This PDF file contains the front matter associated with SPIE Proceedings Volume 9967, including the Title Page, Copyright information, Table of Contents, and Conference Committee listing.

Nine Developments in X-ray Tomography conferences have been held previously, and this paper summarizes data from these conference proceedings. The Developments conference provides snapshots of the x-ray tomography field which spans clinical and biological applications, engineering and industrial studies and physical sciences.

X-ray imaging in absorption contrast mode is well established for hard tissue visualization. However, performance for lower density materials is limited due to a reduced contrast. Our aim is three-dimensional (3D) characterization of micro-morphology of human brain tissues down to (sub-)cellular resolution within a laboratory environment. Using the laboratory-based microtomography (μCT) system nanotom m (GE Sensing and Inspection Technologies GmbH, Wunstorf, Germany) and synchrotron radiation at the Diamond-Manchester Imaging Branchline I13-2 (Diamond Light Source, Didcot, UK), we have acquired 3D data with a resolution down to 0.45 μm for visualization of a human cerebellum specimen down to cellular level. We have shown that all selected modalities, namely laboratory-based absorption contrast micro-tomography (LBμCT), synchrotron radiation based in-line single distance phase contrast tomography (SDPR) and synchrotron radiation based single-grating interferometry (GI), can reach cellular resolution for tissue samples with a size in the mm-range. The results are discussed qualitatively in comparison to optical microscopy of haematoxylin and eosin (HE) stained sections. As phase contrast yields to a better data quality for soft tissues and in order to overcome restrictions of limited beamline access for phase contrast measurements, we have equipped the μCT system nanotom m with a double-grating phase contrast set-up. Preliminary experimental results of a knee sample consisting of a bony part and a cartilage demonstrate that phase contrast data exhibits better quality compared to absorption contrast. Currently, the set-up is under adjustment. It is expected that cellular resolution would also be achieved. The questions arise (1) what would be the quality gain of laboratory-based phase contrast in comparison to laboratory-based absorption contrast tomography and (2) could laboratory-based phase contrast data provide comparable results to synchrotron radiation based phase contrast data.

Magnesium(Mg)-alloys are promising candidates as temporary implants for orthopedic and cranio-facial applications. They can sustain tissues during healing, thanks to favorable mechanical properties, and then they slowly degrade into biocompatible products, avoiding the need of a second surgery for implant removal. They have the potential to benefit a vast number of patients, especially children and elderly patients. However, to be able to tailor their degradation to match the speed of tissue regeneration it is crucial to understand how they actually degrade in the living organism. We utilized high-resolution synchrotron-based tomography at the beamline P05 operated by HZG at the storage ring PETRA III at DESY to study the degradation of 3 novel Mg-alloys in rat bone and the consequent bone response. On threedimensional reconstructions of the bone-implant explants we were able to follow the dynamic transformation that the materials underwent at different healing times and on the basis of absorption coefficients we could distinguish and quantify the amount of remaining implants, the corrosion layers and the new bone. This was a great advantage compared to laboratory CT, for which the limitation in contrast and in resolution made impossible to discriminate between original alloy, degradation products and bone, leading to inaccurate determination of the materials degradation rates. The same samples imaged by tomography were used for non-decalcified histology. The combination of histological and tomographical images provided new insight on the nature of the bone-to-implant interface and of the degradation products, which appeared to have great similarities to the host bone.

The application of x-ray phase contrast computed tomography (PCT) to the field of tissue engineering is dis- cussed. Specific focus is on the edge illumination PCT method, which can be adapted to weakly coherent x-ray sources, permitting PCT imaging in standard (non-synchrotron) laboratory environments. The method was applied to a prominent research topic in tissue engineering, namely the development of effective and reliable decellularization protocols to derive scaffolds from native tissue. Results show that edge illumination PCT provides sufficient image quality to evaluate the microstructural integrity of scaffolds and, thus, to assess the performance of the used decellularization technique. In order to highlight that edge illumination PCT can ultimately comply with demands on a high specimen throughput and low doses of radiation, recently developed strategies for scan time and dose reduction are discussed.

Phase-contrast micro-tomography using synchrotron radiation has yielded superior soft tissue visualization down to the sub-cellular level. The isotropic spatial resolution down to about one micron is comparable to the one of histology. The methods, however, provide different physical quantities and are thus complementary, also allowing for the extension of histology into the third dimension. To prepare for cross-sectional animal studies on epilepsy, we have standardized the specimen’s preparation and scanning procedure for mouse brains, so that subsequent histology remains entirely unaffected and scanning of all samples (n = 28) is possible in a realistic time frame. For that, we have scanned five healthy and epileptic mouse brains at the ID19 beamline, ESRF, Grenoble, France, using grating- and propagation-based phase contrast micro-tomography. The resulting datasets clearly show the cortex, ventricular system, thalamus, hypothalamus, and hippocampus. Our focus is on the latter, having planned kainate-induced epilepsy experiments. The cell density and organization in the dentate gyrus and Ammon’s horn region were clearly visualized in control animals. This proof of principle was required to initiate experiment. The resulting three-dimensional data have been correlated to histology. The goal is a brain-wide quantification of cell death or structural reorganization associated with epilepsy as opposed to histology alone that represents small volumes of the total brain only. Thus, the proposed technique bears the potential to correlate the gold standard in analysis with independently obtained data sets. Such an achievement also fuels interest for other groups in neuroscience research to closely collaborate with experts in phase micro-tomography.

Beam hardening artefacts arise in tomography and microtomography with polychromatic sources. Typically, specimens appear to be less dense in the center of reconstructions because as the path length through the specimen increases, so the X-ray spectrum is shifted towards higher energies due to the preferential absorption of low energy photons. Various approaches have been taken to reduce or correct for these artefacts. Pre-filtering the X-ray beam with a thin metal sheet will reduce soft energy X-rays and thus narrow the spectrum. Correction curves can be applied to the projections prior to reconstruction which transform measured attenuation with polychromatic radiation to predicted attenuation with monochromatic radiation. These correction curves can be manually selected, iteratively derived from reconstructions (this generally works where density is assumed to be constant) or derived from a priori information about the X-ray spectrum and specimen composition. For hard tissue specimens, the latter approach works well if the composition is reasonably homogeneous. In the case of an immersed or embedded specimen (e.g., tooth or bone) the relative proportions of mineral and “organic” (including medium and plastic container) species varies considerably for different ray paths and simple beam hardening correction does not give accurate results. By performing an initial reconstruction, the total path length through the container can be determined. By modelling the X-ray properties of the specimen, a 2D correction transform can then be created such that the predicted monochromatic attenuation can be derived as a function of both the measured polychromatic attenuation and the container path length.

Registration of microscope images to Computed Tomography (CT) 3D volumes is a challenging task because it requires not only multi-modal similarity measure but also 2D-3D or slice-to-volume correspondence. This type of registration is usually done manually which is very time-consuming and prone to errors. Recently we have developed the first automatic approach to localize histological sections in μCT data of a jaw bone. The median distance between the automatically found slices and the ground truth was below 35 μm. Here we explore the limitations of the method by applying it to three tomography datasets acquired with grating interferometry, laboratory-based μCT and single-distance phase retrieval. Moreover, we compare the performance of three feature detectors in the proposed framework, i.e. Speeded Up Robust Features (SURF), Scale Invariant Feature Transform (SIFT) and Affine SIFT (ASIFT). Our results show that all the feature detectors performed significantly better on the grating interferometry dataset than on other modalities. The median accuracy for the vertical position was 0.06 mm. Across the feature detector types the smallest error was achieved by the SURF-based feature detector (0.29 mm). Furthermore, the SURF-based method was computationally the most efficient. Thus, we recommend to use the SURF feature detector for the proposed framework.

X-ray phase contrast imaging is an important mode due to its sensitivity to subtle features of soft biological tissues. Grating-based differential phase contrast (DPC) imaging is one of the most promising phase imaging techniques because it works with a normal x-ray tube of a large focal spot at a high flux rate. However, a main obstacle before this paradigm shift is the fabrication of large-area gratings of a small period and a high aspect ratio. Imaging large objects with a size-limited grating results in data truncation which is a new type of the interior problem. While the interior problem was solved for conventional x-ray CT through analytic extension, compressed sensing and iterative reconstruction, the difficulty for interior reconstruction from DPC data lies in that the implementation of the system matrix requires the differential operation on the detector array, which is often inaccurate and unstable in the case of noisy data. Here, we propose an iterative method based on spline functions. The differential data are first back-projected to the image space. Then, a system matrix is calculated whose components are the Hilbert transforms of the spline bases. The system matrix takes the whole image as an input and outputs the back-projected interior data. Prior information normally assumed for compressed sensing is enforced to iteratively solve this inverse problem. Our results demonstrate that the proposed algorithm can successfully reconstruct an interior region of interest (ROI) from the differential phase data through the ROI.

Early atherosclerosis changes perfusion of the arterial wall due to localized proliferation of the vasa vasorum. When contrast agent passes through the artery, some enters the vasa vasorum and increases radiopacity of the arterial wall. Technical challenges to detecting changes in vasa vasorum density include the thin arterial wall, partial volume averaging at the arterial lumen/wall interface and calcification within the wall. We used a photon-counting spectral CT scanner to study carotid arteries of anesthetized pigs and micro-CT of these arteries to quantify vasa vasorum density. The left carotid artery wall was injected with autologous blood to stimulate vasa vasorum angiogenesis. The scans were performed at 25-120 keV; the tube-current-time product was 550 mAs. A 60 mL bolus of iodine contrast agent was injected into the femoral vein at 5mL/s. Two seconds post injection, an axial scan was acquired at every 3 s over 60 s (i.e., 20 time points). Each time point acquired 28 contiguous transaxial slices with reconstructed voxels 0.16 x 0.16 x 1 mm3. Regions-of-interest in the outer 2/3 of the arterial wall and in the middle 2/3 of the lumen were drawn and their enhancements plotted versus time. Lumenal CT values peaked several seconds after injection and then returned towards baseline. Arterial wall CT values peaked concurrent to the lumen. The peak arterial wall enhancement in the left carotid arterial wall correlated with increased vasa vasorum density observed in micro-CT images of the isolated arteries.

Fracture of nickel-titanium (NiTi) endodontic files is an uncommon but potentially damaging occurrence during root canal preparation. If the broken portion of the file remains inside the tooth canal it can prevent complete preparation of the root canal with consequent negative impact on treatment outcomes. Removal of file fragment from the tooth canal is currently a mechanical process, which due to the limited working space and restricted view can lead to further problems including perforation of the tooth. Electrochemical dissolution is a relatively new method proposed to dissolve a fractured instrument, fully or partially within the canal, to enable its removal. In this article we explore the effects of electrochemical dissolution on the root canal environment using high contrast time delay integration (TDI) X-ray micro-tomography (XMT) designed specifically for dental research.

Forensic anthropologists are routinely asked to estimate a biological profile (i.e., age, sex, ancestry and stature) from a set of unidentified remains. In contrast to the abundance of collections and techniques associated with adult skeletons, there is a paucity of modern, documented subadult skeletal material, which limits the creation and validation of appropriate forensic standards. Many are forced to use antiquated methods derived from small sample sizes, which given documented secular changes in the growth and development of children, are not appropriate for application in the medico-legal setting. Therefore, the aim of this project is to use multi-slice computed tomography (MSCT) data from a large, diverse sample of modern subadults to develop new methods to estimate subadult age and sex for practical forensic applications. The research sample will consist of over 1,500 full-body MSCT scans of modern subadult individuals (aged birth to 20 years) obtained from two U.S. medical examiner’s offices. Statistical analysis of epiphyseal union scores, long bone osteometrics, and os coxae landmark data will be used to develop modern subadult age and sex estimation standards. This project will result in a database of information gathered from the MSCT scans, as well as the creation of modern, statistically rigorous standards for skeletal age and sex estimation in subadults. Furthermore, the research and methods developed in this project will be applicable to dry bone specimens, MSCT scans, and radiographic images, thus providing both tools and continued access to data for forensic practitioners in a variety of settings.

Rapid development of the X-ray phonon-counting detection technology brings tremendous research and application opportunities. In addition to improvements in conventional X-ray imaging performance such as radiation dose utilization and beam hardening correction, photon-counting detectors allows significantly more efficient X-ray fluorescence (XRF) and K-edge imaging, and promises a great potential of X-ray functional, cellular and molecular imaging. XRF is the characteristic emission of secondary X-ray photons from a material excited by initial X-rays. The phenomenon is widely used for chemical and elemental analysis. K-edge imaging identifies a material based on its chemically-specific absorption discontinuity over X-ray photon energy. In this paper, we try to combine XRF and K-edge signals from the contrast agents (e.g., iodine, gadolinium, gold nanoparticles) to simultaneously realize XFCT and K-edge CT imaging for superior image performance. As a prerequisite for this dual-modality imaging, the accurate energy calibration of multi-energy-bin photon-counting detectors is critically important. With the measured XRF data of different materials, we characterize the energy response function of a CZT detector for energy calibration and spectrum reconstruction, which can effectively improve the energy resolution and decrease the inconsistence of the photon counting detectors. Then, a simultaneous K-edge and X-ray fluorescence CT imaging (SKYFI) experimental setup is designed which includes a cone-beam X-ray tube, two separate photon counting detector arrays, a pin-hole collimator and a rotation stage. With a phantom containing gold nanoparticles the two types of XFCT and K-edge CT datasets are collected simultaneously. Then, XFCT and K-edge CT images are synergistically reconstructed in a same framework. Simulation results are presented and quantitative analyzed and compared with the separate XFCT and K-edge CT results.

Scattered x-radiation can be used for computed tomographic reconstruction of the distribution of crystallographic phases within the interior of specimens, and diffraction patterns can be measured for each volume element (voxel) within a reconstructed slice. This modality has been applied to systems as diverse as mineralized tissues and inorganic composites. Use of high energy x-rays (E < 40 keV) offers advantages including the ability to study volumes deep with specimens and to sample large ranges of reciprocal space, i.e., many reflections. The bases of diffraction tomography are reviewed, and the power of the technique is illustrated by the results obtained for specimens containing: a) different materials (SiC/Al composite), b) different polytypes (calcite/aragonite in a bivalve attachment system); c) mixtures of nanocrystalline and amorphous phases; d) a single phase, but volumes with different lattice parameters (hydroxyapatite, hAp, the mineral in bone and tooth); e) a single phase containing a spatial distribution of crystallographic texture (bone); a single phase with a spatial distribution of strains produced by in situ loading (bone). Finally, challenges and future directions are discussed.

A new Transmission X-ray Microscope (TXM), optimized for in-situ nano-tomography experiments, has been designed and built at the Advanced Photon Source (APS). The instrument has been in operation for the last two years and is supporting users over large fields of Science, from energy storage and material science to natural sciences. The flexibility of our X-ray microscope design permits evolutionary geometries and can accommodate relatively heavy, up to 5 kg, and bulky in-situ cells while ensuring high spatial resolution, which is expected to improve steadily thanks to the support of the RD program led by the APS-Upgrade project on Fresnel zone plates (FZP). The robust sample stack, designed with minimum degrees of freedom shows a stability better than 4 nm rms at the sample location. The TXM operates with optics fabricated in-house. A spatial resolution of 30 nm per voxel has been demonstrated when the microscope operates with a 60 nm outermost zone width FZP with a measured efficiency of 18% at 8 keV. 20 nm FZP are also currently available and should be in routine use within the next few months once a new matching condenser is produced. In parallel, efficiency is being improved with opto-mechanical engineering (FZP stacking system) and software developments (more efficient reconstruction algorithms combined with different data acquisition schemes), enabling 3D dynamic studies when sample evolution occurs within a couple of tens of seconds.

Recently, we introduced a nano Computed Tomography (nano-CT) system based on a customized JEOL scanning electron microscope applying the principle of shadow microscopy and yielding a spatial resolution of approximately 3000lp/mm. The system has been upgraded and now comprises a photon counting PIXIRAD-2 detector as well as a customized nano-positioning stage for object and electron target. The latter is a tungsten needle with a tip radius of 100nm produced by electrochemical etching. Here we present for the first time nano-CT volume images of microstructures within an AlCu29 sample recorded by the upgraded system (XRM-II). The quality of the iteratively reconstructed and regularized volumes is assessed by means of detail visibility and line spread. We found the spatial resolution to be at least 300nm. The image processing chain, in particular geometric misalignment correction is of critical importance for a successful nano-CT measurement with the XRM-II.

Cell visualization and counting plays a crucial role in biological and medical research including the study of neurodegenerative diseases. The neuronal cell loss is typically determined to measure the extent of the disease. Its characterization is challenging because the cell density and size already differs by more than three orders of magnitude in a healthy cerebellum. Cell visualization is commonly performed by histology and fluorescence microscopy. These techniques are limited to resolve complex microstructures in the third dimension. Phase- contrast tomography has been proven to provide sufficient contrast in the three-dimensional imaging of soft tissue down to the cell level and, therefore, offers the basis for the three-dimensional segmentation. Within this context, a human cerebellum sample was embedded in paraffin and measured in local phase-contrast mode at the beamline ID19 (ESRF, Grenoble, France) and the Diamond Manchester Imaging Branchline I13-2 (Diamond Light Source, Didcot, UK). After the application of Frangi-based filtering the data showed sufficient contrast to automatically identify the Purkinje cells and to quantify their density to 177 cells per mm³ within the volume of interest. Moreover, brain layers were segmented in a region of interest based on edge detection. Subsequently performed histological analysis validated the presence of the cells, which required a mapping from the two- dimensional histological slices to the three-dimensional tomogram. The methodology can also be applied to further tissue types and shows potential for the computational tissue analysis in health and disease.

The spatio-temporal distribution (4D) of water in porous materials plays a fundamental role in many natural and technological processes. The dynamics of water transport is strongly entangled with the material’s pore-scale structure. Understanding their correlation requires imaging simultaneously the 4D water distribution and the porous microstructure. To date, 4D images with high temporal and spatial resolution have been mainly acquired by attenuation-based X-ray micro-tomography, whereby pure water is substituted by saline solutions with high atomic number components to improve image contrast. The use of saline solutions is however not always desirable, as the altered fluid properties may affect the transport process as well or, as it is the case for hydrating cement-based materials, they may modify the chemical reactions and their kinetics. In this study, we aimed at visualizing pure water transport in porous building materials by a new implementation of fast Talbot interferometry-based multi-contrast X-ray micro-tomography at the P07 beamline of the Helmholtz-Zentrum Geesthacht at DESY. We report results from a mortar specimen imaged at three different stages during evaporative drying. We show the possibility of visualizing simultaneously the microstructure and the pore-scale water redistribution by the phase contrast images. In addition, different solid material phases are clearly distinguished in these images. The higher contrast between water and the porous substrate, achievable in the phase contrast images, compared with the attenuation ones, empowers new analysis and allows investigating the correlation between the drying process and the porous microstructure. The approach offers the possibility of studying other chemically inert or reactive water transport processes without any chemical or physical perturbation of the processes themselves.

Following the principles of “morphology reveals biomechanics”, the anatomical structure of the cartilage-osseous interface and the supporting trabecular network show defined adaptation in their architectural properties to physiological loading. In case of a faulty relationship, the ability to support the load diminishes and the onset of osteoarthritis (OA) may arise and disturb the balanced formation and resorption processes. To describe and quantify the changes occurring, 10 human OA patellae were analysed concerning the architectural parameters of the trabecular network within the first five mms by the evaluation of 3Dmicro-CT datasets. The analysed OA-samples showed a strong irregularity for all trabecular parameters across the trabecular network, no regularity in parameter distribution was found. In general, we saw a decrease of material in the OA population as BV/TV, BS/TV, Tb.N and Tb.Th were decreased and the spacing increased. The development into depth showed a logarithmic dependency, which revealed the greatest difference for all parameters within the first mm in comparison to the physiologic samples. The differences decreased towards the 5th mm. The interpretation of the mathematic dependency leads to the conclusion that the main impact of OA is beneath the subchondral bone plate (SBP) and lessens with depth. Next to the clear difference in material, the architectural arrangement is more rod-like and isotropic just beneath the SBP in comparison to the plate-like and more anisotropic physiological arrangement.

The structure of chocolate, a multicomponent food product, was analyzed using microtomography. Chocolate consists of a semi-solid cocoa butter matrix and a dense network of suspended particles. A detailed analysis of the microstructure is needed to understand mass transport phenomena. Transport of lipids from e.g. a filling or liquid cocoa butter is responsible for major problems in the confectionery industry such as formation of chocolate bloom, which is the formation of visible white spots or a grayish haze on the chocolate surface and leads to consumer rejections and thus large sales losses for the confectionery industry. In this study it was possible to visualize the inner structure of chocolate and clearly distinguish the particles from the continuous phase by taking advantage of the high density contrast of synchrotron radiation. Consequently, particle arrangement and cracks within the sample were made visible. The cracks are several micrometers thick and propagate throughout the entire sample. Images of pure cocoa butter, chocolate without any particles, did not show any cracks and thus confirmed that cracks are a result of embedded particles. They arise during the manufacturing process. Thus, the solidification process, a critical manufacturing step, was simulated with finite element methods in order to understand crack formation during this step. The simulation showed that cracks arise because of significant contraction of cocoa butter, the matrix phase, without any major change of volume of the suspended particles. Tempering of the chocolate mass prior to solidification is another critical step for a good product quality. We found that samples which solidified in an uncontrolled manner are less homogeneous than tempered samples. In summary, our study visualized for the first time the inner microstructure of tempered and untempered cocoa butter as well as chocolate without sample destruction and revealed cracks, which might act as transport pathways.

Heart disease is the number one cause of death worldwide. To improve therapy and patient outcome, the knowledge of anatomical changes in terms of lumen morphology and tissue composition of constricted arteries is crucial for designing a localized drug delivery to treat atherosclerosis disease. Traditional tissue characterization by histology is a pivotal tool, although it brings disadvantages such as vessel morphology modification during decalcification and slicing. X-ray tomography in absorption and phase contrast modes yields a deep understanding in blood vessel anatomy in healthy and diseased stages: measurements in absorption mode make visible highly absorbing tissue components including cholesterol plaques, whereas phase contrast tomography gains better contrast of the soft tissue components such as vessel walls. Established synchrotron radiation-based micro-CT techniques ensure high performance in terms of 3D visualization of highly absorbing and soft tissues.

An entire human head obtained at autopsy was micro-CT scanned in a nano/micro-CT scanner in a 6-hour long session. Despite the size of the head, it could still be scanned with a pixel size of 70 μm. The aim of this study was to obtain an optimal quality 3D data-set to be used as baseline control in a larger study comparing the image quality of various cone beam CT systems currently used in dentistry. The image quality of the micro-CT scans was indeed better than the ones of the clinical imaging modalities, both with regard to noise and streak artifacts due to metal dental implants. Bony features in the jaws, like the trabecular architecture and the thin wall of the alveolar bone were clearly visible. Therefore, the 3D micro-CT data-set can be used as the gold standard for linear, angular, and volumetric measurements of anatomical features in and around the oral cavity when comparing clinical imaging modalities.

Micro computed tomography (mCT) is well established in virtually all fields of biomedical research, allowing for the non-destructive volumetric visualization of tissue morphology. A variety of specimens can be investigated, ranging from soft to hard tissue to engineered structures like scaffolds. Similarly, the size of the objects of interest ranges from a fraction of a millimeter to several tens of centimeters. While synchrotron radiation-based μCT still offers unrivaled data quality, the ever-improving technology of cathodic tube-based machines offers a valuable and more accessible alternative. The Biomaterials Science Center of the University of Basel operates a nanotomOR m (phoenix|x-ray, GE Sensing and Inspection Technologies GmbH, Wunstorf, Germany), with a 180 kV source and a minimal spot size of about 0.9 μm. Through the adjustable focus-specimen and focus-detector distances, the effective pixel size can be adjusted from below 500 nm to about 80 μm. On the high-resolution side, it is for example possible to visualize the tubular network in sub-millimeter thin dentin specimens. It is then possible to locally extract parameters such as tubule diameter, density, or alignment, giving information on cell movements during tooth formation. On the other side, with a horizontal shift of the 3,072 pixels x 2,400 pixels detector, specimens up to 35 cm in diameter can be scanned. It is possible, for example, to scan an entire human knee, albeit with inferior resolution. Lab source μCT machines are thus a powerful and flexible tool for the advancement of biomedical research, and a valuable and more accessible alternative to synchrotron radiation facilities.

Among the clinically relevant imaging techniques, computed tomography (CT) reaches the best spatial resolution. Sub-millimeter voxel sizes are regularly obtained. For investigations on true micrometer level lab-based μCT has become gold standard. The aim of the present study is the hierarchical investigation of a human knee post mortem using hard X-ray μCT. After the visualization of the entire knee using a clinical CT with a spatial resolution on the sub-millimeter range, a hierarchical imaging study was performed using a laboratory μCT system nanotom m. Due to the size of the whole knee the pixel length could not be reduced below 65 μm. These first two data sets were directly compared after a rigid registration using a cross-correlation algorithm. The μCT data set allowed an investigation of the trabecular structures of the bones. The further reduction of the pixel length down to 25 μm could be achieved by removing the skin and soft tissues and measuring the tibia and the femur separately. True micrometer resolution could be achieved after extracting cylinders of several millimeters diameters from the two bones. The high resolution scans revealed the mineralized cartilage zone including the tide mark line as well as individual calcified chondrocytes. The visualization of soft tissues including cartilage, was arranged by X-ray grating interferometry (XGI) at ESRF and Diamond Light Source. Whereas the high-energy measurements at ESRF allowed the simultaneous visualization of soft and hard tissues, the low-energy results from Diamond Light Source made individual chondrocytes within the cartilage visual.

Dental caries, one of the most prevalent infectious bacterial diseases in the world, is caused by specific types of acid-producing bacteria. Caries is a disease continuum resulting from the earliest loss of ions from apatite crystals through gross cavitation. Enamel dissolution starts when the pH-value drops below 5.5. Neutralizing the pH-value in the oral cavity opposes the process of demineralization, and so caries lesions occur in a dynamic cyclic de-mineralizing/remineralizing environment. Unfortunately, biomimetic regeneration of cavitated enamel is not yet possible, although remineralization of small carious lesions occurs under optimal conditions. Therefore, the development of methods that can regenerate carious lesions, and subsequently recover and retain teeth, is highly desirable. For the present proceedings we analyzed one naturally occurring sub-surface and one artificially produced lesion. For the characterization of artificial and natural lesions micro computed tomography is the method of choice when looking to determine three-dimensional mineral distribution and to quantify the degree of mineralization. In this pilot study we elucidate that the de-mineralized enamel in natural and artificially induced lesions shows comparable X-ray attenuation behavior, thereby implying that the study protocol employed herein seems to be appropriate. Once we know that the lesions are comparable, a series of well-reproducible in vitro experiments on enamel regeneration could be performed. In order to quantify further lesion morphology, the anisotropy of the enamel’s nanostructure can be characterized by using spatially resolved, small-angle X-ray scattering. We wanted to demonstrate that the artificially induced defect fittingly resembles the natural carious lesion.

Assessing the three-dimensional architecture of neuronal tissues with sub-cellular resolution presents a significant analytical challenge. Overcoming the limitations associated with serial slicing, phase-contrast x-ray tomography has the potential to contribute to this goal. Even compact laboratory CT at an optimized liquid-metal jet micro- focus source combined with suitable phase-retrieval algorithms and preparation protocols can yield renderings with single cell sensitivity in millimeter sized brain areas of mouse. Here, we show the capabilities of the setup by imaging a Golgi-Cox impregnated mouse brain. Towards higher resolution we extend these studies at our recently upgraded waveguide-based cone-beam holo-tomography instrument GINIX at DESY. This setup allows high resolution recordings with adjustable field of view and resolution, down to the voxel sizes in the range of a few ten nanometers. The recent results make us confident that important issues of neuronal connectivity can be addressed by these methods, and that 3D (virtual) histology with nanoscale resolution will become an attractive modality for neuroscience research.

X-ray computed micro-tomography systems are able to collect data with sub-micron resolution. This high- resolution imaging has many applications but is particularly important in the study of porous materials, where the sub-micron structure can dictate large-scale physical properties (e.g. carbonates, shales, or human bone). Sample preparation and mounting become diffiult for these materials below 2mm diameter: consequently, a typical ultra-micro-CT reconstruction volume (with sub-micron resolution) will be around 3k x 3k x 10k voxels, with some reconstructions becoming much larger. In this paper, we discuss the hardware (MPI-parallel CPU/GPU) and software (python/C++/CUDA) tools used at the ANU CTlab to reconstruct ~186 GigaVoxel datasets.

A new micro-tomography system for materials science has been developed at BL20B2 in SPring-8. The system enables us to do stretching, press and twist of materials with a translation stage and two precise rotation stages arranged opposite to each other. Each deformation can be operated with constant moving rate. The maximum load is about 2 kN because of the hardness of the precision stages. The X-ray image detector consists of visible light conversion system and sCMOS camera. The effective pixel size is variable by changing a tandem lens between 2.7 μm/pixel to 13.2 μm /pixel discretely. As a demonstration of the system, a viscoelastic object was imaged. The experimental conditions are follows, X-ray energy: 25 keV, exposure time: 5 msec, number of projections: 900, single scan time: 7.5 sec, pixel size: 13.2 μm /pixel and field of view: 27.0 mm x 3.9 mm. The stretching rate was 1 μm /sec to 5 μm /sec. A metastable state such as tensile loading of viscoelastic materials is possible with this system.

Recent advances in X-ray imaging technologies have paved the way for use of energy-discriminating photon-counting detector arrays. These detectors show promise in clinical and preclinical applications. Multi-energy or spectral CT images can be visualized in multi-colors. Despite the advantages offered by the spectral dimension of acquired data, higher image resolution is still desirable, especially in challenging tasks such as on-site studies of resected pathological tissues. Here we propose to enhance image resolution of a spectral X-ray imaging system by partially blocking each detector element with an absorption grating (for reduced aperture), commonly used for Talbot-Lau interferometry. After acquiring X-ray data at an initial grating-detector configuration, the grating is shifted to expose previously blocked portions so that each measurement contains new information. All the acquired data are then combined into an augmented system matrix and subsequently reconstructed using an iterative algorithm. Our proof of concept simulations are performed with MCNP6.1 code and the experiment was performed using a Hamamatsu microfocus X-ray source, an absorption grating, and an Xray camera. Our results demonstrate that the gratings commonly used for x-ray phase-contrast imaging have a utility for super-resolution imaging performance.

Synchrotron microtomography typically uses monochromatic beams, because these avoid beam-hardening artifacts and allow imaging above and below the absorption edges of specific elements. However, the monochromator greatly reduces the flux on the sample, and thus increases the data collection time. An alternative is to eliminate the monochromator, instead using absorbers to remove low-energy x-rays and reflection from a mirror to remove high-energy x-rays. This produces a pink beam with a large energy bandwidth and more than 1000 times greater flux. This is useful for dynamic studies, where an entire 3-D dataset can be collected in just a few seconds. We have implemented pink beam tomography at the 13-BM-D beamline at the GeoSoilEnviroCARS sector 13 at the Advanced Photon Source. A key component of such a system is a high-speed detector that can collect over 100 frames/s with excellent signal/noise. We are using a new generation of inexpensive CMOS detectors with very low read noise, large full-well capacity, and high speed. The system performs well, and first experiments in studying fluid imbibition and drainage are presented.

X-ray tensor tomography is a promising imaging modality for probing the micro structure of a sample by reconstructing small-angle scattering densities in different scattering directions. However, the current x-ray grating technique still faces an obstacle when a divergent x-ray beam from a point x-ray source propagates through a large object and reaches large planar gratings. In this situation, tensor interior tomography is essential to perform the image reconstruction over a region of interest (ROI) in the object. Therefore, we propose interior tensor tomography with 2D gratings to extract dark field images isotropically. Our numerical results demonstrate that the proposed methods are promising for reconstruction of local images from truncated dark field projection data.

As one of the state-of-the-art detectors, photon counting detector is used in spectral CT to classify the received photons into several energy channels and generate multichannel projection simultaneously. However, the projection always contains severe noise due to the low counts in each energy channel. How to reconstruct high-quality images from photon counting detector based spectral CT is a challenging problem. It is widely accepted that there exists self-similarity over the spatial domain in a CT image. Moreover, because a multichannel CT image is obtained from the same object at different energy, images among channels are highly correlated. Motivated by these two characteristics of the spectral CT, we employ tensor decomposition and nonlocal means methods for spectral CT iterative reconstruction. Our method includes three basic steps. First, each channel image is updated by using the OS-SART. Second, small 3D volumetric patches (tensor) are extracted from the multichannel image, and higher-order singular value decomposition (HOSVD) is performed on each tensor, which can help to enhance the spatial sparsity and spectral correlation. Third, in order to employ the self-similarity in CT images, similar patches are grouped to reduce noise using the nonlocal means method. These three steps are repeated alternatively till the stopping criteria are met. The effectiveness of the developed algorithm is validated on both numerically simulated and realistic preclinical datasets. Our results show that the proposed method achieves promising performance in terms of noise reduction and fine structures preservation.

Achieving sub-micron resolution in lab-based micro-tomography is challenging due to the geometric instability of the imaging hardware (spot drift, stage precision, sample motion). These instabilities manifest themselves as a distortion or motion of the radiographs relative to the expected system geometry. When the hardware instabilities are small (several microns of absolute motion), the radiograph distortions are well approximated by shift and magnification of the image. In this paper we examine the use of re-projection alignment (RA) to estimate per-radiograph motions. Our simulation results evaluate how the convergence properties of RA vary with: motion-type (smooth versus random), trajectory (helical versus space-filling) and resolution. We demonstrate that RA convergence rate and accuracy, for the space-filling trajectory, is invariant with regard to the motion-type. In addition, for the space-filling trajectory, the per-projection motions can be estimated to less than 0.25 pixel mean absolute error by performing a single quarter-resolution RA iteration followed by a single half-resolution RA iteration. The direct impact is that, for the space-filling trajectory, we need only perform one RA iteration per resolution in our iterative multi-grid reconstruction (IMGR).We also give examples of the effectiveness of RA motion correction method applied to real double-helix and space-filling trajectory micro-CT data. For double-helix Katsevich filtered-back-projection reconstruction (≈2500x2500x5000 voxels), we use a multi-resolution RA method as a pre-processing step. For the space-filling iterative reconstruction (≈2000x2000x5400 voxels), RA is applied during the IMGR iterations.

This paper concerns iterative reconstruction for low-dose and few-view CT by minimizing a data-fidelity term regularized with the Total Variation (TV) penalty. We propose a very fast iterative algorithm to solve this problem. The algorithm derivation is outlined as follows. First, the original minimization problem is reformulated into the saddle point (primal-dual) problem by using the Lagrangian duality, to which we apply the first-order primal-dual iterative methods. Second, we precondition the iteration formula using the ramp filter of Filtered Backprojection (FBP) reconstruction algorithm in such a way that the problem solution is not altered. The resulting algorithm resembles the structure of so-called iterative FBP algorithm, and it converges to the exact minimizer of cost function very fast.

With the GPU computing becoming main-stream, iterative tomographic reconstruction (IR) is becoming a com- putationally viable alternative to traditional single-shot analytical methods such as filtered back-projection. IR liberates one from the continuous X-ray source trajectories required for analytical reconstruction. We present a family of novel X-ray source trajectories for large-angle CBCT. These discrete (sparsely sampled) trajectories optimally fill the space of possible source locations by maximising the degree of mutually independent information. They satisfy a discrete equivalent of Tuy’s sufficiency condition and allow high cone-angle (high-flux) tomog- raphy. The highly isotropic nature of the trajectory has several advantages: (1) The average source distance is approximately constant throughout the reconstruction volume, thus avoiding the differential-magnification artefacts that plague high cone-angle helical computed tomography; (2) Reduced streaking artifacts due to e.g. X-ray beam-hardening; (3) Misalignment and component motion manifests as blur in the tomogram rather than double-edges, which is easier to automatically correct; (4) An approximately shift-invariant point-spread-function which enables filtering as a pre-conditioner to speed IR convergence. We describe these space-filling trajectories and demonstrate their above-mentioned properties compared with a traditional helical trajectories.

X-ray phase contrast imaging provides greater contrast compared to conventional absorption contrast imaging. It has higher sensitivity in discriminating mass density difference in a sample. Therefore phase contrast imaging has broad applications in dynamic tomography in which signal-to-noise ratio is usually traded off to the desired temporal resolution. Single-distance propagation phase contrast tomography is the most popular approach at many synchrotron facilities. The simple and flexible setup facilitates complicated in situ experiments. There are few phase retrieval algorithms available for phase-contrast image data processing. All the algorithms rely on certain models. In this talk we present a phase retrieval algorithm for phase-contrast tomography that is suitable for large propagation distance under phase-attenuation duality assumption. The validity of the algorithm is proved with both simulated and experimental data. The reconstruction results with the new algorithm show improved accuracy compared to other model based algorithms. The framework of this algorithm may be extended to the scenario in which phase-attenuation assumption is not satisfied, therefore a general model-free phase retrieval approach for single-distance phase contrast tomography.

The Helmholtz-Zentrum Geesthacht, Germany, is operating the user experiments for microtomography at the beamlines P05 and P07 using synchrotron radiation produced in the storage ring PETRA III at DESY, Hamburg, Germany. In recent years the software pipeline, sample changing hardware for performing high throughput experiments were developed. In this talk the current status of the beamlines will be given. Furthermore, optimisation and automatisation of scanning techniques, will be presented. These are required to scan samples which are larger than the field of view defined by the X-ray beam. The integration into an optimized reconstruction pipeline will be shown.

With ever-increasing data rates due to stronger light sources and better detectors, X-ray imaging experiments conducted at synchrotron beamlines face bandwidth and processing limitations that inhibit efficient workflows and prevent real-time operations. We propose an experiment platform comprised of programmable hardware and optimized software to lift these limitations and make beamline setups future-proof. The hardware consists of an FPGA-based data acquisition system with custom logic for data pre-processing and a PCIe data connection for transmission of currently up to 6.6 GB/s. Moreover, the accompanying firmware supports pushing data directly into GPU memory using AMD’s DirectGMA technology without crossing system memory first. The GPUs are used to pre-process projection data and reconstruct final volumetric data with OpenCL faster than possible with CPUs alone. Besides, more efficient use of resources this enables a real-time preview of a reconstruction for early quality assessment of both experiment setup and the investigated sample. The entire system is designed in a modular way and allows swapping all components, e.g. replacing our custom FPGA camera with a commercial system but keep reconstructing data with GPUs. Moreover, every component is accessible using a low-level C library or using a high-level Python interface in order to integrate these components in any legacy environment.

In this article we discuss three different developments in Edge Illumination (EI) X-ray phase contrast imaging (XPCi), all ultimately aimed at optimising EI computed tomography (CT) for use in different environments, and for different applications. For the purpose of reducing scan times, two approaches are presented; the reverse projection" acquisition scheme which allows a continuous rotation of the sample, and the single image" retrieval algorithm, which requires only one frame for retrieval of the projected phase map. These are expected to lead to a substantial reduction of EI CT scan times, a prospect which is likely to promote the translation of EI into several applications, including clinical. The last development presented is the "modified local" phase retrieval. This retrieval algorithm is specifically designed to accurately retrieve sample properties (absorption, refraction, scattering) in cases where high-resolution scans are required in non-ideal environments. Experimental results, using both synchrotron radiation and laboratory sources, are shown for the various approaches.

Synchrotron X-ray imaging is constantly achieving higher spatial resolution. In the field of grating-based phase- contrast imaging, these developments allow to directly resolve the interference patterns created by a phase grating without need for a analyzer grating. In this study we analyzed the performance of a single-grating interferometer and compared it to a conventional double-grating interferometer. Based on simulations and measurements of a test phantom we evaluated the sensitivity, resolution and signal to noise ratios of different setup configurations.

We aim at resolving deca-nanometer features in microelectronic samples using a laboratory SEM-based X-ray tomography microscope. Such a system produces X-rays through the interaction between a focused SEM electron beam and a metallic target. The effective source size of the X-ray beam can be adjusted by varying the target material and geometry. For instance, the use of tungsten nanowires (few hundred nanometers of length) combined with a high electron beam current leads to an increased X-ray flux generated in a reduced volume, necessary for detecting interface details of the analyzed object. It improves resolution and signal-to-noise ratio (SNR), but is also sensitive to electron beam-target instabilities during the scan. To improve robustness, a FFT-based image correlation is integrated in the process through a closed-loop control scheme. It allows stabilizing the electron beam on the target and to preserve the X-ray flux intensity and alignment. Also, a state of the art high-resolution scientific-CMOS (sCMOS) X-ray detector was installed, allowing to reduce noise and to increase quantum efficiency. Results show that such numerical and equipment improvements lead to significant gains in spatial resolution, SNR and scanning time of the SEM-based tomography. It paves the way to routine, high resolution, 3D X-ray imaging in the laboratory.

BL13W, an X-ray imaging beamline has been built and opened to users since May 6, 2009. More than 70 user proposals per year are granted and implemented at the beamline, with about 500 user visits/year. Up to now, X-ray microtomography (XMCT) is the dominated method for BL13W user operation, more than 70% user experiments were carried out with XMCT, covering the research fields in material science, biomedicine, physics, environmental science, archaeology and paleontology. To meet the user requirements, micro-CT imaging methods based on a variety of contrast mechanisms, including absorption, phase contrast, X-ray fluorescence, have been developed. Algorithms and related software have been developed achieve the low dose and fast data collection. Quantitative analysis to the three dimensional CT images is highly emphasized and related software for 3D information extraction with high precision and high efficiency, has been developed. Three-dimensional structure evolution has been attracting more and more attention in many scientific research fields. Two-Hertz dynamic phase contrast CT based on monochromatic SR beam was established at SSRF. The limitation of fluorescence X-ray CT from practical applications is the data-collection efficiency. The ordered-subsets expectation maximization algorithm was inducted to improve practicability of X-ray fluorescence computed tomography (XFCT), greatly. A scheme for full field XFCT was also proposed.

Industrial Computed Tomography (CT) has recently gained a prominent role in the field of dimensional metrology as a powerful 3D coordinate measurement technique. Its main advantage is the ability of measuring both inner and outer features of geometrically complex workpieces without altering or damaging them. The settings with which CT data are acquired can contribute to the uncertainty of measurements; these settings are chosen by the users in an intuitive way, resulting in high variability of the measurement outcome. There is currently no available holistic model that can (1) describe the relationship between CT setup parameters and measurement uncertainty, or (2) determine the optimal parameters for a given measurement task. In this study, we propose an analytical method to optimize imaging parameters for multimaterial measurements. The proposed method takes as input information about the nominal workpiece geometry and material composition. For a given workpiece position and orientation, the optimal photon energy is calculated to maximize edge detectability and minimize image noise. Subsequently, tube voltage and prefilter are chosen to ensure that the generated X-ray spectrum is quasi-monochromatic around the optimal photon energy. Focal spot size is chosen to minimize resolution, while also avoiding blurring. Then, the corresponding tube power is evaluated as well as the tube current. Finally, integration time is minimized so that the gray values of air are still in the linear range of the detector. The presented method was implemented into a software application and validated through simulation of CT scans of multimaterial workpieces. Measurements with predicted parameters were found to be more accurate than those performed with parameters chosen by expert users.

We have launched a project to promote grating-based X-ray phase imaging/tomography extensively. Here, two main activities are presented for enabling dynamic, or four-dimensional, X-ray phase tomography and nanoscopic X-ray phase tomography by grating interferometry. For the former, while some demonstrations in this direction were performed with white synchrotron radiation, improvement in image quality by spectrum tuning is described. A preliminary result by a total reflection mirror is presented, and as a next step, preparation of a 10% bandpass filter by a multilayer mirror is reported. For the latter, X-ray microscopes available both at synchrotron radiation facilities and laboratories equipped with a Fresnel zone plate are combined with grating interferometry. Here, a preliminary result with a combination of a Lau interferometer and a laboratory-based X-ray microscope is presented.

Extruded styrenic foams are low density foams that are widely used for thermal insulation. It is difficult to precisely characterize the structure of the cells in low density foams by traditional cross-section viewing due to the frailty of the walls of the cells. X-ray computed tomography (CT) is a non-destructive, three dimensional structure characterization technique that has great potential for structure characterization of styrenic foams. Unfortunately the intrinsic artifacts of the data and the artifacts generated during image reconstruction are often comparable in size and shape to the thin walls of the foam, making robust and reliable analysis of cell sizes challenging. We explored three different image processing methods to clean up artifacts in the reconstructed images, thus allowing quantitative three dimensional determination of cell size in a low density styrenic foam. Three image processing approaches - an intensity based approach, an intensity variance based approach, and a machine learning based approach - are explored in this study, and the machine learning image feature classification method was shown to be the best. Individual cells are segmented within the images after the images were cleaned up using the three different methods and the cell sizes are measured and compared in the study. Although the collected data with the image analysis methods together did not yield enough measurements for a good statistic of the measurement of cell sizes, the problem can be resolved by measuring multiple samples or increasing imaging field of view.

The Advanced Light Source (ALS) is a third-generation synchrotron X-ray source that operates as a user facility with more than 40 beamlines hosting over 2000 users per year. Synchrotron sources like the ALS provide high quality X-ray beams, with flux that is several orders of magnitude higher than lab-based sources. This is particularly advantageous for dynamic applications because it allows for high-speed, high-resolution imaging and microscale tomography. The hard X-ray beamline 8.3.2 at the Advanced Light Source enables imaging of samples at high temperatures and pressures, with mechanical loading and other realistic conditions using environmental test cells. These test cells enable experimental observation of samples undergoing dynamic microstructural changes in-situ. We present recent instrumentation developments that allow for continuous tomography with scan rates approaching 1 Hz per 3D image. In addition, our use of iterative reconstruction techniques allows for improved image quality despite fewer images and low exposure times used during fast tomography compared to traditional Fourier reconstruction methods.

Many diseases trigger morphological changes in affected tissue. Today, classical histology is still the “gold standard” used to study and describe those changes. Classical histology, however, is time consuming and requires chemical tissue manipulations that can result in significant tissue distortions. It is sometimes difficult to separate tissue-processing artifacts from changes caused by the disease process. We show that synchrotron X-ray phase-contrast micro-computed tomography (micro-CT) can be used to examine non-embedded, hydrated tissue at a resolution comparable to that obtained with classical histology. The data analysis from stacks of reconstructed micro-CT images is more flexible and faster than when using the classical, physically embedded sections that are by necessity fixed in a particular orientation. We show that in a three-dimensional (3D) structure with meticulous structural details such as the cochlea and the kidney, micro-CT is more flexible, faster and more convenient for morphological studies and disease diagnoses.

Digital breast tomosynthesis (DBT) can provide quasi three-dimensional (3D) structural information using a sequence of projection views that are acquired at a small number of views over a limited angular range. Nevertheless, the quantitative accuracy of the image can be significantly compromised by severe artifacts and poor resolution in depth dimension resulting from the incomplete data. The purpose of this work is: (a) investigate a variety of boundary artifacts representing as the decline tendency of the attenuation coefficients which is caused by insufficient projection data; (b) employ the 3D breast surface information we proposed in this study into the simultaneous algebraic reconstruction technique (SART) for artifacts reduction. Numerical experiments demonstrated that such boundary artifacts could be suppressed with the proposed algorithm. Compared to SART without using prior information, a 9.57% decrease in root mean square error (RMSE) is achieved for the central 40 slices. Meanwhile, the spatial resolution of potential masses and micro calcifications (MCs) in the reconstructed image is relatively enhanced. The full-width at half maximum (FWHM) of the artifact spread function (ASF) for proposed algorithm and SART are 17.87 and 19.68, respectively.

This paper deals with tomographic image reconstruction under the situation where some of projection data bins are contaminated with abnormal data. Such situations occur in various instances of tomography. We propose a new reconstruction algorithm called the Fault-Tolerant reconstruction outlined as follows. The least-squares (L²- norm) error function || Ax- b||²₂ used in ordinary iterative reconstructions is sensitive to the existence of abnormal data. The proposed algorithm utilizes the L¹-norm error function || Ax- b||¹₁ instead of the L²-norm, and we develop a row-action-type iterative algorithm using the proximal splitting framework in convex optimization fields. We also propose an improved version of the L¹-norm reconstruction called the L¹-TV reconstruction, in which a weak Total Variation (TV) penalty is added to the cost function. Simulation results demonstrate that reconstructed images with the L²-norm were severely damaged by the effect of abnormal bins, whereas images with the L¹-norm and L¹-TV reconstructions were robust to the existence of abnormal bins.

Dual energy computed tomography (DECT) has significant impacts on material characterization, bone mineral density inspection, nondestructive evaluation and so on. In spite of great progress has been made recently on reconstruction algorithms for DECT, there still exist two main problems: 1) For polyenergetic X-ray source, the tube spectrum needed in reconstruction is not always available. 2) The reconstructed image of DECT is very sensitive to noise which demands special noise suppression strategy in reconstruction algorithm design. In this paper, we propose a novel method for DECT reconstruction that reconstructs tube spectrum from projection data and suppresses image noise by introducing ℓ1-norm based regularization into statistical reconstruction for polychromatic DECT. The contribution of this work is twofold. 1) A three parameters model is devised to represent spectrum of ployenergetic X-ray source. And the parameters can be estimated from projection data by solving an optimization problem. 2) With the estimated tube spectrum, we propose a computation framework of ℓ1-norm regularization based statistical iterative reconstruction for polychromatic DECT. Simulation experiments with two phantoms were conducted to evaluate the proposed method. Experimental results demonstrate the accuracy and robustness of the spectrum model in terms of that comparable reconstruction image quality can be achieved with the estimated and ideal spectrum, and validate that the proposed method works with attractive performance in terms of accuracy of reconstructed image. The root mean square error (RMSE) between the reconstructed image and the ground truth image are 7.648 × 10^-4 and 2.687 x 10^-4 for the two phantoms, respectively.

In the context of large-angle cone-beam tomography (CBCT), we present a practical iterative reconstruction (IR) scheme designed for rapid convergence as required for large datasets. The robustness of the reconstruction is provided by the “space-filling” source trajectory along which the experimental data is collected. The speed of convergence is achieved by leveraging the highly isotropic nature of this trajectory to design an approximate deconvolution filter that serves as a pre-conditioner in a multi-grid scheme. We demonstrate this IR scheme for CBCT and compare convergence to that of more traditional techniques.

Despite the significantly practical utilities of interior tomography, it still suffers from severe degradation of direct current (DC) shift artifact. Existing literature suggest to introducing prior information of object support (OS) constraint or the zeroth order image moment, i.e., the DC value into interior reconstruction to suppress the shift artifact, while the prior information is not always available in practice. Aimed at alleviating the artifacts without prior knowledge, in this paper, we reported an approach on the estimation of the object support which could be employed to estimate the zeroth order image moment, and hence facilitate the DC shift artifacts removal in interior reconstruction. Firstly, by assuming most of the reconstructed object consists of soft tissues that are equivalent to water, we reconstructed a virtual OS that is symmetrical about the interior region of interest (ROI) for the DC estimation. Hence the DC value can be estimated from the virtual reconstruction. Secondly, a statistical iterative reconstruction incorporated with the sparse representation in terms of learned dictionary and the constraint in terms of image DC value was adopted to solve the interior tomography. Experimental results demonstrate that the relative errors of the estimated zeroth order image moment are 4.7% and 7.6%, corresponding to the simulated data of a human thorax and the real data of a sheep lung, respectively. Reconstructed images with the constraint of the estimated DC value exhibit greatly superior image quality to that without DC value constraint.

Multiphase abdominal CT is an imaging protocol in which the patient is scanned at different phases before and after the injection of a contrast agent. Reconstructed images with different concentrations of contrast material provide useful information for effective detection of abnormalities. However, several scanning during a short period of time eventually increase the patient radiation dose to a remarkable value up to a risky level. Reducing the patient dose by modulating the x-ray tube current or acquiring the projection data through a small number of views are known to degrade the image quality and reduce the possibility to be useful for diagnosis purpose. In this work, we propose a novel multiphase abdominal CT imaging protocol with patient dose reduction and high image quality. The image reconstruction cost function consists of two terms, namely the data fidelity term and penalty term to enforce the anatomical similarity in successive contrast phase reconstruction. The prior information, named phase-induced swap prior (PISP) is computed using total variation minimization of image acquired from different contrast phases. The new method is evaluated through a simulation study using digital abdominal phantom and real data and results are promising.

The timing of ossification of middle ear ossicles has been extensively studied in humans. This is an exception since it is vastly unknown in the +5000 extant species of placentals. As a preliminary approach, a cow foetus (around 115 days of gestation) was visualized using X-ray microtomography (μCT) and the ossicles including stapes, incus, and malleus could be extracted from the data set. All three bones have already undergone substantial ossification, which allow comparison to adult middle ear bones. Their ossification at this stage parallels ossification in humans at a comparable stage of gestation. While full ossification is not yet achieved almost all the morphological characters of the ossicles are observed. Bone tissue is still very porous, the stapes does not have the characteristic plate-like footplate, the lenticular process of the incus is missing and the manubrium of the malleus is very thin and not yet complete. Despite all this, the ossicles are articulate with each other and perfectly with the bony labyrinth. The stapes footplate is positioned on the oval window but is smaller than the latter while it should perfectly fit to transmit sound vibrations to the cochlea. All ossicles, especially the stapes, have not yet reached adult size, while the bony labyrinth already has. This is the first detailed description of a set of middle ear bones in a placental at mid-gestation based on high-resolution μCT. Similarities in ossification timing with humans encourage more work to be done on foetuses to understand if a general rule for placental mammals exists.

For early detection and targeted therapy, receptor expression profiling is instrumental to classifying breast cancer into sub-groups. In particular, human epidermal growth factor receptor 2 (HER2) expression has been shown to have both prognostic and predictive values. Recently, an increasingly more complex view of HER2 in breast cancer has emerged from genome sequencing that highlights the role of inter- and intra-tumor heterogeneity in therapy resistance. Studies on such heterogeneity demand high-content, high-resolution functional and molecular imaging in vivo, which cannot be achieved using any single imaging tool. Clearly, there is a critical need to develop a multimodality approach for breast cancer imaging. Since 2006, grating-based x-ray imaging has been developed for much-improved x-ray images. In 2014, the demonstration of fluorescence molecular tomography (FMT) guided by x-ray grating-based micro-CT was reported with encouraging results and major drawbacks. In this paper, we propose to integrate grating-based x-ray tomography (GXT) and high-dimensional optical tomography (HOT) into the first-of-its-kind truly-fused GXT-HOT (pronounced as “Get Hot”) system for imaging of breast tumor heterogeneity, HER2 expression and dimerization, and therapeutic response. The primary innovation lies in developing a brand-new high-content, high-throughput x-ray optical imager based on several contemporary techniques to have MRI-type soft tissue contrast, PET-like sensitivity and specificity, and micro-CT-equivalent resolution. This system consists of two orthogonal x-ray Talbot-Lau interferometric imaging chains and a hyperspectral time-resolved single-pixel optical imager. Both the system design and pilot results will be reported in this paper, along with relevant issues under further investigation.

Segmentation of lung features is one of the most important steps for computer-aided detection (CAD) of pulmonary nodules with computed tomography (CT). However, irregular shapes, complicated anatomical background and poor pulmonary nodule contrast make CAD a very challenging problem. Here, we propose a novel scheme for feature extraction and classification of pulmonary nodules through dictionary learning from training CT images, which does not require accurately segmented pulmonary nodules. Specifically, two classification-oriented dictionaries and one background dictionary are learnt to solve a two-category problem. In terms of the classification-oriented dictionaries, we calculate sparse coefficient matrices to extract intrinsic features for pulmonary nodule classification. The support vector machine (SVM) classifier is then designed to optimize the performance. Our proposed methodology is evaluated with the lung image database consortium and image database resource initiative (LIDC-IDRI) database, and the results demonstrate that the proposed strategy is promising.

The development of energy-resolving photon-counting detectors makes it possible to collect data in different energy bins. These detectors lead to emerging spectral computed tomography (CT), which is also called multi-energy CT, energy-selective CT, color CT, etc. Spectral CT can provide additional information in comparison with conventional CT in which energy integrating detectors are used to form polychromatic projection of an object being investigated. The photon counting detectors in spectral CT can acquire projections of the object in different energy levels as they are able to reliably distinguish the received photon energies. In recent years, different methods have been developed to acquire additional information hidden in different energy levels of spectral CT images. Different regularization methods have been adopted for reconstructing the noisy image in the last decade. In this work, we numerically evaluate the performance of different regularizers such as total variation, Huber, non-local means and anisotropic diffusion regularization in spectral CT. The goal is to provide some practical guidance to accurately reconstruct the attenuation distribution of each energy channel of the spectral CT data.

The use of degradable magnesium based implants is becoming clinically relevant, e.g. for the use as bone screws. Still there is a lack of analyzing techniques to characterize the in vitro degradation behavior of implant prototypes. The aim of this study was to design an in situ environment to continuously monitor the degradation processes under physiological conditions by time-lapse SRμCT. The use of physiological conditions was chosen to get a better approach to the in vivo situation, as it could be shown by many studies, that these conditions change on the one hand the degradation rate and on the other hand also the formed degradation products. The resulting in situ environment contains a closed bioreactor system to control and monitor the relevant parameters (37°C, 5 % O₂, 20 % CO₂) and to grant sterility of the setup. A flow cell was designed and manufactured from polyether etherketone (PEEK), which was chosen because of the good mechanical properties, high thermal and chemical resistance and radiographic translucency. Sterilization of the system including the sample was reached by a transient flush with 70 % ethanol and subsequent replacement by physiological medium (Modified Eagle Medium alpha). As proof of principle it could be shown that the system remained sterile during a beamtime of several days and that the continuous SRμCT imaging was feasible.