This PDF file contains the Front Matter associated with SPIE Proceedings Volume 7804, including the Title page, Copyright information, Table of Contents, Conference Committee listing, and introduction.

Trends in micro- and nanoComputed Tomography (CT) from January 2008 through July 2010 are the subject of this brief report which takes up where a previous report in Developments in X-ray Tomography VI (2008) concluded. First, the number of systems operating world-wide is estimated. The main focus is on what searches of three citation indices (Web of Science, Compendex and PubMed) reveal about the field of micro- and nanoCT. Given research-fielddependent and disparate terminology used by investigators, searches were on "microtomography", "microCT" and "synchrotron tomography".

X-ray tomography is a workhorse tool of non-destructive imaging. It is used to probe three-dimensional structures across a wide range of length scales for objects that offer good absorption contrast to x-rays. In recent years extremely high resolution imaging (on the order of tens of nanometres) has become possible due to technological advances in x-ray optics. At the same time the requirement for strong absorption contrast has been relaxed thanks to the advent of new experimental and algorithmic techniques in phase imaging. Advances in both resolution and phase imaging can be combined to image biological samples at the sub-cellular level. I will report on recent advances in our work including improvements to the current approaches in extracting phase information at high resolution from measurements of the diffracted intensity from a sample. I will also discuss our current experimental status.

Many objects relevant to materials science, biology and medicine are weakly absorbing to the hard energy x rays typically produced by laboratory sources. However, these samples can produce significant shifts in the phase of the x rays, which can be exploited using in-line phase contrast. This paper describes the work carried out to optimize phase contrast tomography using a polychromatic laboratory source. A variety of different phase retrieval algorithms are compared for two samples, one of uniformly low absorption contrast, the other comprising soft and hard materials, with a view to establishing basic guidelines for laboratory phase contrast tomography.

Taking advantage of the fact that an X-ray Talbot interferometer functions with X-rays of a broad energy bandwidth, high-speed X-ray phase tomography has been demonstrated by using white synchrotron light. Time resolution in addition to three-dimensional spatial resolution has been attained, and we report this achievement as the first four-dimensional (4D) X-ray phase tomography. Moire image movies of samples rotating at a speed of 1 or 2 rps generated by a Talbot interferometer were recorded at a frame rate of up to 1 kf/s, and differential phase image movies of the same frame rate were created by the Fourier-transform method. Consequently, a sub-second time resolution was achieved in the 4D phase tomography, while the spatial resolution was below 0.1 mm and 0.05 mm in axial and in-plane directions, respectively. An X-ray Talbot interferometer generates visibility images in addition to differential phase images, showing the distribution of microstructures, which cause ultra-small angle scattering but cannot be resolved individually with system spatial resolution. Tomographic image reconstruction from the visibility images was also demonstrated.

In this paper we describe the design of different X-ray Talbot interferometers that have been built at the tomography beamline ID19 of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, and give a short review of performance characteristics, of current developments, and of the results obtained with these instruments so far. Among the applications so far, soft-tissue imaging has been a particular focus, as demonstrated in a recent paper by Schulz et al. (J. Roy. Soc. Interface, in press).

X-ray phase-contrast radiography and tomography enables to increase contrast for weakly absorbing materials. Recently, x-ray grating interferometers were developed which extend the possibility of phase-contrast imaging from highly brilliant radiation sources like third-generation synchrotron even to non-coherent sources. Here, we present a setup of an x-ray grating interferometer designed and installed at low-coherence wiggler source at the GKSS beamline W2 (HARWI II) operated at the second-generation synchrotron storage ring DORIS at the Deutsches Elektronen-Synchrotron (DESY, Hamburg, Germany). The beamline is dedicated to imaging in materials science. Equipped with the grating interferometer, it is the first synchrotron radiation beamline with a three-grating setup combining the advantages of phase-contrast imaging with monochromatic radiation with very high flux and a sufficiently large field of view for centimeter sized objects. Examples of radiography on laser-welded aluminum and magnesium joints are presented to demonstrate the high potential of the new gratingbased setup in the field of materials science. In addition, the results of an off-axis phase-contrast tomography of a human urethra with 15 mm in diameter are presented showing internal structures, which cannot be resolved by the conventional tomography in absorption mode.

Phase contrast imaging with conventional X-ray tubes as e.g. in computer tomography scanners (CTscanners) requires a setup of three different types of optical gratings. One grating is used to obtain a spatially coherent radiation, the second grating defines a periodic phase shift and the third is used as a periodic absorption grating. In order to absorb high energy radiation, absorption gratings with periods of a few microns only and extreme aspect ratios (>80) are fabricated, employing a modified LIGA process. However, above a critical structural height, structures collapse due to e.g. capillary effects. To overcome this limitation a new variant of the LIGA process has been developed. It is characterized by structuring of a resist on both sides of a membrane, resulting in a moderate aspect ratio on both sides of the membrane instead of an extreme aspect ratio on one side. To get a perfect overlay of both structures the grating structure on the front side of a membrane patterned by the standard LIGA-process is used as the mask for structuring the second resist layer on the backside of the membrane. A second electroforming step fills the gaps on the backside.

A facility for x-ray computed microtomography (CMT) is operating as a national user facility for earth and environmental sciences research on the bending magnet beamline at the GeoSoilEnviroCARS sector at the Advanced Photon Source (APS). We present an analysis of the source of noise in the reconstructed data, compared to data on similar samples from another instrument. We also report on careful characterization of the CCD detector, on new highspeed data collection strategies, and applications to high-pressure tomography.

The unique beam characteristics of PETRA III at DESY promote novel applications for many scientific fields, including imaging applications. For tomography these are techniques like high-speed and in-situ measurements marked by highest density resolutions and spatial resolutions down to the nanometer range. Furthermore, the high coherence enables phase contrast applications in an exceptional way. Therefore, the Imaging Beamline IBL is equipped with two dedicated endstations, one for micro and one for nano tomography. In addition, a very flexible X-ray and light optics concept is implemented. The micro tomography endstation is designed for samples requiring (sub-) micrometer resolution. The technical specifications of the nano tomography endstation aim for a spatial resolution of below 100 nm. The nanometer resolution will be achieved by using different combinations of compound refractive lenses as X-ray optics. The overall setup is designed to be very flexible, which allows also the implementation of other optical elements as well as the application of different magnifying techniques.

Micro computed tomography has been developed to a powerful technique for the characterization of hard and soft human and animal tissues. Soft tissues including the urethra, however, are difficult to be analyzed, since the microstructures of interest exhibit X-ray absorption values very similar to the surroundings. Selective staining using highly absorbing species is a widely used approach, but associated with significant tissue modification. Alternatively, one can suitably embed the soft tissue, which requires the exchange of water. Therefore, the more recently developed phase contrast modes providing much better contrast of low X-ray absorbing species are especially accommodating in soft tissue characterization. The present communication deals with the morphological characterization of sheep, pig and human urethras on the micrometer scale taking advantage of micro computed tomography in absorption and phase contrast modes. The performance of grating-based tomography is demonstrated for freshly explanted male and female urethras in saline solution. The micro-morphology of the urethra is important to understand how the muscles close the urethra to reach continence. As the number of incontinent patients is steadily increasing, the function under static and, more important, under stress conditions has to be uncovered for the realization of artificial urinary sphincters, which needs sophisticated, biologically inspired concepts to become nature analogue.

Biocompatible materials such as porous bioactive calcium phosphate ceramics or titanium are regularly applied in dental surgery: ceramics are used to support the local bone regeneration in a given defect, afterwards titanium implants replace lost teeth. The current gold standard for bone reconstruction in implant dentistry is the use of autogenous bone grafts. But the concept of guided bone regeneration (GBR) has become a predictable and well documented surgical approach using biomaterials (bioactive calcium phosphate ceramics) which qualify as bone substitutes for this kind of application as well. We applied high resolution synchrotron microtomography and subsequent 3d image analysis in order to investigate bone formation and degradation of the bone substitute material in a three-dimensional manner, extending the knowledge beyond the limits of classical histology. Following the bone regeneration, titanium-based implants to replace lost teeth call for high mechanical precision, especially when two-piece concepts are used in order to guaranty leak tightness. Here, synchrotron-based radiography in comparison with classical laboratory radiography yields high spatial resolution in combination with high contrast even when exploiting micro-sized features in these kind of highly attenuating objects. Therefore, we could study micro-gap formation at interfaces in two-piece dental implants with the specimen under different mechanical load. We could prove the existence of micro-gaps for implants with conical connections as well as to study the micromechanical behavior of the mating zone of conical implants during loading. The micro-gap is a potential issue of failure, i. e. bacterial leakage which can induce an inflammatory process.

Minimally invasive deep brain neurosurgical interventions require a profound knowledge of the morphology of the human brain. Generic brain atlases are based on histology including multiple preparation steps during the sectioning and staining. In order to correct the distortions induced in the anisotropic, inhomogeneous soft matter and therefore improve the accuracy of brain atlases, a non-destructive 3D imaging technique with the required spatial and density resolution is of great significance. Micro computed tomography provides true micrometer resolution. The application to post mortem human brain, however, is questionable because the differences of the components concerning X-ray absorption are weak. Therefore, magnetic resonance tomography has become the method of choice for three-dimensional imaging of human brain. Because the spatial resolution of this method is limited, an alternative has to be found for the three-dimensional imaging of cellular microstructures within the brain. Therefore, the present study relies on the synchrotron radiationbased micro computed tomography in the recently developed grating-based phase contrast mode. Using data acquired at the beamline ID 19 (ESRF, Grenoble, France) we demonstrate that grating-based tomography yields premium images of human thalamus, which can be used for the correction of histological distortions by 3D non-rigid registration.

Multiple-source cone-beam scanning is a promising mode for dynamic volumetric CT/micro-CT. The first dynamic CT system is the Dynamic Spatial Reconstructor (DSR) built in 1979. The pursuance for higher temporal resolution has largely driven the development of CT technology, and recently led to the emergence of Siemens dual-source CT scanner. Given the impact and limitation of dual-source cardiac CT, triple-source cone-beam CT seems a natural extension for future cardiac CT. Our work shows that trinity (triple-source architecture) is superior to duality (dual-source architecture) for helical cone-beam CT in terms of exact reconstruction. In particular, a triple-source helical scan allows a perfect mosaic of longitudinally truncated cone-beam data to satisfy the Orlov condition and yields better noise performance than the dual-source counterpart. In the (2N+1)-source helical CT case, the more sources, the higher temporal resolution. In the N-source saddle CT case, a triple-source scan offers the best temporal resolution for continuous dynamic exact reconstruction of a central volume. The recently developed multi-source cone-beam algorithms include an exact backprojection-filtration (BPF) approach and a "slow" exact filtered-backprojection (FBP) algorithm for (2N+1)-source helical CT, two fast quasi-exact FBP algorithms for triple-source helical CT, as well as a fast exact FBP algorithm for triple-source saddle CT. Some latest ideas will be also discussed, such as multi-source interior tomography and multi-beam field-emission x-ray CT.

In 1981, Elliott and Dover designed an X-ray microtomography scanner as a means of measuring the local mineral concentration in teeth. Although slow, this first generation system gave accurate measurements of the X-ray linear attenuation coefficient (LAC) due to its use of energy dispersive photon counting apparatus. Attaining such accuracy with integrating detectors in third generation scanners is difficult, but has been the goal of our ongoing development. The current "MuCat 2" system uses a 6cm square CCD chip with a parallel fibre-optic faceplate coupled to a CsI scintillator. Time delay integration readout (with sliding camera) is used to eliminate ring artefacts and enable high dynamic range X-ray projections to be acquired. The beam is collimated with a moving aperture (tracking the camera) to reduce X-ray scatter. Beam hardening is reduced by the use of filtering and corrected using data from an aluminium step wedge to optimise a model of polychromatic X-ray generation, attenuation and detection. Adjustments can be made to the model to allow for known specimen composition. Projections are corrected for distortion and repeatable wobble in the rotation stage. Where high absolute accuracy of the LAC is required, a pure aluminium wire is included in the scan and used to "fine-tune" the grey level after reconstruction.

We present a simple, robust, and versatile solution to the problem of blurred tomographic images as a result of imperfect geometric hardware alignment. The necessary precision for the alignment between the various components of a tomographic instrument is in many cases technologically difficult to implement, or requires impractical stability. Misaligned projection sets are not self-consistent and give blurred tomographic reconstructions. We have developed an off-line software method that utilises a geometric model to parameterise the alignment, and an algorithm for determining the alignment parameter set that gives the sharpest tomogram. It is an adaptation of passive auto-focus methods that have been used to obtain sharp images in optical instruments for decades. To minimise computation time, the auto-focus strategy is a multi-scale iterative technique implemented on a selection of 2D cross-sections of the tomogram. For each cross-section, the sharpness is evaluated while scanning over various combinations of alignment parameters. The parameter set that maximises sharpness is used to reconstruct the 3D tomogram. To apply the corrections, the projection data are re-mapped, or the reconstruction algorithm is modified. The entire alignment process takes less time than that of a full-scale 3D reconstruction. It can in principle be applied to any cone or parallel beam CT with circular, helical, or more general trajectories. It can also be applied retrospectively to archived projection data without any additional information. This concept is fully tested and implemented for routine use in the ANU micro-CT reconstruction software suite and has made the entire reconstruction pipeline robust and autonomous.

Nowadays, thanks to the high brilliance available at modern, third generation synchrotron facilities and recent developments in detector technology, it is possible to record volumetric information at the micrometer scale within few minutes. High signal-to-noise ratio, quantitative information on very complex structures like the brain micro vessel architecture, lung airways or fuel cells can be obtained thanks to the combination of dedicated sample preparation protocols, in-situ acquisition schemes and cutting-edge imaging analysis instruments. In this work we report on recent experiments carried out at the TOMCAT beamline of the Swiss Light Source [1] where synchrotron-based tomographic microscopy has been successfully used to obtain fundamental information on preliminary models for cerebral fluid flow [2], to provide an accurate mesh for 3D finite-element simulation of the alveolar structure of the pulmonary acinus [3] and to investigate the complex functional mechanism of fuel cells [4]. Further, we introduce preliminary results on the combination of absorption and phase contrast microscopy for the visualization of high-Z nanoparticles in soft tissues, a fundamental information when designing modern drug delivery systems [5]. As an outlook we briefly discuss the new possibilities offered by high sensitivity, high resolution grating interferomtery as well as Zernike Phase contrast nanotomography [6].

We are creating a state-of-the-art 2D and 3D imaging atlas of zebrafish development. The atlas employs both 2D histology slides and 3D benchtop and synchrotron micro CT results. Through this atlas, we expect to document normal and abnormal organogenesis, to reveal new levels of structural detail, and to advance image informatics as a form of systems biology. The zebrafish has become a widely used model organism in biological and biomedical research for studies of vertebrate development and gene function. In this work, we will report on efforts to optimize synchrotron microCT imaging parameters for zebrafish at crucial developmental stages. The aim of these studies is to establish protocols for high-throughput phenotyping of normal, mutant and diseased zebrafish. We have developed staining and embedding protocols using different heavy metal stains (osmium tetroxide and uranyl acetate) and different embedding media (Embed 812 and glycol methacrylate). We have explored the use of edge subtraction and multi-energy techniques for contrast enhancement and we have examined the use of different sample-detector distances with unstained samples to explore and optimize phase-contrast enhancement effects. We will report principally on our efforts to optimize energy choice for single- and multi-energy studies as well as our efforts to optimize the degree of phase contrast enhancement.

Conventional X-ray CT is not usually sufficient to determine microscopic compositional distributions. A dataconstrained microstructure modeling (DCM) methodology has been developed which uses multiple CT data sets acquired with different X-ray spectra, and incorporates them as model constraints. The DCM approach has been applied to predict the distributions of corrosion inhibitor and filler in a polymer matrix. The DCM-predicted compositional microstructures have a reasonable agreement with EDX images taken on the sample surface.

Over the past decade computed tomography (CT) with conventional x-ray sources has evolved from an imaging method in medicine to a well established technology for industrial applications in fields such as material science, light metals and plastics processing, microelectronics and geology. By using modern microfocus and nanofocus X-ray tubes, parts can be scanned with sub-micrometer resolutions. Currently, micro-CT is a technology increasingly used for metrology applications in the automotive industry. CT offers big advantages compared with conventional tactile or optical coordinate measuring machines (CMMs). This is of greater importance if complex parts with hidden or difficult accessible surfaces have to be measured. In these cases, CT offers the advantage of a high density of measurement points and a non-destructive and fast capturing of the sample's complete geometry. When using this growing technology the question arises how precise a μCT based CMM can measure as compared to conventional and established methods for coordinate measurements. For characterizing the metrological capabilities of a tactile or optical CMM, internationally standardized parameters like length measurement error and probing error are defined and used. To increase the acceptance of CT as a metrological method, our work seeks to clarify the definition and usage of parameters used in the field of metrology as these apply to CT. In this paper, an overview of the process chain in CT based metrology will be given and metrological characteristics will be described. For the potential user of CT as 3D metrology tool it is important to show the measurement accuracy and repeatability on realistic samples. Following a discussion of CT metrology techniques, two samples are discussed. The first compares a measured CT Data set to CAD data using CMM data as a standard for comparison of results. The second data second realistic data set will compare the results of applying both the CMM method of measurement and the CT method of measurement within the same CT data set. A comparison of these results to the data obtained by means of CT shows that state of the art high resolution CT can provide measurement accuracy on the order of established coordinate measurement techniques.

We present a description of our departments work flow that utilises X-ray micro-tomography in the observation and prediction of physical properties of porous rock. These properties include fluid flow, dissolution/deposition, fracture mapping, and mechanical processes, as well as measurement of three-dimensional (3D) morphological attributes such as pore/grain size and shape distributions, and pore/grain connectivity. To support all these areas there is a need for well integrated and parallel research programs in hardware development, structural description and physical property modelling. Since we have the ability to validate simulation with physical measurement, (and vice versa), an important part of the integration of all these techniques is calibration at every stage of the work flow. For example, we can use high-resolution scanning electron microscopy (SEM) images to verify or improve our sophisticated segmentation algorithm based on image grey-levels and gradients. The SEM can also be used to obtain sub-resolution porosity information estimated from tomographic grey-levels and texture. Comparing experimental and simulated mercury intrusion porosimetry can quantify the effective resolution of tomograms and the accuracy of segmentation. The foundation of our calibration techniques is a robust and highly optimised 3D to 3D image-based registration method. This enables us to compare the tomograms of successively disturbed (e.g., dissolved, fractured, cleaned, ...) specimens with an original undisturbed state. A two-dimensional (2D) to 3D version of this algorithm allows us to register microscope images (both SEM and quantitative electron microscopy) of prepared 2D sections of each specimen. This can assist in giving a multimodal assessment of the specimen.

Most X-ray systems are limited in spatial resolution by the x-ray source performance. In laboratory sources, x-rays are generated by the interaction of an electron beam with a metal target. Bulk target sources produce a spot size in the micron range. Thin layer targets allow a spot size improvement down to hundreds of nanometers, but with a significant flux reduction. Until now a spatial resolution under 100 nm could only be achieved by imaging with Fresnel zone plates with limited depth of focus, typically - several microns. This is acceptable for imaging of flat objects, but it creates a problem for tomography, which requires all parts of a bulk object to be in focus. To overcome the limitations, we invented an x-ray source with a new type of target. Because x-ray cameras can only collect photons from a small angle, the new emitter is physically shaped in such way that the camera can see it as a small dot, but it has a big length along the direction perpendicular to the camera creating a significant flux without compromising the resolution. Evaluation shows that structures down to 50 nm can be distinguished while maintaining a significant x-ray flux and infinite depth of focus required for nano-tomographical reconstruction.

High resolution x-ray computed tomography is a powerful non-destructive 3-D imaging method. It can offer superior resolution on objects that are opaque or low contrast for optical microscopy. Synchrotron based x-ray computed tomography systems have been available for scientific research, but remain difficult to access for broader users. This work introduces a lab-based high-resolution x-ray nanotomography system with 50nm resolution in absorption and Zernike phase contrast modes. Using this system, we have demonstrated high quality 3-D images of polymerized photonic crystals which have been analyzed for band gap structures. The isotropic volumetric data shows excellent consistency with other characterization results.

We have developed an x-ray computer tomography (CT) add-on to perform X-ray micro- and nanotomography in any scanning electron microscope (SEM). The electron beam inside the SEM is focused on a metal target to generate x-rays. Part of the X-rays pass through the object that is installed on a rotation stage. Shadow X-ray images are collected by a CCD camera with direct photon detection mounted on the external wall of the SEM specimen chamber. An extensive description on the working principles of this micro/nano-CT add-on together with some examples of CT-scans will be given in this paper. The resolution that can be obtained with this set-up and the influence of the shape of the electron beam are discussed. Furthermore, possible improvements on this SEM-CT set-up will be discussed: replacing the backilluminated CCD with a fully depleted CCD with improved quantum efficiency (QE) for higher energies, reduces the exposure time by 6 when using metal targets with x-ray characteristic lines around 10 keV.

Proper selection of modern key components allows eliminating most artifacts in micro-CT and nano-CT systems already during data acquisition. X-ray cameras with direct photon detection allow avoiding ring artifacts. Newly developed fully depleted CCD sensors show an energy response similar to traditional cameras with a thin scintillator, but without any geometrical distortions and flashes from x-ray photons penetrating through the fiber optics. Air-bearing rotation stages and piezo-positioning minimizes mechanical inaccuracies in acquiring angular projections. Beam hardening can be eliminated by energy-selective photon counting imaging.

While classic CT theory targets exact reconstruction of a whole cross-section or of an entire object from complete projections, practical applications often focus on much smaller internal ROIs. Traditional CT methods cannot exactly reconstruct an internal ROI only from local truncated projections associated with x-rays through the ROI, because this interior problem does not have a unique solution. When applying approximate local CT algorithms for interior reconstruction from truncated projection data, features outside the ROI may create artifacts overlapping inside features, rendering the images inaccurate or useless. Recently, novel solutions for the interior problem were published by our group with numerical results demonstrating that the interior problem can be solved in a theoretically exact and numerically stable fashion aided by some prior knowledge, such as a small known sub-region inside the ROI or the ROI can modeled by piecewise constant/polynomial function. In this invited paper, we will review the recent progress in local reconstruction. The topic includes lambda tomography, analytic and iterative interior reconstructions, with an emphasis on total variation minimization based soft-threshold methods and statistical based interior reconstruction algorithms.

In the field of restoration of ancient handworks, X-ray tomography is a powerful method to reconstruct the internal structure of the object in non-invasive way. In some cases, such as small objects fully realized with hard metals and completely hidden by clay or products of oxidation, the tomography, although necessary to obtain the 3D appearance of the object, does not give any additional information on its internal monolithic structure. We present here the application of the shape-from-silhouette technique on X-ray images to reconstruct the 3D profile of handworks. The acquisition technique is similar to tomography, since several X-ray images are taken while the object is rotated. Some reference points are placed on a structure co-rotating with the object and are acquired on the images for calibration and registration. The shape-from-silhouette algorithm gives finally the 3D appearance of the handwork. We present the analysis of a tin pendant of VI-VIII century b.C. (Venetian area) completely hidden by solid ground. The 3D reconstruction shows surprisingly that the pendant is a very elaborated piece, with two embraced figures that were completely invisible before restoration.

Scintillators, optical systems and CCD cameras used to record projections also blur them. Therefore the recorded projections are smooth functions of spatial variables. This can be used to construct special methods to suppress ring artefacts. Several such algorithms based on ideas of the theory of inverse and ill-posed problems and using various forms of Tikhonov functional are proposed: a fast ring artefact suppression algorithm in a case of homogeneous specimens and its modified versions for anisotropically attenuated samples.

Highly brilliant X-rays delivered by third generation synchrotron facilities coupled with modern detector technology permit routinely acquisition of high resolution tomograms in few minutes, making high throughput experiments a reality and bringing real-time tomography closer. New solutions for fast post-processing of such large amount of data are mandatory to fully exploit advantages provided by the high acquisition speed enabling new experiments until recently even unimaginable. The TOMCAT beamline¹ is well equipped for fast and high throughput experiments^{2, 3}. Here, we will focus on our solutions regarding the reconstruction process and discuss a fast reconstruction algorithm⁴, based on the Fourier Transform method as opposed to slower standard Filtered Back-Projection routines. We perform the critical step of such method, the polar-to-Cartesian mapping in the Fourier space, by convolution with the Fourier transform of functions with particular characteristics. This convolution approach combines speed with accuracy, making real-time data postprocessing closer to reality. This fast reconstruction algorithm implemented at TOMCAT also features several plug-ins, aimed at taming reconstruction artifacts. Here, we will discuss a new approach for removing rings from reconstructed datasets arising from defective detector pixels and/or damaged scintillator screens. This new method is based on a combined wavelet- FFT decomposition⁵. Another important feature of the presented reconstruction algorithm deals with local tomographic datasets, characterized by incomplete data. We show here that ad-hoc padding of the sinograms prior to reconstruction significantly reduces typical artifacts related to data incompleteness, making local tomography a valuable acquisition mode when small volumes in relatively large samples are of interest.

Laminography is a technique for 3D volume reconstruction, extending the classical tomography to the estimation of local areas in lamellar objects. We demonstrate X-ray phase laminography by using an X-ray Talbot interferometer consisting of two transmission gratings, which has been used only for X-ray phase tomography. In this presentation, experiments using 17.7 keV synchrotron radiation through a double-crystal monochromator are reported. The X-rays passed through the sample placed in front of the first phase grating. The rotation axis of the sample was set almost parallel to the sample plane normal, and inclined from the X-ray beam. Behind the second amplitude grating, moiré fringe patterns were measured by displacing one of the gratings in the direction parallel to its diffraction vector. Differential phase information were extracted through the fringe-scanning method. For the reconstruction of the three-dimensional volume from the differential phase information, the filtered back projection method was used with a specific filtering function. Promising results of phase laminography reconstruction are obtained for simulation data as well as weakly absorbing lamellar objects such as a polymer meshes and other samples. This advancement extends experiments with X-ray Talbot volume reconstruction to a larger variety of samples.

Photon counting detectors are of growing importance in medical imaging because they enable routine measurement of photon energy. Detectors such as Medipix2 and Medipix3 record the energy of incident photons with minimal loss of spatial resolution. Their use is being investigated for both pre-clinical and clinical applications of X-ray CT. The Medipix3 detector has 256 x 256 55 μm pixels and a silicon or cadmium telluride detector layer, giving a spatial resolution comparable to mammographic film. Each Medipix pixel can be seen as an individual spectral detector. The logic circuits for each pixel (some 1300 transistors) can analyze incoming events at megahertz rates, comparing the charge of the electron-hole cloud with preset levels, giving a resolution of about 2 keV across the range of 8 - 140 keV. A prototype CT scanner has been developed for laboratory animals and excised specimens. Applications under investigation include: K-edge imaging: Using spectral information to measure heavy elements (e.g., preparations of iodine, barium, and gadolinium) and Soft tissue contrast: Dual energy systems have shown that image contrast for soft tissue can be improved, e.g., distinguishing between iron and calcium within vascular plaques.

We have constructed a helical trajectory X-ray micro-CT system which enables high-resolution tomography within practical acquisition times. In the quest for ever-increasing resolution, lab-based X-ray micro-CT systems are limited by the spot size of the X-ray source. Unfortunately, decreasing the spot size reduces the X-ray flux, and therefore the signal-to-noise ratio (SNR). The reduced source flux can be offset by moving the detector closer to the source, thereby capturing a larger solid angle of the X-ray beam. We employ a helical scanning trajectory, accompanied by an exact reconstruction method to avoid the artifacts resulting from the use of large cone-angles with circular trajectories. In this paper, we present some challenges which arise when adopting this approach in a high-resolution cone-beam micro-CT system.

Traditionally, phase proportions in igneous rocks have been estimated by optical microscopy of thin-sectioned rocks to study the mineralogy and identify the proportions of equilibrium phases. For example, an in-depth investigation of basaltic igneous rocks recovered from the oceanic crust at Hess Deep, 110Km west of the Galapagos Islands used phase proportions estimated from petrography to verify results calculated from chemical analyses of the basaltic samples. Chemical analysis divided these samples into two groupings based on their relative FeO content. Those with low-FeO contents dominated the volcanic rock subset and those with higher-FeO contents dominated the intrusive subset. Calculations based on the chemical analyses suggested that plagioclase (an Fe-poor phase) had accumulated in magmas and resulted in the low-FeO group. Petrographic microscopy supported the calculations by verifying that plagioclase exist in relatively greater abundance in the low-FeO group compared to the high-FeO group. Optical microscopy requires the rock samples be sectioned and polished, and then each section is individually imaged in only two dimensions by the petrographic microscope. From these images modal percent of phases is determined for a threedimensional sample. Using nondestructive x-ray tomography and three-dimensional image analysis, we produce a more accurate assessment of phase proportions using an intact lava sample from the low-FeO group, and provide a threedimensional perspective on the relationship between phases in the rocks unavailable with standard petrographic microscopy techniques.

Direct composite fillings belong to widespread tooth restoration techniques in dental medicine. The procedure consists of successive steps, which include etching of the prepared tooth surface, bonding and placement of composite in incrementally built up layers. Durability and lifespan of the composite inlays strongly depend on the accurate completion of the individual steps to be also realized by students in dental medicine. Improper handling or nonconformity in the bonding procedure often lead to air enclosures (bubbles) as well as to significant gaps between the composite layers or at the margins of the restoration. Traditionally one analyzes the quality of the restoration cutting the tooth in an arbitrarily selected plane and inspecting this plane by conventional optical microscopy. Although the precision of this established method is satisfactory, it is restricted to the selected two-dimensional plane. Rather simple micro computed tomography (μCT) systems, such as SkyScan 1174™, allows for the non-destructive three-dimensional imaging of restored teeth ex vivo and virtually cutting the tomographic data in any desired direction, offering a powerful tool for inspection of the restored tooth with micrometer resolution before cutting and thus also to select a two-dimensional plane with potential defects. In order to study the influence of the individual steps on the resulted tooth restoration, direct composite fillings were placed in mod cavities of extracted teeth. After etching, an adhesive was applied in half of the specimens. From the tomographic datasets, it becomes clear that gaps occur more frequently when bonding is omitted. The visualization of air enclosures offers to determine the probability to find a micrometer-sized defect using an arbitrarily selected cutting plane for inspection.

An integrated microCT/microXRF system has been designed and built at SkyScan. The two sub-systems are aligned. The microCT provides 3D morphological information of the sample, which can be also used for attenuation correction during microXRF reconstruction. The microXRF, based on a pin-hole collimator and a photon-counting energy-sensitive 2Ddetector, obtains 2D projections of 3D chemical composition inside the sample with 50-70 microns spatial resolution. The reconstruction of 3D microXRF scans is challenging because of very low photon counting statistics due to limited power of laboratory x-ray sources and the strong self-absorption of the low-energy fluorescence photons. We have developed a maximum-likelihood expectation-maximization (ML-EM) algorithm based on Poisson model. This algorithm has proven to be rather robust and good reconstructions have been obtained with sample scans. Regularization is necessary to achieve stable reconstruction. One method is to apply smoothing between iterations. Two different smoothing kernels have been evaluated: 3D symmetric Gaussian kernel and minimization of total variation. For further improvement, a multi-ray resolution recovery technique has been evaluated. The self-absorption is currently compensated by a simplified method: the correction coefficients are pre-calculated and obtained by forward-projecting the attenuation map for both the primary X-rays and the fluorescence photons. The attenuation maps at the energy of fluorescence photons are approximated from the CT image.

X-ray fluorescence (XRF) allows imaging of the chemical composition of a specimen. We developed a 2^nd generation prototype laboratory system that can produce 3D chemical maps using microXRF as well as volumetric microCT images. The latter can be used to overlay morphological information on top of the XRF image for co-registration. It is also employed for attenuation correction during the tomographic reconstruction of the XRF images. The new system has various hardware and software changes to improve the performance, stability and flexibility. A deep depleted CCD was employed to improve the detection efficiency for high-energy fluorescence X rays. The use of a deep depleted CCD requires signal-clustering techniques to correct for charge diffusion in the CCD to obtain the correct energy of the fluorescence x rays. Furthermore, energy drift correction techniques were put in place to ensure stability of energy measurement during very long scan times. To minimize the contribution of the long CCD readout times to the total scan time, the exposure frames are dynamically adjust during the scan to the maximum time allowed for operation under photon counting mode. The XRF component has a spatial resolution of 70 μm and an energy resolution of 180 eV at 6.4 keV.

This paper presents a feasibility study of using emission tomography (ET) systems for synchrotron X-ray fluorescence computer tomography (XFCT). The proposed detection system combines high-resolution semiconductor detectors with multiple-pinhole apertures. The key advantage of using an ET-based detection system is that 3D distributions of trace elements can be built up with much reduced scanning motion and potentially without need for tomographic reconstruction. In comparison to the conventional line-by-line scanning scheme, the ET-based imaging system allows a great reduction in imaging time, which has been one of the major hurdles for current XFCT studies. In order to compare different imaging schemes for XFCT studies, we developed an analytical performance index that is based on the fundamental tradeoffs between image noise and spatial resolution achievable with given detection configurations. To further demonstrate the feasibility of using SPECT apertures for XFCT, a prototype CCD-based multiple-pinhole imaging system was set up at the Advanced Photon Source (APS) for imaging phantoms that contain solutions of several trace metals. Simultaneously acquired 3D distributions of these elements are presented.

Cone-beam computed tomography, also termed digital volume tomography, has become a standard technique in dentistry, allowing for fast 3D jaw imaging including denture at moderate spatial resolution. More detailed X-ray images of restricted volumes for post-mortem studies in dental anthropology are obtained by means of micro computed tomography. The present study evaluates the impact of the pipe smoking wear on teeth morphology comparing the abraded tooth with its contra-lateral counterpart. A set of 60 teeth, loose or anchored in the jaw, from 12 dentitions have been analyzed. After the two contra-lateral teeth were scanned, one dataset has been mirrored before the two datasets were registered using affine and rigid registration algorithms. Rigid registration provides three translational and three rotational parameters to maximize the overlap of two rigid bodies. For the affine registration, three scaling factors are incorporated. Within the present investigation, affine and rigid registrations yield comparable values. The restriction to the six parameters of the rigid registration is not a limitation. The differences in size and shape between the tooth and its contra-lateral counterpart generally exhibit only a few percent in the non-abraded volume, validating that the contralateral tooth is a reasonable approximation to quantify, for example, the volume loss as the result of long-term clay pipe smoking. Therefore, this approach allows quantifying the impact of the pipe abrasion on the internal tooth morphology including root canal, dentin, and enamel volumes.

During the last decade, several tissues and biomaterials for medical applications in replacing bony tissues have been developed. Three-dimensional cell clusters and mandibular bone grafts are two distinct examples of these developments. The characterization of the complex three-dimensional structures, however, is still mainly restricted on the twodimensional analysis of histological slices. The present paper examines the quantitative analysis of mandibular bone grafts and three-dimensional cell clusters on the basis of synchrotron radiation-based micro computed tomography measurements. An automated search of pre-defined microstructures through component labeling is applied to the real datasets in order to identify features that reside independently from other components. The examples demonstrate three levels of complexity: rather large pieces of bone augmentation material that touch each other, individual adipocytes difficult to automatically segment in a wet cluster and osmium-stained adipocyte exhibiting higher X-ray absorption than the surrounding tissue. Although the structures of interest such as the cells can be labeled, de-clustering of the components requires the incorporation of erosion and dilation algorithms.

The increased susceptibility to fracture of root canal- and post-treated teeth is less affected by alterations of the dentin structure, but seems to crucially depend on the loss of coronal tooth substance. The surface, available for adhesion of the composite material in the root canal and in the coronal part of the tooth, is assumed to be of key importance for the fracture resistance. Thus, an appropriate three-dimensional method should be identified to determine the adhesive surface with necessary precision. For this purpose, severely decayed teeth were simulated decapitating clinical crowns. After root canal filling and post space preparation, impressions of the root canal and the amputation surface were obtained using silicone. Micro computed tomography scans of these impressions were acquired. For one selected specimen, an additional high-resolution scan was recorded at a synchrotron radiation source. Software of ImageLab served for the extraction of the amputation interface, the post surface and the post volume from the tomography data, which have been finally correlated with the Young's modulus and the maximal load derived from mechanical tests. The morphological parameters show a realistic relationship to the mechanical tests performed after the restoration treatments and are consequently important for improving the dental skills.

The long-standing interior problem has been recently revisited, leading to promising results on exact local reconstruction also referred to as interior tomography. To date, there are two key computational ingredients of interior tomography. The first ingredient is inversion of the truncated Hilbert transform with prior sub-region knowledge. The second is compressed sensing (CS) assuming a piecewise constant or polynomial region of interest (ROI). Here we propose a statistical approach for interior tomography incorporating the aforementioned two ingredients as well. In our approach, projection data follows the Poisson model, and an image is reconstructed in the maximum a posterior (MAP) framework subject to other interior tomography constraints including known subregion and minimized total variation (TV). A deterministic interior reconstruction based on the inversion of the truncated Hilbert transform is used as the initial image for the statistical interior reconstruction. This algorithm has been extensively evaluated in numerical and animal studies in terms of major image quality indices, radiation dose and machine time. In particular, our encouraging results from a low-contrast Shepp-Logan phantom and a real sheep scan demonstrate the feasibility and merits of our proposed statistical interior tomography approach.

The world-wide explosion of commercial microComputed Tomography (microCT) system emplacement has led to dayin, day-out access to laboratory scanners. Most biologically-oriented microCT facilities must characterize large numbers of samples rapidly at moderate spatial resolution (e.g., 10-20 μm isotropic volume elements, voxels). Scanning multiple specimens simultaneously is one efficient solution. Sample positioning is critical if the region of interest of each specimen is to be imaged without increasing the number of slices recorded (i.e., data acquisition and reconstruction times). Three very different, multiple sample data acquisitions are reported: mouse heart tissue calcification, rat spinal fusion and mouse tibial bone cancer models

Shape memory alloys (SMAs) belong to 'intelligent' materials since the metal alloy can change its macroscopic shape as the result of the temperature-induced, reversible martensite-austenite phase transition. SMAs are often applied for medical applications such as stents, hinge-less instruments, artificial muscles, and dental braces. Rapid prototyping techniques, including selective laser melting (SLM), allow fabricating complex porous SMA microstructures. In the present study, the macroscopic shape changes of the SMA test structures fabricated by SLM have been investigated by means of micro computed tomography (μCT). For this purpose, the SMA structures are placed into the heating stage of the μCT system SkyScan 1172™ (SkyScan, Kontich, Belgium) to acquire three-dimensional datasets above and below the transition temperature, i.e. at room temperature and at about 80°C, respectively. The two datasets were registered on the basis of an affine registration algorithm with nine independent parameters - three for the translation, three for the rotation and three for the scaling in orthogonal directions. Essentially, the scaling parameters characterize the macroscopic deformation of the SMA structure of interest. Furthermore, applying the non-rigid registration algorithm, the three-dimensional strain field of the SMA structure on the micrometer scale comes to light. The strain fields obtained will serve for the optimization of the SLM-process and, more important, of the design of the complex shaped SMA structures for tissue engineering and medical implants.

Quantitation of coherent x-ray scatter traditionally involves measuring the intensity of the scattered x-ray over a range of angles (θ) from the illuminating monochromatic x-ray beam. Spectral x-ray imaging produces the same information at a single θ when bremsstrahlung x-ray exposure is used. We used a 200μm thick sheet-illumination of a phantom (lucite cylinder containing holes with water, polyethylene, collagen, polycarbonate, and nylon) and a polycapillary x-ray optic collimator to provide measurements at a fixed θ. A Medipix2 x-ray detection array (256² (55μm)² pixels) provided the spectral (E, 10 - 22 keV in 3keV energy bins) spread needed to generate the momentum transfer (q) profile information at one angle. The tungsten x-ray source anode (aluminum filter) was operated at 35kVp at 20mA. The detected scatter intensity was corrected for attenuation of the incident and the scattered x-ray by use of the regular CT image of the phantom generated at the same energy bins. The phantom was translated normal to the plane of the fan beam in 65, 0.2mm, steps to generate the 3D image data. The momentum transfer profiles generated with this approach were compared to published momentum transfer profiles obtained by other methods.

Propagation-based phase contrast imaging allows low absorbing materials to be studied non-destructively using hard xrays, generating additional edge contrast through interference effects. Here we will present recent work undertaken at Manchester University's "Henry Moseley X-ray Imaging Facility" studying the applicability of lab-based phase contrast tomography to the imaging of spider specimens preserved in a range of amber types. New spider species are identified using distinctive anatomical features, including the modified structures of the anterior leg-like appendages (pedipalps) of mature males. We will describe three different strategies adopted in dealing with the phase artefacts inherent to the technique, giving a clean segmentation of important features and resulting in the classification of new species.