performance and accuracy. The present article proposes a set of protocols to systematically analyze and compare the results of unsupervised classification methods used for segmentation of synchrotron‐based data. The proposed dataflow for Materials Segmentation and Metrics (MSM) provides 3D micro‐tomography image segmentation algorithms, such as statistical region merging (SRM), k‐means algorithm and parallel Markov random field (PMRF), while offering different metrics to evaluate segmentation quality, confidence and conformity with standards. Both experimental and synthetic data are assessed, illustrating quantitative results through the MSM dashboard, which can return sample information such as media porosity and permeability. The main contributions of this work are: (i) to deliver tools to improve material design and quality control; (ii) to provide datasets for benchmarking and reproducibility; (iii) to yield good practices in the absence of standards or ground‐truth for ceramic composite analysis.     

Evaluation of the improved three‐dimensional resolution of a synchrotron radiation computed tomograph using a micro‐fabricated test pattern

A micro test pattern prepared by focused ion beam milling was used to evaluate the three‐dimensional resolution of a microtomograph at the BL20B2 beamline of SPring‐8. The resolutions along the direction within the tomographic slice plane and perpendicular to it were determined from the modulation transfer functions. The through‐plane resolution perpendicular to the tomographic slice was evaluated to be 8 µm, which corresponds to the spatial resolution of two‐dimensional radiographs. In contrast, the in‐plane resolution within the slice was evaluated to be 12 µm. Real‐space interpolation was performed prior to the tomographic reconstruction, giving an improved in‐plane resolution of 8.5 µm. However, the 8 µm pitch pattern was resolved in the interpolated slice image. To reflect this result, another resolution measure from the peak‐to‐valley difference plot was introduced. This resolution measure gave resolution limits of 7.4 µm for the in‐plane direction and 6.1 µm for the through‐plane direction. The three‐dimensional test pattern along with the interpolated reconstruction enables the quantitative evaluation of the spatial resolution of microtomographs.     

The 3D characteristics of post‐traumatic syringomyelia in a rat model: a propagation‐based synchrotron radiation microtomography study

Many published literature sources have described the histopathological characteristics of post‐traumatic syringomyelia (PTS). However, three‐dimensional (3D) visualization studies of PTS have been limited due to the lack of reliable 3D imaging techniques. In this study, the imaging efficiency of propagation‐based synchrotron radiation microtomography (PB‐SRµCT) was determined to detect the 3D morphology of the cavity and surrounding microvasculature network in a rat model of PTS. The rat model of PTS was established using the infinite horizon impactor to produce spinal cord injury (SCI), followed by a subarachnoid injection of kaolin to produce arachnoiditis. PB‐SRµCT imaging and histological examination, as well as fluorescence staining, were conducted on the animals at the tenth week after SCI. The 3D morphology of the cystic cavity was vividly visualized using PB‐SRµCT imaging. The quantitative parameters analyzed by PB‐SRµCT, including the lesion and spared spinal cord tissue area, the minimum and maximum diameters in the cystic cavity, and cavity volume, were largely consistent with the results of the histological assessment. Moreover, the 3D morphology of the cavity and surrounding angioarchitecture could be simultaneously detected on the PB‐SRµCT images. This study demonstrated that high‐resolution PB‐SRµCT could be used for the 3D visualization of trauma‐induced spinal cord cavities and provides valuable quantitative data for cavity characterization. PB‐SRµCT could be used as a reliable imaging technique and offers a novel platform for tracking cavity formation and morphological changes in an experimental animal model of PTS.     

Using synchrotron radiation inline phase‐contrast imaging computed tomography to visualize three‐dimensional printed hybrid constructs for cartilage tissue engineering

Synchrotron radiation inline phase‐contrast imaging combined with computed tomography (SR‐inline‐PCI‐CT) offers great potential for non‐invasive characterization and three‐dimensional visualization of fine features in weakly absorbing materials and tissues. For cartilage tissue engineering, the biomaterials and any associated cartilage extracellular matrix (ECM) that is secreted over time are difficult to image using conventional absorption‐based imaging techniques. For example, three‐dimensional printed polycaprolactone (PCL)/alginate/cell hybrid constructs have low, but different, refractive indices and thicknesses. This paper presents a study on the optimization and utilization of inline‐PCI‐CT for visualizing the components of three‐dimensional printed PCL/alginate/cell hybrid constructs for cartilage tissue engineering. First, histological analysis using Alcian blue staining and immunofluorescent staining assessed the secretion of sulfated glycosaminoglycan (GAGs) and collagen type II (Col2) in the cell‐laden hybrid constructs over time. Second, optimization of inline PCI‐CT was performed by investigating three sample‐to‐detector distances (SDD): 0.25, 1 and 3 m. Then, the optimal SDD was utilized to visualize structural changes in the constructs over a 42‐day culture period. The results showed that there was progressive secretion of cartilage‐specific ECM by ATDC5 cells in the hybrid constructs over time. An SDD of 3 m provided edge‐enhancement fringes that enabled simultaneous visualization of all components of hybrid constructs in aqueous solution. Structural changes that might reflect formation of ECM also were evident in SR‐inline‐PCI‐CT images. Summarily, SR‐inline‐PCI‐CT images captured at the optimized SDD enables visualization of the different components in hybrid cartilage constructs over a 42‐day culture period.     

Performance of the micro‐PIC gaseous area detector in small‐angle X‐ray scattering experiments

The application of a two‐dimensional photon‐counting detector based on a micro‐pixel gas chamber (µ‐PIC) to high‐resolution small‐angle X‐ray scattering (SAXS), and its performance, are reported. The µ‐PIC is a micro‐pattern gaseous detector fabricated by printed circuit board technology. This article describes the performance of the µ‐PIC in SAXS experiments at SPring‐8. A dynamic range of >10⁵ was obtained for X‐ray scattering from a polystyrene sphere solution. A maximum counting rate of up to 5 MHz was observed with good linearity and without saturation. For a diffraction pattern of collagen, weak peaks were observed in the high‐angle region in one accumulation of photons.     

The emerging role of 4D synchrotron X‐ray micro‐tomography for climate and fossil energy studies: five experiments showing the present capabilities at beamline 8.3.2 at the Advanced Light Source

Continuous improvements at X‐ray imaging beamlines at synchrotron light sources have made dynamic synchrotron X‐ray micro‐computed tomography (SXR‐µCT) experiments more routinely available to users, with a rapid increase in demand given its tremendous potential in very diverse areas. In this work a survey of five different four‐dimensional SXR‐µCT experiments is presented, examining five different parameters linked to the evolution of the investigated system, and tackling problems in different areas in earth sciences. SXR‐µCT is used to monitor the microstructural evolution of the investigated sample with the following variables: (i) high temperature, observing in situ oil shale pyrolysis; (ii) low temperature, replicating the generation of permafrost; (iii) high pressure, to study the invasion of supercritical CO₂ in deep aquifers; (iv) uniaxial stress, to monitor the closure of a fracture filled with proppant, in shale; (v) reactive flow, to observe the evolution of the hydraulic properties in a porous rock subject to dissolution. For each of these examples, it is shown how dynamic SXR‐µCT was able to provide new answers to questions related to climate and energy studies, highlighting the significant opportunities opened recently by the technique.     

Microvascular imaging using synchrotron radiation

In vascular diseases, the involvement of small vessels can be very crucial physiologically. Morphological changes of vasculature and alterations may be promising characteristic criteria for investigating disease progression and for evaluating therapeutic effects. Visualization of microvasculatures is an important step in understanding the mechanism of early vessel disorders and developing effective therapeutic strategies. However, the microvessels involved are beyond the detection limit of conventional angiography, i.e. 200 µm. Thus, faster and higher‐resolution imaging technologies are desired to capture the early anatomical structure changes of vasculatures in study of the disease. A new angiography system, synchrotron radiation microangiography, has been developed in this study. It allows for enhanced sensitivity to contrast agents and superior image quality in spatial resolution. Iodine and barium sulfate were used as blood vessel contrast agents. Physiological features of whole‐body mouse microvasculature were investigated using synchrotron radiation for the first time. The intracranial vascular network and other blood vessels were observed clearly, and the related anatomy and vessel diameters were studied. Dynamic angiography in mouse brain was performed with a high spatial image resolution of around 20–30 µm. Future research will focus on the development of novel specific targeting contrast agents for blood vessel imaging in vivo with a long half‐life and fewer side effects.     

Development of a two‐dimensional imaging system of X‐ray absorption fine structure

A two‐dimensional imaging system of X‐ray absorption fine structure (XAFS) has been developed at beamline BL‐4 of the Synchrotron Radiation Center of Ritsumeikan University. The system mainly consists of an ionization chamber for I₀ measurement, a sample stage, and a two‐dimensional complementary metal oxide semiconductor (CMOS) image sensor for measuring the transmitted X‐ray intensity. The X‐ray energy shift in the vertical direction, which originates from the vertical divergence of the X‐ray beam on the monochromator surface, is corrected by considering the geometrical configuration of the monochromator. This energy correction improves the energy resolution of the XAFS spectrum because each pixel in the CMOS detector has a very small vertical acceptance of ～0.5 µrad. A data analysis system has also been developed to automatically determine the energy of the absorption edge. This allows the chemical species to be mapped based on the XANES feature over a wide area of 4.8 mm (H) × 3.6 mm (V) with a resolution of 10 µm × 10 µm. The system has been applied to the chemical state mapping of the Mn species in a LiMn₂O₄ cathode. The heterogeneous distribution of the Mn oxidation state is demonstrated and is considered to relate to the slow delocalization of Li⁺‐defect sites in the spinel crystal structure. The two‐dimensional‐imaging XAFS system is expected to be a powerful tool for analyzing the spatial distributions of chemical species in many heterogeneous materials such as battery electrodes.     

Elemental depth profile of faux bamboo paint in Forbidden City studied by synchrotron radiation confocal µ‐XRF

A three‐dimensional (3D) analysis of micro x‐ray fluorescence (XRF), namely confocal µ‐XRF, has been constructed at 4W1B beamline of the Beijing synchrotron radiation facility (BSRF). A KB mirror is applied to focus the incident beam and a polycapillary half‐lens in front of the Si(Li) detector is used to limit the visual field of the detector. The faux bamboo paint in Emperor Qianlong's Lodge of Retirement in Forbidden City was analyzed nondestructively by this method. A stratified structure in the paint is disclosed and the results show that the painting was probably restored once in the past, following the same painting technique as originally used. Copyright © 2008 John Wiley & Sons, Ltd.     

Monte Carlo simulation code for confocal 3D micro‐beam X‐ray fluorescence analysis of stratified materials

Stratified materials are of great importance for many branches of modern industry, e.g. electronics or optics and for biomedical applications. Examination of chemical composition of individual layers and determination of their thickness helps to get information on their properties and function. A confocal 3D micro X‐ray fluorescence (3D µXRF) spectroscopy is an analytical method giving the possibility to investigate 3D distribution of chemical elements in a sample with spatial resolution in the micrometer regime in a non‐destructive way. Thin foils of Ti, Cu and Au, a bulk sample of Cu and a three‐layered sandwich sample, made of two thin Fe/Ni alloy foils, separated by polypropylene, were used as test samples. A Monte Carlo (MC) simulation code for the determination of elemental concentrations and thickness of individual layers in stratified materials with the use of confocal 3D µXRF spectroscopy was developed. The X‐ray intensity profiles versus the depth below surface, obtained from 3D µXRF experiments, MC simulation and an analytical approach were compared. Correlation coefficients between experimental versus simulated, and experimental versus analytical model X‐ray profiles were calculated. The correlation coefficients were comparable for both methods and exceeded 99%. The experimental X‐ray intensity profiles were deconvoluted with iterative MC simulation and by using analytical expression. The MC method produced slightly more accurate elemental concentrations and thickness of successive layers as compared to the results of the analytical approach. This MC code is a robust tool for simulation of scanning confocal 3D µXRF experiments on stratified materials and for quantitative interpretation of experimental results. Copyright © 2011 John Wiley & Sons, Ltd.     

X‐ray nanotomography and focused‐ion‐beam sectioning for quantitative three‐dimensional analysis of nanocomposites

Knowing the relationship between three‐dimensional structure and properties is paramount for complete understanding of material behavior. In this work, the internal nanostructure of micrometer‐size (～10 µm) composite Ni/Al particles was analyzed using two different approaches. The first technique, synchrotron‐based X‐ray nanotomography, is a nondestructive method that can attain resolutions of tens of nanometers. The second is a destructive technique with sub‐nanometer resolution utilizing scanning electron microscopy combined with an ion beam and `slice and view' analysis, where the sample is repeatedly milled and imaged. The obtained results suggest that both techniques allow for an accurate characterization of the larger‐scale structures, while differences exist in the characterization of the smallest features. Using the Monte Carlo method, the effective resolution of the X‐ray nanotomography technique was determined to be ～48 nm, while focused‐ion‐beam sectioning with `slice and view' analysis was ～5 nm.     

In vivo high‐resolution synchrotron radiation imaging of collagen‐induced arthritis in a rodent model

In vivo microstructures of the affected feet of collagen‐induced arthritic (CIA) mice were examined using a high‐resolution synchrotron radiation (SR) X‐ray refraction technique with a polychromatic beam issued from a bending magnet. The CIA models were obtained from six‐week‐old DBA/1J mice that were immunized with bovine type II collagen and grouped as grades 0–3 according to a clinical scoring for the severity of arthritis. An X‐ray shadow of a specimen was converted into a visual image on the surface of a CdWO₄ scintillator that was magnified using a microscopic objective lens before being captured with a digital charge‐coupled‐device camera. Various changes in the joint microstructure, including cartilage destruction, periosteal born formation, articular bone thinning and erosion, marrow invasion by pannus progression, and widening joint space, were clearly identified at each level of arthritis severity with an equivalent pixel size of 2.7 µm. These high‐resolution features of destruction in the CIA models have not previously been available from any other conventional imaging modalities except histological light microscopy. However, thickening of the synovial membrane was not resolved in composite images by the SR refraction imaging method. In conclusion, in vivo SR X‐ray microscopic imaging may have potential as a diagnostic tool in small animals that does not require a histochemical preparation stage in examining microstructural changes in joints affected with arthritis. The findings from the SR images are comparable with standard histopathology findings.     

Design of an ultrahigh‐energy‐resolution and wide‐energy‐range soft X‐ray beamline

A new ultrahigh‐energy‐resolution and wide‐energy‐range soft X‐ray beamline has been designed and is under construction at the Shanghai Synchrotron Radiation Facility. The beamline has two branches: one dedicated to angle‐resolved photoemission spectroscopy (ARPES) and the other to photoelectron emission microscopy (PEEM). The two branches share the same plane‐grating monochromator, which is equipped with four variable‐line‐spacing gratings and covers the 20–2000 eV energy range. Two elliptically polarized undulators are employed to provide photons with variable polarization, linear in every inclination and circular. The expected energy resolution is approximately 10 meV at 1000 eV with a flux of more than 3 × 10¹⁰ photons s^?1 at the ARPES sample positions. The refocusing of both branches is based on Kirkpatrick–Baez pairs. The expected spot sizes when using a 10 µm exit slit are 15 µm × 5 µm (horizontal × vertical FWHM) at the ARPES station and 10 µm × 5 µm (horizontal × vertical FWHM) at the PEEM station. The use of plane optical elements upstream of the exit slit, a variable‐line‐spacing grating and a pre‐mirror in the monochromator that allows the influence of the thermal deformation to be eliminated are essential for achieving the ultrahigh‐energy resolution.     

In‐line Bragg magnifier based on V‐shaped germanium crystals

In this work an X‐ray imaging system based on a recently developed in‐line two‐dimensional Bragg magnifier composed of two monolithic V‐shaped crystals made of dislocation‐free germanium is presented. The channel‐cut crystals were used in one‐dimensional and in two‐dimensional (crossed) configurations in imaging applications and allowed measurement of phase‐contrast radiograms both in the edge‐enhanced and in the holographic regimes. The measurement of the phase gradient in two orthogonal directions is demonstrated. The effective pixel size attained was 0.17 µm in the one‐dimensional configuration and 0.5 µm in the two‐dimensional setting, offering a twofold improvement in spatial resolution over devices based on silicon. These results show the potential for applying Bragg magnifiers to imaging soft matter at high resolution with reduced dose owing to the higher efficiency of Ge compared with Si.     

A feasibility study of X‐ray phase‐contrast mammographic tomography at the Imaging and Medical beamline of the Australian Synchrotron

Results are presented of a recent experiment at the Imaging and Medical beamline of the Australian Synchrotron intended to contribute to the implementation of low‐dose high‐sensitivity three‐dimensional mammographic phase‐contrast imaging, initially at synchrotrons and subsequently in hospitals and medical imaging clinics. The effect of such imaging parameters as X‐ray energy, source size, detector resolution, sample‐to‐detector distance, scanning and data processing strategies in the case of propagation‐based phase‐contrast computed tomography (CT) have been tested, quantified, evaluated and optimized using a plastic phantom simulating relevant breast‐tissue characteristics. Analysis of the data collected using a Hamamatsu CMOS Flat Panel Sensor, with a pixel size of 100 µm, revealed the presence of propagation‐based phase contrast and demonstrated significant improvement of the quality of phase‐contrast CT imaging compared with conventional (absorption‐based) CT, at medically acceptable radiation doses.     

Capabilities of through‐the‐substrate microdiffraction: application of Patterson‐function direct methods to synchrotron data from polished thin sections

Some theoretical and practical aspects of the application of transmission microdiffraction (µXRD) to thin sections (≤30 µm thickness) of samples fixed or deposited on substrates are discussed. The principal characteristic of this technique is that the analysed micro‐sized region of the thin section is illuminated through the substrate (tts‐µXRD). Fields that can benefit from this are mineralogy, petrology and materials sciences since they often require in situ lateral studies to follow the evolution of crystalline phases or to determine new crystal structures in the case of phase transitions. The capability of tts‐µXRD for performing structural studies with synchrotron radiation is shown by two examples. The first example is a test case in which tts‐µXRD intensity data of pure aerinite are processed using Patterson‐function direct methods to directly solve the crystal structure. In the second example, tts‐µXRD is used to study the transformation of laumonite into a new aluminosilicate for which a crystal structure model is proposed.     

A high‐spatial‐resolution three‐dimensional detector array for 30–200 keV X‐rays based on structured scintillators

A three‐dimensional X‐ray detector for imaging 30–200 keV photons is described. It comprises a set of semi‐transparent structured scintillators, where each scintillator is a regular array of waveguides in silicon, and with pores filled with CsI. The performance of the detector is described theoretically and explored in detail through simulations. Based on available hardware, a spatial resolution of 1 µm is obtainable. The resolution of a single screen is shown to be determined only by the pitch, at least up to 100 keV. In comparison with conventional homogeneous screens, an improvement in efficiency by a factor of 5–15 is obtainable. The cross‐talk between screens in the three‐dimensional detector is shown to be negligible. The three‐dimensional concept enables ray‐tracing and super‐resolution algorithms to be applied.     

Depth‐selective elemental imaging of microSD card by confocal micro XRF analysis

A semiconductor device, a microSD card, was measured by using two XRF instruments. 2D elemental images were obtained using a micro‐XRF system with a spatial resolution of 10 µm. Elemental distributions of the near‐surface region of the sample were clearly shown. Titanium was observed in the resin constituting the sample. Nickel and gold were observed on a terminal and localization of the sample. Elemental distribution of copper reflected the circuit structure of the measurement area that was in the neighborhood of the sample surface. Moreover, the elemental depth distributions of the sample were measured by using a confocal micro‐XRF instrument. The confocal micro‐XRF instrument was constructed in the laboratory with fine‐focus polycapillary x‐ray optics. The depth resolution of the developed spectrometer was 13.7 µm at an energy of Au Lβ (11.4 keV). The elemental images obtained at near‐surface by confocal micro‐XRF were the same as the results obtained from 2D micro‐XRF. However, different Cu images were obtained at a depth of several tens of micrometers. This indicates that microSD cards consist of a few different Cu‐circuit structure designs. The elemental depth distributions of each circuit structure of the semiconductor device were clearly shown by confocal micro‐XRF. Copyright © 2013 John Wiley & Sons, Ltd.     

Potential of propagation‐based synchrotron X‐ray phase‐contrast computed tomography for cardiac tissue engineering

Hydrogel‐based cardiac tissue engineering offers great promise for myocardial infarction repair. The ability to visualize engineered systems in vivo in animal models is desired to monitor the performance of cardiac constructs. However, due to the low density and weak X‐ray attenuation of hydrogels, conventional radiography and micro‐computed tomography are unable to visualize the hydrogel cardiac constructs upon their implantation, thus limiting their use in animal systems. This paper presents a study on the optimization of synchrotron X‐ray propagation‐based phase‐contrast imaging computed tomography (PCI‐CT) for three‐dimensional (3D) visualization and assessment of the hydrogel cardiac patches. First, alginate hydrogel was 3D‐printed into cardiac patches, with the pores filled by fibrin. The hydrogel patches were then surgically implanted on rat hearts. A week after surgery, the hearts including patches were excised and embedded in a soft‐tissue‐mimicking gel for imaging by using PCI‐CT at an X‐ray energy of 25 keV. During imaging, the sample‐to‐detector distances, CT‐scan time and the region of interest (ROI) were varied and examined for their effects on both imaging quality and radiation dose. The results showed that phase‐retrieved PCI‐CT images provided edge‐enhancement fringes at a sample‐to‐detector distance of 147 cm that enabled visualization of anatomical and microstructural features of the myocardium and the implanted patch in the tissue‐mimicking gel. For visualization of these features, PCI‐CT offered a significantly higher performance than the dual absorption‐phase and clinical magnetic resonance (3 T) imaging techniques. Furthermore, by reducing the total CT‐scan time and ROI, PCI‐CT was examined for lowering the effective dose, meanwhile without much loss of imaging quality. In effect, the higher soft tissue contrast and low‐dose potential of PCI‐CT has been used along with an acceptable overall animal dose to achieve the high spatial resolution needed for cardiac implant visualization. As a result, PCI‐CT at the identified imaging parameters offers great potential for 3D assessment of microstructural features of hydrogel cardiac patches.     

On the use of clessidra prism arrays in long‐focal‐length X‐ray focusing

Clessidra (hour‐glass) X‐ray lenses have an overall shape of an old hour glass, in which two opposing larger triangular prisms are formed of smaller identical prisms or prism‐like objects. In these lenses, absorbing and otherwise optically inactive material was removed with a material‐removal strategy similar to that used by Fresnel in the lighthouse lens construction. It is verified that when the single prism rows are incoherently illuminated they can be operated as independent micro‐lenses with coinciding image positions for efficient X‐ray beam concentration. Experimental data for the line width and the refraction efficiency in one‐dimensional focusing are consistent with the expectations. Imperfections in the structures produced by state‐of‐the‐art deep X‐ray lithography directed only 35% of the incident intensity away from the image and widened it by just 10% to 125 µm. An array of micro‐lenses with easily feasible prism sizes is proposed as an efficient retrofit for the refocusing optics in an existing beamline, where it would provide seven‐fold flux enhancement.