Trends in the type and number of published micro- and nano-CT studies are reviewed in this paper. The literature of the last decade is covered, i.e., from 2005 to 2014, and some active fields of research are highlighted.

Cardiovascular diseases are the number one cause of death and morbidity in the world. Understanding disease development in terms of lumen morphology and tissue composition of constricted arteries is essential to improve treatment and patient outcome. X-ray tomography provides non-destructive three-dimensional data with micrometer-resolution. However, a common problem is simultaneous visualization of soft and hard tissue-containing specimens, such as atherosclerotic human coronary arteries. Unlike absorption based techniques, where X-ray absorption strongly depends on atomic number and tissue density, phase contrast methods such as grating interferometry have significant advantages as the phase shift is only a linear function of the atomic number. We demonstrate that grating interferometry-based phase tomography is a powerful method to three-dimensionally visualize a variety of anatomical features in atherosclerotic human coronary arteries, including plaque, muscle, fat, and connective tissue. Three formalin-fixed, human coronary arteries were measured using advanced laboratory μCT. While this technique gives information about plaque morphology, it is impossible to extract the lumen morphology. Therefore, selected regions were measured using grating based phase tomography, sinograms were treated with a wavelet-Fourier filter to remove ring artifacts, and reconstructed data were processed to allow extraction of vessel lumen morphology. Phase tomography data in combination with conventional laboratory μCT data of the same specimen shows potential, through use of a joint histogram, to identify more tissue types than either technique alone. Such phase tomography data was also rigidly registered to subsequently decalcified arteries that were histologically sectioned, although the quality of registration was insufficient for joint histogram analysis.

The grating based approach to phase contrast imaging is rather inefficient in the use of the available x-ray flux due to the presence of two absorption gratings and it requires longer scan times compared to conventional CT because multiple images are needed at each projection angle. To avoid these drawbacks, a proof-of-principle experiment was developed to obtain absorption, phase contrast (DPC) and dark field images (DCI) in a single exposure using only a non-absorbing phase grating, a micro-focus source in cone-beam geometry and a highresolution x-ray detector.

This article discusses two experimental setups of edge illumination (EI) x-ray phase contrast imaging (XPCi) as well as the theory that is required to reconstruct quantitative tomographic maps using established methods, e.g. filtered back projection (FBP). Tomographic EI XPCi provides the option to reconstruct volumetric maps of different physical quantities, amongst which are the refractive index decrement from unity and the absorption coefficient, which can be used for dual-mode imaging. EI XPCi scans of a custom-built wire phantom using synchrotron and x-ray tube generated radiation were carried out, and tomographic maps of both parameters were reconstructed. This article further discusses the theoretical basis for the tomographic reconstruction of images showing combined phase and attenuation contrast. Corresponding experimental results are presented.

Conventional absorption-based imaging often lacks in good contrast at special applications like visualization of soft tissue or weak absorbing material in general. To overcome this limitation, several new X-ray phase-contrast imaging methods have been developed at synchrotron radiation facilities. Our aim was to establish the possibility of different phase-contrast imaging modalities at the Imaging Beamline (IBL, P05) and the High Energy Material Science beamline (HEMS, P07) at Petra III (DESY, Germany). Here we present the instrumentation and the status of the currently successfully established phase-contrast imaging techniques. First results from measurements of biomedical samples will be presented as demonstration.

The high utility and wide applicability of x-ray imaging has led to a rapidly increased number of CT scans over the past years, and at the same time an elevated public concern on the potential risk of x-ray radiation to patients. Hence, a hot topic is how to minimize x-ray dose while maintaining the image quality. The low-dose CT strategies include modulation of x-ray flux and minimization of dataset size. However, these methods will produce noisy and insufficient projection data, which represents a great challenge to image reconstruction. Our team has been working to combine statistical iterative methods and advanced image processing techniques, especially dictionary learning, and have produced excellent preliminary results. In this paper, we report recent progress in dictionary learning based low-dose CT reconstruction, and discuss the selection of regularization parameters that are crucial for the algorithmic optimization. The key idea is to use a “balancing principle” based on a model function to choose the regularization parameters during the iterative process, and to determine a weight factor empirically for address the noise level in the projection domain. Numerical and experimental results demonstrate the merits of our proposed reconstruction approach.

Image registration is a powerful tool in various tomographic applications. Our main focus is on microCT applications in which samples/animals can be scanned multiple times under different conditions or at different time points. For this purpose, a registration tool capable of handling fairly large volumes has been developed, using a novel pseudo-3D method to achieve fast and interactive registration with simultaneous 3D visualization. To reduce computation complexity in 3D registration, we decompose it into several 2D registrations, which are applied to the orthogonal views (transaxial, sagittal and coronal) sequentially and iteratively. After registration in each view, the next view is retrieved with the new transformation matrix for registration. This reduces the computation complexity significantly. For rigid transform, we only need to search for 3 parameters (2 shifts, 1 rotation) in each of the 3 orthogonal views instead of 6 (3 shifts, 3 rotations) for full 3D volume. In addition, the amount of voxels involved is also significantly reduced. For the proposed pseudo-3D method, image-based registration is employed, with Sum of Square Difference (SSD) as the similarity measure. The searching engine is Powell's conjugate direction method. In this paper, only rigid transform is used. However, it can be extended to affine transform by adding scaling and possibly shearing to the transform model. We have noticed that more information can be used in the 2D registration if Maximum Intensity Projections (MIP) or Parallel Projections (PP) is used instead of the orthogonal views. Also, other similarity measures, such as covariance or mutual information, can be easily incorporated. The initial evaluation on microCT data shows very promising results. Two application examples are shown: dental samples before and after treatment and structural changes in materials before and after compression. Evaluation on registration accuracy between pseudo-3D method and true 3D method has been performed.

X-ray computed tomography (CT) is an established tool for industrial non-destructive testing purposes. Yet conventional CT devices pose limitations regarding specimen dimensions and material thicknesses. Here we introduce a novel CT system capable of inspecting very large objects (VLO) like automobiles or sea freight containers in 3-D and discuss strategies for efficient scanning and reconstruction methods. The system utilizes a 9 MeV linear accelerator to achieve high penetration lengths in both dense and high-Z materials. The line detector array has an overall length of 4 meters. The presented system allows for reconstruction volumes of 3.2 meters in diameter and 5 meters in height. First we outline the general capabilities of high energy CT imaging and compare it with state of the art 450 kV X-ray systems. The imaging performance is shown based on experimental results. The second part addresses the problem of considerably higher scanning times when using line detectors compared to area detectors. Reducing the number of projections considerably causes image artifacts with standard reconstruction methods like filtered back projection (FBP). Alternative methods which can provide significantly better results are algebraic reconstruction techniques (ART). One of these is compressed sensing (CS) based ART which we discuss regarding its suitability in respect to FBP. We could prove the feasibility of inspecting VLOs like complete automobiles based on experimental data. CS allows for achieving sufficient image quality in terms of spatial and contrast resolution while reducing the number of projections significantly resulting in faster scanning times.

We explore the use of referenceless multi-material beam hardening correction methods, with an emphasis on maintaining data quality for real-world imaging of geologic materials with a view towards automation. In particular, we consider cases where the sample of interest is surrounded by a container of uniform material and propose a novel container-only pre-correction technique to allow automation of the segmentation process required for such correction methods. The effectiveness of the new technique is demonstrated using both simulated and experimental data.

Micro scale computed tomography (CT) can resolve many features in cellular structures, bone formations, minerals properties and composite materials not seen at lower spatial-resolution. Those features enable us to build a more comprehensive model for the object of interest. CT resolution is limited by a fundamental trade off between source size and signal-to-noise ratio (SNR) for a given acquisition time. There is a limit on the X-ray flux that can be emitted from a certain source size, and fewer photons cause a lower SNR. A large source size creates penumbral blurring in the radiograph, limiting the effective spatial-resolution in the reconstruction. High cone-angle CT improves SNR by increasing the X-ray solid angle that passes through the sample. In the high cone-angle regime current source deblurring methods break down due to incomplete modelling of the physical process. This paper presents high cone-angle source de-blurring models. We implement these models using a novel multi-slice Richardson-Lucy (M-RL) and 3D Conjugate Gradient deconvolution on experimental high cone-angle data to improve the spatial-resolution of the reconstructed volume. In M-RL, we slice the back projection volume into subsets which can be considered to have a relative uniform convolution kernel. We compare these results to those obtained from standard reconstruction techniques and current source deblurring methods (i.e. 2D Richardson-Lucy in the radiograph and the volume respectively).

Biological materials are complex and their investigation demands advanced characterization tools capable of elucidating their structure in three dimensions without the need for complicated sample preparation. Herein, we discuss our implementation of diffraction/scattering computed tomography (DSCT). DSCT is based on the use of diffraction information for tomographic reconstructions rather than linear attenuation as in regular μ-CT. This provides much additional information on the material under investigation. We illustrate the use of DSCT by discussion of data on a biomineralized attachment organ from a marine mussel. DSCT allowed mapping the spatial distribution of calcium carbonate polymorphs aragonite and calcite even though they were indistinguishable in absorption tomography. Detailed analysis of reconstructed diffraction patterns may provide additional insights as exemplified in the present case by mapping of the degree of chemical substitution in calcite.

In microelectronics, more and more attention is paid to the physical characterization of interconnections, to get a better understanding of reliability issues like voiding, cracking and performance degradation. Those interconnections have a 3D architecture with features in the deep sub-micrometer range, requiring a probe with high spatial resolution and high penetration depth. Third generation synchrotron sources are the ideal candidate for that, and we show hereafter the potential of synchrotron-based hard x-ray nanotomography to investigate the morphology of through silicon vias (TSVs) and copper pillars, using projection (holotomography) and scanning (fluorescence) 3D imaging, based on a series of experiments performed at the ESRF. In particular, we highlight the benefits of the method to characterize voids, but also the distribution of intermetallics in copper pillars, which play a critical role for the device reliability. Beyond morphological imaging, an original acquisition scheme based on scanning Laue tomography is introduced. It consists in performing a raster scan (z,θ) of a sample illuminated by a synchrotron polychromatic beam while recording diffraction data. After processing and image reconstruction, it allows for 3D reconstruction of grain orientation, strain and stress in copper TSV and also in the surrounding Si matrix.

Owing to the high photon flux of synchrotron radiation, the exposure time is greatly reduced, and the total data-acquisition time of a tomography scan has been shortened to second level. Thus a four dimensional (3D structural and temporal) imaging technique can be utilized to capture the structural evolvement of 3D systems. Utilizing this technique, we studied the structural evolvement and particle-scale dynamics of three dimensional (3D) granular packing under tapping. We conducted a tomographic scan of the packing after each tapping, and the displacement of each particle was captured through a tracking algorithm. An averaged 3D flow field of the packing under tapping was also calculated. The major conclusion of this work is that the local particle fluctuation displacements are correlated with local packing structures, which are characterized through the size and shape of the Voronoi cells.

In laboratory X-ray microtomography (XMT) systems, the signal-to-noise ratio (SNR) is typically determined by the X-ray exposure due to the low flux associated with microfocus X-ray tubes. As the exposure time is increased, the SNR improves up to a point where other sources of variability dominate, such as differences in the sensitivities of adjacent X-ray detector elements. Linear time-delay integration (TDI) readout averages out detector sensitivities on the critical horizontal direction and equiangular TDI also averages out the X-ray field. This allows the SNR to be increased further with increasing exposure. This has been used in dentistry to great effect, allowing subtle variations in dentine mineralisation to be visualised in 3 dimensions. It has also been used to detect ink in ancient parchments that are too damaged to physically unroll. If sufficient contrast between the ink and parchment exists, it is possible to virtually unroll the tomographic image of the scroll in order that the text can be read. Following on from this work, a feasibility test was carried out to determine if it might be possible to recover images from decaying film reels. A successful attempt was made to re-create a short film sequence from a rolled length of 16mm film using XMT. However, the “brute force” method of scaling this up to allow an entire film reel to be imaged presents a significant challenge.

The power and brightness of electron-impact micro-focus X-ray sources have long been limited by thermal damage in the anode. Here we describe a novel X-ray microfocus source based on a new anode concept, the liquid-metal-jet anode (MetalJet). The regenerative nature of this anode allows for significantly higher e-beam power density than on conventional anodes, resulting in this source generating significantly higher brightness than other X-ray tubes in the microfocus regime (~5-50 μm). We describe the fundamental properties of the technology and will review the current status specifically in terms of spot size, stability, lifetime, flux, acceleration voltage and brightness.

The purpose of this study is to derive optimized parameters for a detector module employing an off-the-shelf X-ray camera and a pinhole array collimator applicable for a range of different SPECT systems. Monte Carlo simulations using the Geant4 application for tomographic emission (GATE) were performed to estimate the performance of the pinhole array collimators and were compared to that of low energy high resolution (LEHR) parallel-hole collimator in a four head SPECT system. A detector module was simulated to have 48 mm by 48 mm active area along with 1mm, 1.6mm and 2 mm pinhole aperture sizes at 0.48 mm pitch on a tungsten plate. Perpendicular lead septa were employed to verify overlapping and non-overlapping projections against a proper acceptance angle without lead septa. A uniform shape cylindrical water phantom was used to evaluate the performance of the proposed four head SPECT system of the pinhole array detector module. For each head, 100 pinhole configurations were evaluated based on sensitivity and detection efficiency for 140 keV ɣ-rays, and compared to LEHR parallel-hole collimator. SPECT images were reconstructed based on filtered back projection (FBP) algorithm where neither scatter nor attenuation corrections were performed. A better reconstruction algorithm development for this specific system is in progress. Nevertheless, activity distribution was well visualized using the backprojection algorithm. In this study, we have evaluated several quantitative and comparative analyses for a pinhole array imaging system providing high detection efficiency and better system sensitivity over a large FOV, comparing to the conventional four head SPECT system. The proposed detector module is expected to provide improved performance in various SPECT imaging.

The NanoXCT project aims at developing a laboratory nano-CT system for non-destructive testing applications in the micro- and nano-technology sector. The system concept omits the use of X-ray optics, to be able to provide up to 1 mm FOV (at 285 nm voxel size) and down to 50 nm voxel size (at 0.175 mm FOV) while preserving the flexibility of stateof- the-art micro-CT systems. Within the project a suitable X-ray source, detector and manipulation system are being developed. To cover the demand for elemental analysis, the project will additionally include X-ray spectroscopic techniques. These will be reported elsewhere while this paper is focused on the imaging part of the project. We introduce the system concept including design goals and constraints, and the individual components. We present the current state of the prototype development including first results.

Analysis of large tomographic datasets at synchrotron light sources is becoming progressively more challenging due to the increasing data acquisition rates that new technologies in X-ray sources and detectors enable. The next generation of synchrotron facilities that are currently under design or construction throughout the world will provide diffraction limited X-ray sources and is expected to boost the current data rates by several orders of magnitude and stressing the need for the development and integration of efficient analysis tools more than ever. Here we describe in detail an attempt to provide such a collaborative framework for the analysis of synchrotron tomographic data that has the potential to unify the effort of different facilities and beamlines performing similar tasks. The proposed Python/C++ based framework is open-source, OS and data format independent, parallelizable and supports functional programming that many researchers prefer. This collaborative platform will affect all major synchrotron facilities where new effort is now dedicated into developing new tools that can be deployed at the facility for real time processing as well as distributed to users for off site data processing.

The imaging beamline (IBL/P05) operated by Helmholtz Zentrum Geesthacht (HZG) at the DESY PETRA III storage ring consists of two experimental stations: A micro tomography and a nano tomography end station. Here an overview of the experimental setups and the data acquisition will be given. In addition some first results out of the wide range of applications using the micro tomography station at P05 will be shown. Furthermore, we present first results of the nano tomography end station. These were obtained with an x–ray microscopy setup, which currently operates at energies of 17.4 and 30 keV using polymer compound refractive lenses (CRLs) and rolled prism lenses. Taken together these results clearly show the high potential of the newly built imaging beamline IBL.

Angiogenesis, i.e. the formation of vessels, is one of the key processes during tumor development. The newly formed vessels transport oxygen and nutrients from the healthy tissue to the tumor and gives tumor cells the possibility to replicate. The principle of anti-angiogenic therapy is to block angiogenic process in order to stop tumor growth. The aim of the present study is the investigation of murine glioma vascular architecture at early (7 days), intermediate (10 and 15 days) and late (23 days) stage of growth by means of grating-based phase contrast microtomography. We demonstrate that this technique yields premium contrast between healthy and cancerous parts of murine brain tissues.

We use propagation based hard x-ray phase contrast tomography to explore the three dimensional structure of neuronal tissues from the organ down to sub-cellular level, based on combinations of synchrotron radiation and laboratory sources. To this end a laboratory based microfocus tomography setup has been built in which the geometry was optimized for phase contrast imaging and tomography. By utilizing phase retrieval algorithms, quantitative reconstructions can be obtained that enable automatic renderings without edge artifacts. A high brightness liquid metal microfocus x-ray source in combination with a high resolution detector yielding a resolution down to 1.5 μm. To extend the method to nanoscale resolution we use a divergent x-ray waveguide beam geometry at the synchrotron. Thus, the magnification can be easily tuned by placing the sample at different defocus distances. Due to the small Fresnel numbers in this geometry the measured images are of holographic nature which poses a challenge in phase retrieval.

Hippocampal sclerosis is a common cause of epilepsy, whereby a neuronal cell loss of more than 50% cells is characteristic. If medication fails the best possible treatment is the extraction of the diseased organ. To analyze the microanatomy of the diseased tissue we scanned a human hippocampus extracted from an epilepsy patient. After the identification of degenerated tissue using magnetic resonance imaging the specimen was reduced in size to fit into a cylindrical container with a diameter of 6 mm. Using synchrotron radiation and grating interferometry we acquired micro computed tomography datasets of the specimen. The present study was one of the first successful phase tomography measurements at the imaging beamline P05 (operated by HZG at the PETRA III storage ring, DESY, Hamburg, Germany). Ring and streak artefacts were reduced by enhanced flat-field corrections, combined wavelet-Fourier filters and bilateral filtering. We improved the flat-field correction by the consideration of the correlation between the projections and the flat-field images. In the present study, the correlation that was based on mean squared differences and evaluated on manually determined reference regions leads to the best artefact reduction. A preliminary segmentation of the abnormal tissue reveals that a clinically relevant study requires the development of even more sophisticated artifact reduction tools or a phase contrast measurement of higher quality.

X-ray phase imaging is sensitive to structural variation of soft tissue, and offers excellent contrast resolution for characterization of cancerous tissues. Also, the cross-section of x-ray phase shift is a thousand times greater than that of x-ray attenuation in soft tissue over the diagnostic energy range, allowing a much higher signal-to-noise ratio at a substantially lower radiation dose than attenuation-based x-ray imaging. In this paper, we present a second order approximation model with respect to phase shift based on the paraxial Fresnel-Kirchhoff diffraction theory, and also discuss in-line dark-field imaging based on the second order model. This proposed model accurately establishes a quantitative correspondence between phases and recorded intensity images, outperforming the linear phase approximation model widely used in the conventional methods of x-ray in-line phase-contrast imaging. This new model can be iteratively solved using the algebraic reconstruction technique (ART). The state of the art compressive sensing ingredients can be incorporated to achieve high quality image reconstruction. Our numerical simulation studies demonstrate the feasibility of the proposed approach that is more accurate and stable, and more robust against noise than the conventional approach.

According to the World Health Organization (WHO), in 2010 hearing loss affected more than 278 million people worldwide. The loss of hearing and communication has significant consequences on the emotional well-being of each affected individual. The estimated socio-economic impact is about $100 billion in unrealized household income per year. Despite this impact on society, no Food and Drug Administration (FDA) approved drug intervention is available today that would either protect or reverse the effects of hearing loss. A limiting factor for all efforts to validate drugs for treatment relates to the time consuming animal experiments and subsequent histology. Here, we present an imaging method that is superior to current gold standard methods in flexibility and time for evaluation of histology. Tissue processing times are reduced from weeks to hours. As an example, we show that Brain Derived Neurotrophic Factor (BDNF) reduces the effect of noise induced hearing loss.

Remote electron microscopy sessions are featured at a number of imaging centers. Similarly, many synchrotron light sources offer routine “mail-in” crystallography and powder diffractometry. At imaging beam lines, small numbers of (preliminary) scans are sometimes performed by staff, in the absence of the investigator, to demonstrate feasibility of the proposed study or as an industrial service. In the 1990s, one of us (SRS) participated in processing experiments where samples were couriered between Georgia Tech and SSRL and synchrotron microCT followed the spatial distribution of densification. Here, the authors report results of remote microCT experiments, i.e., where the investigator who knows the sample interacts via the web with the beam line scientist operating the apparatus and provides real-time feedback on where to scan based upon radiographs and on the most recent reconstructions. Local tomography imaged sea urchin teeth with 350 nm isotropic volume element (voxel) at beam line ID-19, ESRF. Sea urchin teeth form by growing parallel plates of high Mg calcite, each of which is 2-5 μm away from its neighbors, and very high Mg calcite columns later link the plates. The remote imaging session focused on tooth positions where the columns were just forming, and column shapes and dimensions were measured, something which has previously only been done with destructive sample preparation and scanning electron microscopy. The experiments were successful despite a separation of 4,400 miles and seven time zones.

In a dental office, every day X rays of teeth within the oral cavity are obtained. Caries induces a mineral loss and, therefore, becomes visible by reduced X-ray absorption. The detailed spatial distribution of the mineral loss, however, is inaccessible in conventional dental radiology, since the dose for such studies is intolerable. As a consequence, such measurements can only be performed after tooth extraction. We have taken advantage of synchrotron radiation-based micro computed tomography to characterize a human tooth with a rather small, natural caries lesion and an artificially induced lesion provoked by acidic etching. Both halves of the tooth were separately visualized from 2400 radiographs recorded at the beam line P07 / PETRA III (HASYLAB at DESY, Hamburg, Germany) with an asymmetric rotation axis at photon energy of 45 keV. Because of the setup, one finds an energy shift in the horizontal plane, to be corrected. After the appropriate three-dimensional registration of the data with the ones of the same crown using the better accessible phoenix nanotom® m of General Electric, Wunstorf, Germany, one can determine the joint histogram, which enable to calibrate the system with the conventional X-ray source.

X-ray computed tomography (CT) has become an established technique in the biomedical imaging or materials science research. Its ability to non-destructively provide high-resolution images of samples makes it attractive for diverse fields of research especially the paleontology. Exceptionally, the Precambrian is a geological time of rocks deposition containing several fossilized early animals, which still need to be investigated in order to predict the origin and evolution of early life. Corumbella werneri is one of those fossils skeletonized in Corumbá (Brazil). Here, we present a study on selected specimens of Corumbella werneri using absorption-based contrast imaging at diverse tomographic setups. We investigated the potential of conventional laboratory-based device and synchrotron radiation sources to visualize internal structures of the fossils. The obtained results are discussed as well as the encountered limitations of those setups.

Malfunction of oxygen regulation in kidney and liver may lead to the pathogenesis of chronic diseases. The underlying mechanisms are poorly understood. In kidney, it is hypothesized that renal gas shunting from arteries to veins eliminates excess oxygen. Such shunting is highly dependent on the structure of the renal vascular network. The vascular tree has so far not been quantified under maintenance of its connectivity as three-dimensional imaging of the vessel tree down to the smallest capillaries, which in mouse model are smaller than 5 μm in diameter, is a challenging task. An established protocol uses corrosion casts and applies synchrotron radiation-based micro-computed tomography (SRμCT), which provides the desired spatial resolution with the necessary contrast. However, SRμCT is expensive and beamtime access is limited. We show here that measurements with a phoenix nanotomrm (General Electric, Wunstorf, Germany) can provide comparable results to those obtained with SRμCT, except for regions with small vessel structures, where the signal-to-noise level was significantly reduced. For this purpose the nanotom®m measurement was compared with its corresponding measurement acquired at the beamline P05 at PETRA III at DESY, Hamburg, Germany.

Synchrotron radiation is a good candidate for 3D imaging at high resolution. However, the difficult access to 3rd generation synchrotron sources is prohibitive for daily analyses and we present hereafter a step towards x-ray nanotomography using a laboratory system. To have a lens-free system, we use the electron beam of an SEM to produce x-rays through the interaction between the SEM electron beam and a metallic anode. The inherent x-ray source size can be properly shaped using different anode materials and geometries. This flexible system makes it possible to perform xray imaging at energies of up to 10keV and resolution down to 100nm. Because of a low SNR, the exposure time is long and forces to have a low angular sampling. This is counterbalanced by using algebraic reconstruction algorithms. The technique has been applied to the study of plasma FIB-prepared macroporous silicon samples. Those samples come from the controlled porosification of 200mm silicon wafer, with thicknesses from few nm to few hundreds of micrometers. We quantified the 3D pore network, which is of interest for the optimization of the production of such materials.

“Can brute-force high-contrast tomography techniques and image processing techniques retrieve textual content from damaged heritage materials?” The Dental Institute at Queen Mary University of London (QMUL) is the leading centre for very high contrast X-Ray Microtomography imaging. The Apocalypto Project is our collaboration with the heritage community and experts in Computer Vision systems in the Computer Science Department at Cardiff University. This collaboration has developed techniques and a workflow that allows us to reveal textual content from moisture-damaged parchment rolls. This article will also present some initial results from burned and heat shrunken parchment rolls, an insect damaged Mamluk cap and a birch bark roll.

Direct study of pore-scale fluid displacements, and other dynamic (i.e. time-dependent) processes is not feasible with conventional X-ray micro computed tomography (μCT). We have previously verified that a priori knowledge of the underlying physics can be used to conduct high-resolution, time-resolved imaging of continuous, complex processes, at existing X-ray μCT facilities. In this paper we present a maximum a posteriori (MAP) model of the dynamic tomography problem, which allows us to easily adapt and generalise our previous dynamic μCT approach to systems with more complex underlying physics.

In this paper, we develop a dual-energy ordered subsets convex method for transmission tomography based on material matching with a material dictionary. This reconstruction includes a constrained update forcing material characteristics of reconstructed atomic number (Z) and density (p) volumes to follow a distribution according to the material database provided. We also propose a probabilistic classification technique in order to manage this material distribution. The overall process produces a chemically segmented volume data and outperforms sequential labelling computed after tomographic reconstruction.

We address several acquisition questions that have arisen for the high cone-angle helical-scanning micro-CT facility developed at the Australian National University. These challenges are generally known in medical and industrial cone-beam scanners but can be neglected in these systems. For our large datasets, with more than 2048³ voxels, minimising the number of operations (or iterations) is crucial. Large cone-angles enable high signal-to-noise ratio imaging and a large helical pitch to be used. This introduces two challenges: (i) non-uniform resolution throughout the reconstruction, (ii) over-scan beyond the region-of-interest significantly increases re- quired reconstructed volume size. Challenge (i) can be addressed by using a double-helix or lower pitch helix but both solutions slow down iterations. Challenge (ii) can also be improved by using a lower pitch helix but results in more projections slowing down iterations. This may be overcome using less projections per revolution but leads to more iterations required. Here we assume a given total time for acquisition and a given reconstruction technique (SART) and seek to identify the optimal trajectory and number of projections per revolution in order to produce the best tomogram, minimise reconstruction time required, and minimise memory requirements.

High-resolution X-ray computed tomography has become a vital technique to study fossils down to the true micrometer level. Paleontological research requires the non-destructive analysis of internal structures of fossil specimens. We show how X-ray computed tomography enables us to visualize the inner ear of extinct and extant ruminants without skull destruction. The inner ear, a sensory organ for hearing and balance has a rather complex three-dimensional morphology and thus provides relevant phylogenetical information what has been to date essentially shown in primates. We made visible the inner ears of a set of living and fossil ruminants using the phoenix x-ray nanotom®m (GE Sensing and Inspection Technologies GmbH). Because of the high absorbing objects a tungsten target was used and the experiments were performed with maximum accelerating voltage of 180 kV and a beam current of 30 μA. Possible stem ruminants of the living families are known in the fossil record but extreme morphological convergences in external structures such as teeth is a strong limitation to our understanding of the evolutionary history of this economically important group of animals. We thus investigate the inner ear to assess its phylogenetical potential for ruminants and our first results show strong family-level morphological differences.

A new control system for high-throughput experiments (X-Ray, Neutrons) is introduced in this article. The system consists of several software components which are required to make optimized use of the beamtime and to fulfill the demand to implement the new standardized data format established within the Helmholtz Association in Germany. The main components are: PreExperiment Data Collector; Status server; Data Format Server. Especially for tomography a concept for an online reconstruction based on GPU computing is presented. One of the main goals of the system is to collect data that extends standard experimental data, e.g. instrument’s hardware state, preinvestigation data, experiment description data etc. The collected data is stored together with the experiment data in the permanent storage of the user. The stored data is then used for post processing and analysis of the experiment.

In this article we present the quantitative characterization of CCD and CMOS sensors which are used at the experiments for microtomography operated by HZG at PETRA III at DESY in Hamburg, Germany. A standard commercial CCD camera is compared to a camera based on a CMOS sensor. This CMOS camera is modified for grating-based differential phase-contrast tomography. The main goal of the project is to quantify and to optimize the statistical parameters of this camera system. These key performance parameters such as readout noise, conversion gain and full-well capacity are used to define an optimized measurement for grating-based phase-contrast. First results will be shown.

Contrast agents with high-Z elements have K-absorption edges which significantly change X-ray attenuation coefficients. The K-edge characteristics is different for various kinds of contrast agents, which offers opportunities for material decomposition in biomedical applications. In this paper, we propose a new K-edge imaging method, which not only quantifies a distribution of a contrast agent but also provides an optimized contrast ratio. Our numerical simulation tests demonstrate the feasibility and merits of the proposed methodology.

Noninvasive determination of plaque vulnerability has been a holy grail of medical imaging. Despite advances in tomographic technologies , there is currently no effective way to identify vulnerable atherosclerotic plaques with high sensitivity and specificity. Computed tomography (CT) and magnetic resonance imaging (MRI) are widely used, but neither provides sufficient information of plaque properties. Thus, we are motivated to combine CT and MRI imaging to determine if the composite information can better reflect the histological determination of plaque vulnerability. Two human endarterectomy specimens (1 symptomatic carotid and 1 stable femoral) were imaged using Scanco Medical Viva CT40 and Bruker Pharmascan 16cm 7T Horizontal MRI / MRS systems. μCT scans were done at 55 kVp and tube current of 70 mA. Samples underwent RARE-VTR and MSME pulse sequences to measure T1, T2 values, and proton density. The specimens were processed for histology and scored for vulnerability using the American Heart Association criteria. Single modality-based analyses were performed through segmentation of key imaging biomarkers (i.e. calcification and lumen), image registration, measurement of fibrous capsule, and multi-component T1 and T2 decay modeling. Feature differences were analyzed between the unstable and stable controls, symptomatic carotid and femoral plaque, respectively. By building on the techniques used in this study, synergistic CT+MRI analysis may provide a promising solution for plaque characterization in vivo.

With the increasing use of microspheres and nanoparticles for diagnostic and therapeutic purposes, the need to quantify the spatial distribution and concentration of those particles in a minimally invasive manner, such as by imaging, is required. In the case of CT-imaging, labelling of those particles with elements that have high contrast, and when possible that is specific for that element, is an obvious approach, but this still begs the question as to what extent particles that are smaller than the detector pixel can be quantified over relatively large volumes of tissue. This study is an exploration of three approaches to quantify the spatial distribution and/or size of those microscopic particles by use of; (i) a model of the impact of high contrast opaque particle on the detected x-ray attenuation, (ii) quasi-monochromatic energy CT and (iii) the statistics of random clustering of particles resulting in clusters that are larger than detector pixels and using that information to extrapolate to sub-resolution information about individual particles. To explore the role of particle size relative to detector pixel size we recorded x-ray attenuation in detector pixels smaller than the particle and then retrospectively increased the effective detector pixel size by summing the x-ray signal in contiguous pixels around the particle location.

Since its recent inception, simultaneous image reconstruction for multimodality fusion has received a great deal of attention due to its superior imaging performance. On the other hand, the compressed sensing (CS)-based image reconstruction methods have undergone a rapid development because of their ability to significantly reduce the amount of raw data. In this work, we combine computed tomography (CT) and magnetic resonance imaging (MRI) into a single CS-based reconstruction framework. From a theoretical viewpoint, the CS-based reconstruction methods require prior sparsity knowledge to perform reconstruction. In addition to the conventional data fidelity term, the multimodality imaging information is utilized to improve the reconstruction quality. Prior information in this context is that most of the medical images can be approximated as piecewise constant model, and the discrete gradient transform (DGT), whose norm is the total variation (TV), can serve as a sparse representation. More importantly, the multimodality images from the same object must share structural similarity, which can be captured by DGT. The prior information on similar distributions from the sparse DGTs is employed to improve the CT and MRI image quality synergistically for a CT-MRI scanner platform. Numerical simulation with undersampled CT and MRI datasets is conducted to demonstrate the merits of the proposed hybrid image reconstruction approach. Our preliminary results confirm that the proposed method outperforms the conventional CT and MRI reconstructions when they are applied separately.

The three-dimensional (3D) microstuructural evolution in a Pb-free solder system undergoing accelerated electromigration (EM) testing is characterized using a custom, lab-scale, cone-beam, micro x-ray computed tomography (μXCT) instrument. A micro-scale Sn-0.7Cu butt -joint was subjected to a current density of 10⁴A/cm² at 100°C. The experimentation was enabled by the design of a miniature fixture for in situ imaging under accelerating EM testing conditions. The fixture is friendly to surface imaging and μXCT scanning. The migrating species, copper and tin, are observed volumetrically through substrate dissolution, solder build-up, and the formation of reaction products in the solder joint by μXCT imaging. The migration of the copper substrate and the formation of copper-tin reaction products is quantified.

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 from around the world. Users of the Hard X-ray Micro-Tomography Beamline (8.3.2) often collect more than 1 Terabyte of raw data per day that in turn generates additional Terabytes of processed data. The data rate continues to increase rapidly due to faster detectors and new sample automation capabilities. We will present the development and deployment of a computational pipeline, fed by data from the ALS, and powered by the storage, networking, and computing resources of the local National Energy Research Scientific Computing Center (NERSC) and the Energy Sciences Network (ESNET). After one year of operation, the system contained 70,000 datasets and 350 TB of data from 85 users. All datasets now collected at the Hard X-ray Tomography Beamline are automatically reconstructed using parameters set by users and/or that are automatically detected from the data acquisition control system. Results are presented to users for visualization through a secure web portal. Users can then download their data or launch a (currently limited but) growing number of operations based on the data-such as filtering, segmentation, and simulation. The massive computational resources of NERSC are thus made available on a level that is easily accessible to the full range of micro-tomography users.