This PDF file contains the front matter associated with SPIE Proceedings Volume 7078, including the Title Page, Copyright information, Table of Contents, Introduction (if any), and the Conference Committee listing.

Because x-rays can penetrate almost any object and yield information of the interior of specimens opaque to visible light, they have been used as a powerful tool for the investigation of all kinds of materials and bodies right from their discovery by Conrad Roentgen¹ in 1895. Among the multitude of different ways such studies can be performed the imaging methods play a predominant and most important role. The intent is to describe some interesting and relevant ways x-ray imaging has been employed up to now. Clinical tomography will be excluded here. Recent surveys exist in the literature, e.g.².

The way in which microtomography developed in the authors' laboratory in the early 1980s is described, together with some background material. Later developments in scanning geometries and detectors, mainly in other laboratories, are described. Some present problems and possible future directions will be considered.

Trends in the type and distribution of published micro- and nano-CT studies are reviewed in this paper. The focus is on the temporal evolution of the literature over the last decade and on the distribution of study types and on the distribution of locations where such studies have appeared. Data analysis and representations are also briefly considered.

A BFU is an organ's smallest assembly of diverse cells that functions like the organ, such as the liver's hepatic lobules. There are approximately 10⁷ BFUs in a human organ. These 100-200 μm structures are perfused by capillaries fed by a terminal arteriole (15μm diameter). BFU sizes, function and number per organ vary with disease, either by loss of BFUs and/or their decrease in function. The BFU is the upper limit of a spherical assembly of cells, immersed in a suitably nutrient medium, which can survive without its own blood supply. However, each BFU has its own blood supply to support the extra energy and/or solutes needed for providing its physiological function (e.g., contraction or secretion). A BFU function is best evaluated by its micro-perfusion, which can be readily evaluated with whole-body CT. Resolution of individual BFUs within in-situ organs, using clinical imaging devices, would require high radiation doses and/or the intolerably long scan-durations needed for suitable signal-to-noise image-data. However, it is possible to obtain a statistical description of the BFU number, size and function from wholebody CT by way of a model. In this study we demonstrate this capability by using the distribution of myocardial terminal arteriolar perfusion territories by way of a nested, multiple, regions-of-interest analysis of the heart wall imaged during transient opacification of its blood supply.

Dual source CT (DSCT) has the potential to solve remaining limitations of conventional multi-detector row CT (MDCT)-scanners, such as insufficient temporal resolution for ECG-controlled cardiac imaging. A DSCT is equipped with two X-ray tubes and two corresponding detectors that are mounted onto the rotating gantry with an angular offset of 90°. The key benefit of DSCT for cardiac scanning is improved temporal resolution equivalent to a quarter of the gantry rotation time (83 ms at 0.33 s rotation time). Additionally, both X-ray tubes can be operated at different kV- and mA-settings, enabling the acquisition of dual energy data. The acquisition of dual energy CT data can add functional information to the morphological information based on different X-ray attenuation coefficients that is usually obtained in a CT examination.

The need for table motion in multi-detector CT causes image volumes acquired for whole organ motion and perfusion studies to lack temporal uniformity. The next revolution in clinical CT, dynamic volume CT, mitigates this limitation by providing the ability to acquire an entire organ with isotropic resolution in a single gantry rotation with no table movement. The first dynamic volume CT scanner has recently been introduced and comprises 320 detector rows of 0.5mm channel thickness, covering 16cm of anatomy in one rotation of 0.35sec. This scanner offers many advancements in terms of temporal uniformity, reconstruction, and radiation dose. This system significantly reduces motion artifact and eliminates contrast phase differences within the volume. Because this scanner does not require helical acquisition for volumetric imaging, it delivers significantly less dose for applications such as CT coronary angiography exams as well as reduced dose in most other applications. Furthermore, by eliminating table motion, the need for complex interpolation methods that can distort cardiac images is removed. Image quality is not sacrificed compared with standard 64-row CT scanners, as demonstrated via low contrast, resolution, and accuracy measurements presented in this work. By capturing the entire brain in one rotation, brain perfusion, bone subtraction, and quantitative perfusion analysis are now possible with a single low dose exam. Dynamic volume CT offers to change the way medicine approaches stroke patients, myocardial perfusion studies, and imaging of other moving body parts such as the lung and joints.

High resolution micro-CT scanners are becoming widely used for in vivo imaging of small laboratory animals. However, imaging of chest area remains a challenging task due to periodic respiratory and cardiac motion, where respiratory motion dominates. To reduce motion artifacts and to allow dynamic imaging, we propose a retrospective synchronization method for scans of chest area in our in vivo micro-CT scanners. In this synchronization method, we acquire projection images in a step-and-shoot mode, where multiple images are acquired covering more than one motion cycle at each step with exact time marks of every acquisition. In the meanwhile motion signals are recorded. An offline sorting program has been developed to sort images into corresponding motion phases. We have evaluated our method on respiratory motion. Compared to prospective synchronization methods, our method has several advantages: 1. flexible in sorting; 2. continuous imaging: maximum utilization of radiation dose applied to the animal; 3. possibility for 4D dynamic imaging; 4. can be used during irregular breathing cycle. This method has been applied to two of SkyScan in-vivo scanners. Initial results indicate that the proposed method is adequate.

Understanding the morphology of anatomical structures is a cornerstone of biology. For small animals, classical methods such as histology have provided a wealth of data, but such techniques can be problematic due to destruction of the sample. More importantly, fixation and physical slicing can cause deformation of anatomy, a critical limitation when precise three-dimensional data are required. Modern techniques such as confocal microscopy, MRI, and tabletop x-ray microCT provide effective non-invasive methods, but each of these tools each has limitations including sample size constraints, resolution limits, and difficulty visualizing soft tissue. Our research group at the Advanced Photon Source (Argonne National Laboratory) studies physiological processes in insects, focusing on the dynamics of breathing and feeding. To determine the size, shape, and relative location of internal anatomy in insects, we use synchrotron microtomography at the beamline 2-BM to image structures including tracheal tubes, muscles, and gut. Because obtaining naturalistic, undeformed anatomical information is a key component of our studies, we have developed methods to image fresh and non-fixed whole animals and tissues. Although motion artifacts remain a problem, we have successfully imaged multiple species including beetles, ants, fruit flies, and butterflies. Here we discuss advances in biological imaging and highlight key findings in insect morphology.

Cancer belongs to the primary diseases these days. Although different successful treatments including surgery, chemical, pharmacological, and radiation therapies are established, the aggressive proliferation of cancerous cells and the related formation of blood vessels has to be better understood to develop more powerful strategies against the different kinds of cancer. Angiogenesis is one of the crucial steps for the survival and metastasis formation of malignant tumors. Although therapeutic strategies attempting to inhibit these processes are being developed, the biological regulation is still unclear. This study concentrates on the three-dimensional morphology of vessels formed in a mouse tumor xenograft model post mortem. Synchrotron radiation-based micro computed tomography (SRμCT) could provide the necessary information that is essential for validating the simulations. Using mouse and human brain tissue, the different approaches to extract the vessel tree from SRμCT data are discussed. These approaches include corrosion casting, the application of contrast agents such as barium sulfate, tissue embedding, all of them regarded as materials science based. Alternatively, phase contrast tomography was used, which gave rise to promising results but still not reaches the spatial resolution to uncover the smallest capillaries.

Investigations of bony tissues are often performed using micro computed tomography based on X-rays, since the calcium distribution leads to superior contrast. Osteoporotic bone, for example, can be well compared with healthy one with respect to density and morphology. Degenerative and rheumatoid diseases usually start, however, at the bone-cartilage-interface, which is hardly accessible. The direct influence on the bone itself becomes only visible at later stage. For the development of suitable therapies against degenerative cartilage damages the exact three-dimensional description of the bone-cartilage interface is vital, as demonstrated for transplanted cartilage-cells or bone-cartilage-constructs in animal models. So far, the morphological characterization was restricted to magnetic resonance imaging (MRI) with poor spatial resolution or to time-consuming histological sectioning with appropriate spatial resolution only in two rather arbitrarily chosen directions. Therefore, one should develop μCT to extract the features of low absorbing cartilage. The morphology and the volume of the inter-vertebral cartilage disc of lumbar motion segments have been determined for one PMMA embedded specimen. Tomograms were recorded using nanotom® (Phoenix|x-ray, Wunstorf, Germany), μCT 35^TM (Scanco Medical, Brütisellen, Switzerland), 1172^TM and 1174^TM (both Skyscan, Kontich, Belgium), as well as using the SRμCT at HASYLAB/DESY. Conventional and SRμCT can provide the morphology and the volume of cartilage between bones. Increasing the acquisition time, the signal-to-noise ratio becomes better and better but the prominent artifacts in conventional μCT as the result of inhomogeneously distributed bony tissue prevents the exact segmentation of cartilage. SRμCT allows segmenting the cartilage but requires long periods of expensive beam-time to obtain reasonable contrast.

Evolutionary research in biology relies on the comparison of different individuals of different species in order to explore the history of today's biodiversity. Synchrotron radiation based high resolution X-ray tomography (SRμCT) rapidly generates detailed three dimensional datasets. At the beamlines W2 and BW2 of the storage ring DORIS at DESY, Hamburg, Germany, we used SRμCT to study the cranial anatomy of different species and different developmental stages of caecilians (Lissamphibia: Gymnophiona). Here we describe a work-flow for analysis of the SRμCT data that covers segmentation of tissues in Amira® (Mercury Computer Systems), photorealistic rendering and animation in Maya^TM, rapid prototyping, and morphometrics. The integration of different analyses of SRμCT data in our study resulted in a comprehensive understanding of form, function, and evolution of caecilian skulls. SRμCT imaging has the potential to become a standard technique for life sciences applications in the near future.

The investigation of micro-vessel dimensions in 3D is currently problematic due to their complex structures and fine scale. Quantification of vascular parameters is important in several fields of biomedicine; including embryogenesis, wound healing, diseases characterized by uncontrolled angiogenesis (e.g. tumor growth and metastasis) and the development of implantable bio-materials where a functional vascular supply is critical to their successful integration into host tissue. However, techniques that can resolve the micron-scaled features of these capillary beds, such as scanning electron and confocal microscopy, do not allow for total image reconstitution in 3D in thick tissue samples [1]. The present study describes the use of an in vivo corrosion casting technique that provides a stable replica of the microvascular network and the subsequent evaluation of three different μCT systems in order to accurately quantify vessel dimensions. Stable replicas of micro-vascular networks in neonatal mouse eyes were first created using in vivo vascular corrosion casting and then imaged using a unique, laboratory scale, μCT unit. This system combines a LaB₆ cathode with high-performance electron optics to obtain a high resolution x-ray source. Novel image analysis was then applied to the reconstructions to quantify the morphological parameters of the hyaloid vascular plexi in the developing eyes of post-natal day 2 (P2) wild-type mice. These results are compared to synchrotron scans, establishing vascular casting and x-ray μCT as a valid laboratory scale experimental method for accurate 3D quantification of the microvasculature, with potential applications to a wide variety of fields in biological and medical research.

The conventional wisdom states that the interior problem (reconstruction of an interior region from projection data along lines only through that region) is NOT uniquely solvable. While it remains correct, our recent theoretical and numerical results demonstrated that this interior problem CAN be solved in a theoretically exact and numerically stable fashion if a sub-region within the interior region is known. In contrast to the well-established lambda tomography, the studies on this type of exact interior reconstruction are referred to as "interior tomography". In this paper, we will overview the development of interior tomography, involving theory, algorithms and applications. The essence of interior tomography is to find the unique solution from highly truncated projection data via analytic continuation. Such an extension can be done either in the filtered backprojection or backprojection filtration formats. The key issue for the exact interior reconstruction is how to invert the truncated Hilbert transform. We have developed a projection onto convex set (POCS) algorithm and a singular value decomposition (SVD) method and produced excellent results in numerical simulations and practical applications.

The Radon transform and its inversion are the mathematical keys that enable tomography. Radon transforms are defined for continuous objects with continuous projections at all angles in [0,π). In practice, however, we pre-filter discrete projections taken at a discrete set of angles and reconstruct a discrete object. Since we are approximating a continuous transform, it would seem that acquiring more projections at finer projection resolutions is the path to providing better reconstructions. Alternatively, a discrete Radon transform (DRT) and its inversion can be implemented. Then the angle set and the projection resolution are discrete having been predefined by the required resolution of the tomogram. DRT projections are not necessarily evenly spaced in [0, π), but are concentrated in directions which require more information due to the discrete square [or cubic] grid of the reconstruction space. A DRT, by design, removes the need for interpolation, speeding up the reconstruction process and gives the minimum number of projections required, reducing the acquisition time and minimizing the required radiation dose. This paper reviews the concept of a DRT and demonstrates how they can be used to reconstruct objects from X-ray projections more efficiently in terms of the number of projections and to enable speedier reconstruction. This idea has been studied as early as 1977 by Myron Katz. The work begun by Katz has continued and many methods using different DRT versions have been proposed for tomographic image reconstruction. Here, results using several of the prominent DRT formalisms are included to demonstrate the different techniques involved. The quality and artifact structure of the reconstructed images are compared and contrasted with that obtained using standard filtered back projection.

In this paper, a hybrid helix-saddle trajectory scanning mode is proposed for bolus-chasing CT angiography. By combining the conventional helical trajectory and saddle trajectory appropriately, an optimal curve can be obtained with a capability of localized volumetric imaging at desirable locations. In this context, a condition for the PI-line existence is determined. Then, both filtered-backprojection (FBP), backprojection filtration (BPF) and reduced-scan FBP algorithms are developed. Numerical studies with the 3D Shepp-Logan phantom support the validity and merits of the proposed trajectories and associated algorithms.

In the cone-beam composite-circling mode, the trajectory is composited by two circular motions. An x-ray focal spot within an x-ray source is rotated at constant or variable speeds on a plane facing a short object to be reconstructed, while the x-ray tube is rotated around the object on the gantry plane. In this paper, we describe an algorithm for determining the boundary surface of the region for PI-line-based exact reconstruction using composite-circling curves. Such an exact reconstruction region consists of all PI-segments on the scanning curve. For different combinations of scanning parameters, we find the radius of the largest sphere centered at the origin that can be embedded in the region. The exact reconstruction region is found to be the largest, reaching the radius of the focal spot circling facing the object, when the ratio of the focal spot circling frequency to the x-ray tube rotation frequency is two. The numerical results are also compared with those of standard saddle curves.

In this paper, we propose an exact shift-invariant filtered backprojection (FBP) algorithm for triple-source saddle-curve cone-beam CT. In this imaging geometry, the sources are symmetrically positioned along a circle, and the trajectory of each x-ray source is a saddle. Then, we extend Yang's formula from the single-source case to the triple-source case. The saddles can be divided into four parts to specify four datasets. Each of them contains three data segments associated with different saddles. Then, images can be reconstructed on the planes orthogonal to the z-axis. Each plane intersects the trajectories at six pointes which can be used to define the filtering directions. With our triple-source approach, the scanning time is only one-third of that with the single-source saddle trajectory, and the reconstructed image quality is excellent in our numerical studies. These new features are important for cardiac imaging and small animal imaging.

The root/periodontal ligament/bone (RPB) interface is important for a correct understanding of the load transfer mechanism of masticatory forces and orthodontic loads. It is the aim of this study to assess the three-dimensional structure of the RPB interface using high-resolution microtomography. A human posterior jaw segment, obtained at autopsy from a 22-year old male donor was first scanned using a tomograph at the HASYLAB/DESY synchrotron facility (Hamburg, Germany) at 31μm resolution. Afterwards the first molar and its surrounding bone were removed with a 10mm hollow core drill. From this cylindrical sample smaller samples were drilled out in the buccolingual direction with a 1.5mm hollow core drill. These samples were scanned at 4μm resolution. The scans of the entire segment showed alveolar bone with a thin lamina dura, supported by an intricate trabecular network. Although featuring numerous openings between the PDL and the bone marrow on the other side to allow blood vessels to transverse, the lamina dura seems smooth at this resolution. First at high resolution, however, it becomes evident that it is irregular with bony spiculae and pitted surfaces. Therefore the stresses in the bone during physiological or orthodontic loading are much higher than expected from a smooth continuous alveolus.

Synchrotron radiation-based micro computed tomography (SRμCT) is well established to determine the degree of mineralization in bony tissue. The present study demonstrates that the method can be likewise used for three-dimensional analyses of dentin de- and remineralization. Four dentin discs about 4 mm in diameter and 0.8 mm thick were prepared from freshly extracted human third molars. In order to study the de- and re-mineralization, three of them were treated with 10% citric acid for the period of 10 min. Nano-particulate bioactive glass made of SiO₂, P₂O₅, CaO, Na₂O served for the re-mineralization in physiological saline. This process was carried out at the incubation temperature of 37 °C for 1 and 7 d, respectively. The native and the treated discs were comparatively examined by SRμCT in absorption contrast mode. Already the visual inspection of the tomograms obtained reveals remarkable differences related to the mean X-ray absorption and internal microstructure. The de-mineralization led to a surface morphology characteristic for the treated dentin collagen matrix. The re-mineralized discs show a dependence on the period of the treatment with the bio-active glass suspension. Initial signs of the remineralization were clearly present already after 24 h of incubation. The disc incubated for 7 d exhibits a degree of mineralization comparable to the native control disc. Thus, SRμCT is a powerful non-destructive technique for the analysis of dentin de- and re-mineralization.

Three-dimensional images are vital for the diagnosis in dentistry and cranio-maxillofacial surgery. Artifacts caused by highly absorbing components such as metallic implants, however, limit the value of the tomograms. The dominant artifacts observed are blowout and streaks. Investigating the artifacts generated by metallic implants in a pig jaw, the data acquisition for the patients in dentistry should be optimized in a quantitative manner. A freshly explanted pig jaw including related soft-tissues served as a model system. Images were recorded varying the accelerating voltage and the beam current. The comparison with multi-slice and micro computed tomography (CT) helps to validate the approach with the dental CT system (3D-Accuitomo, Morita, Japan). The data are rigidly registered to comparatively quantify their quality. The micro CT data provide a reasonable standard for quantitative data assessment of clinical CT.

MIRRORCLE is a noble hard X-ray source, which is quite different from either X-ray tubes or synchrotron light sources (SLS) in many regards. MIRRORCLE generates very parallel and high-density photons like SLS, but the source emitter size is much smaller than SLS as well as tube. The radiation angular spread is much wider than SLS and similar to tube. Thus diagnosis of human body size is possible. The X-ray spectrum is polychromatic peaking around 30-200 keV, which is higher than SLS, while X-ray tube uses characteristic X-rays. The photon energy is selectable with MIRRORCLE by changing the target material and thickness. Because of these wonderful features the imaging by MIRRORCLE demonstrates 10 to 100 times magnifications, extremely sharp edge enhancement due to the phase contrast, and one micron order spatial resolution without optical elements. Density mapping is demonstrated in a simple plane magnified imaging. When tomography is applied, density volume mapping is obtained.

X-ray fluorescence computed tomography (XFCT) is a synchrotron-based imaging modality employed for mapping the distribution of elements within slices or volumes of intact specimens. A pencil beam of external radiation is used to stimulate emission of characteristic X-rays from within a sample, which is scanned and rotated through the pencil beam in a first-generation tomographic geometry. While this line-by-line acquisition is slow, it does provide remarkable flexibility in sampling, since the sampling intervals and patterns are not limited by detector hardware as they are in many imaging modalities. In this work we discuss several ways of exploiting this flexibility to increase imaging speed without sacrificing image quality. This includes: (1) scanning only the half of the object nearest the detector while rotating through 360 degrees, (2) performing so-called interlaced sampling in which the sampling patterns at even and odd projection views are offset relative to one another, and (3) performing 3D helical scanning in which only the half of the object nearest the detector is scanned. The helical sampling is coupled with a novel Fourier-based interpolation scheme we have previously introduced for helical CT.

We have developed a compact laboratory scanner, which combines X-ray microtomography (microCT) with X-ray microfluorescence tomography (3D microXRF). This dual-modality scanner opens possibility for nondestructive threedimensional volumetric analysis of local chemical composition, enhanced by morphological information provided by the built-in microCT. Unlike known microXRF methods based on collimated beam and detector, our microXRF scanner includes a full-field acquisition system based on an energy-sensitive detector with 512x512 pixels operating in photon counting mode. It allows detection of two-dimensional photon energy distribution in the range of 3...20keV. Up to 8 sets of energy windows can be selected for independent and simultaneous collection of microXRF images. By object rotation the scanner acquires projections in transmission and fluorescence mode for subsequent 3D reconstruction. The system acquires data in such a way that the CT scans and XRF scans match each other in magnification and angular position. This makes image registration much easier and more accurate. MicroCT data is reconstructed with a FBP algorithm. All microXRF datasets are reconstructed by a maximum likelihood iterative algorithm, which uses corresponding CT images for absorption correction.

X-ray fluorescence computed tomography (XFCT) is a synchrotron-based imaging modality employed for mapping the distribution of elements within slices or volumes of intact specimens. A pencil beam of external radiation is used to stimulate emission of characteristic X-rays from within a sample, which is scanned and rotated through the pencil beam in a first-generation tomographic geometry. It has long been believed that for each slice, the acquired measurement lines must span the entire object at every projection view over 180 degrees to avoid reconstructing images with so-called truncation artifacts. However, recent developments in tomographic reconstruction theory have overturned those long-held beliefs about minimum-data requirements and shown that it is possible to obtain exact reconstruction of ROIs from truncated projections. In this work, we show how to exploit these developments to allow for region of interest imaging in XFCT.

In the field of tissue engineering, micro computed tomography (μCT) should allow non-destructively assessing the extra-cellular matrix deposited by cells within porous scaffolds in-vitro. While synchrotron radiation-based μCT combines micrometer resolution with a high signal-to-noise ratio (contrast), recent advances in desktop μCT devices have achieved comparable results with benefits in availability and user-friendliness. In this study we compare the performance of the commercially available, entry-level desktop device 1174 (SkyScan, Belgium) with the μCT at HASYLAB (DESY, Hamburg, Germany) by characterizing porous interconnected 3D scaffolds and monitoring the development of engineered human bone constructs upon culture in such an environment. Expansion of human osteogenic cells has been performed with the use of perfusion bioreactors and 3D scaffolds, serving as cell carriers. Constructs based on low X-ray absorbing, rapid-prototyped fibrous scaffolds were analyzed with a nominal spatial resolution of better than 5 μm. Direct 3D image analysis allowed for the accurate quantification of the scaffold morphometry parameters, where both μCT techniques yielded comparable results. However, due to the monochromatic nature of X-rays available at the synchrotron radiation source, drastically reduced beam hardening effects and higher density resolution (higher dynamic range) has been obtained at HASYLAB. Studies in this direction could be useful to highlight the mechanisms that are involved in bone-like tissue growth and to further understand how it can be affected by the choice of cell type, 3D culture environment and scaffold type and architecture.

Nowadays, X-ray tube-based high-resolution CT systems are widely used in scientific research and industrial applications. But the potential, convenience and economy of these lab systems is often underestimated. The present paper shows the comparison of sophisticated conventional μCT with synchrotron radiation-based μCT (SRμCT). The different aspects and characteristics of both approaches like spatial and density resolution, penetration depth, scanning time or sample size is described in detail. The tube-based μCT measurements were performed with a granite-based nanotom®-CT system (phoenix|x-ray, Wunstorf, Germany) equipped with a 180 kV - 15 W high-power nanofocus® tube with tungsten or molybdenum targets. The tube offers a wide range of applications from scanning low absorbing samples in nanofocus® mode with voxel sizes below 500 nm and highly absorbing objects in the high power mode with focal spot and voxel sizes of a few microns. The SRμCT measurements were carried out with the absorption contrast set-up at the beamlines W 2 and BW 2 at HASYLAB/DESY, operated by the GKSS Research Center. The range of samples examined covers materials of very different absorption levels and related photon energies for the CT scans. Both quantitative and qualitative comparisons of CT scans using biomedical specimens with rather low X-ray absorption such as parts of the human spine as well as using composites from the field of materials science are shown.

Over the last decade, synchrotron-based X-ray tomographic microscopy has established itself as a fundamental tool for non-invasive, quantitative investigations of a broad variety of samples, with application ranging from space research and materials science to biology and medicine. Thanks to the brilliance of modern third generation sources, voxel sizes in the micrometer range are routinely achieved by the major X-ray microtomography devices around the world, while the isotropic 100 nm barrier is reached and trespassed only by few instruments. The beamline for TOmographic Microscopy and Coherent rAdiology experiments (TOMCAT) of the Swiss Light Source at the Paul Scherrer Institut, operates a multimodal endstation which offers tomographic capabilities in the micrometer range in absorption contrast - of course - as well as phase contrast imaging. Recently, the beamline has been equipped with a full field, hard X-rays microscope with a theoretical pixel size down to 30 nm and a field of view of 50 microns. The nanoscope performs well at X-ray energies between 8 and 12 keV, selected from the white beam of a 2.9 T superbend by a [Ru/C]₁₀₀ fixed exit multilayer monochromator. In this work we illustrate the experimental setup dedicated to the nanoscope, in particular the ad-hoc designed X-ray optics needed to produce a homogeneous, square illumination of the sample imaging plane as well as the magnifying zone plate. Tomographic reconstructions at 60 nm voxel size will be shown and discussed.

The BAMline at the BESSY light source in Berlin and the TopoTomo beamline at the ANKA synchrotron facility in Karlsruhe (both Germany) operate in the hard X-ray regime (above 6 keV) with similiar photon flux density. For typical imaging applications, a double multilayer monochromator or a filtered white beam is used. In order to optimise the field of view and the resolution of the available indirect pixel detectors, different optical systems have been installed, adapted, respectively, to a large field of view (macroscope) and to high spatial resolution (microscope). They can be combined with different camera systems, ranging from 16-bit dynamic range slow-scan CCDs to fast CMOS cameras. The spatial resolution can be brought substantially beyond the micrometer limit by using a Bragg magnifier. The moderate flux of both beamlines compared to other 3rd generation light sources is compensated by a dedicated scintillator concept. For selected applications, X-ray beam collimation has proven to be a reliable approach to increase the available photon flux density. Absorption contrast, phase contrast, holotomography and refraction-enhanced imaging are used depending on the application. Additionally, at the TopoTomo beamline digital white beam synchrotron topography is performed, using the digital X-ray pixel detectors installed.

Due to the high brilliance of the new storage ring PETRA III at DESY in Hamburg, the low emittance of 1 nmrad and the high fraction of coherent photons also in the hard X-ray range extremely intense and sharply focused X-ray light will be provided. These advantages of the beam fulfill excellently the qualifications for the planned Imaging BeamLine IBL and the High Energy Materials Science Beamline (HEMS) at PETRA III, i.e. for absorption tomography, phase enhanced and phase contrast experiments, for diffraction, for nano focusing, for nano tomography, and for high speed or in-situ experiments with highest spatial resolution. The existing HARWI II beamline at the DORIS III storage ring at DESY completes the GKSS beamline concept with setups for high energy tomography (16-150 keV) and diffraction (16-250 keV), characterized by a large field of view and an excellent absorption contrast with spatial resolutions down to 2 μm.

X-ray computed tomography (XCT) is a powerful non-invasive imaging tool for biomedical applications. It provides not only morphology but also the absolute value of the linear attenuation coefficient distribution of the specimen in three dimensions, which is helpful in osteoporosis and other component-sensitive studies. Spatial resolution and specimen size are coupled through the detector's field of view (FOV) and the number of elements in the area detector. When the FOV is smaller than the specimen size, the truncated-data problem arises, which can cause large errors in the values of the volume elements (voxels) in the reconstruction. Zoom-in tomography is a technique that images a small region of interest (ROI) in a large-size specimen with high resolution and uses low-resolution data for the entire specimen to reduce reconstruction errors in the ROI. We developed a method to estimate the residual error in linear attenuation coefficient values persisting in zoom-in tomography and used it to judge the accuracy of zoom-in tomographic reconstructions. In this work, we imaged a sample of trabecular bone with zoom-in tomography and quantified differences in voxel values, concentrating on comparisons of low and high mineral regions of the bone.

The sensitivity of X-ray phase tomography based on Talbot(-Lau) interferometry is discussed. A criterion is described to evaluate the superiority of the technique in comparison to the conventional absorption-contrast method. An experimental result of X-ray phase tomography with a Talbot interferometer is compared with the criterion. The advantage of X-ray phase tomography based on Talbot(-Lau) interferometry is more prominent when smaller structures are observed with smaller pixels.

In X-ray phase-contrast tomography imaging studies, the object of interest may be larger than the field of view (FOV) of the imaging system, resulting in a set of truncated tomographic projections. In this work, we adapt recent advancements in conventional reconstruction theory to X-ray phase-contrast tomography, and demonstrate that the Laplacian of the refractive index distribution can be reconstructed exactly within certain regions-of-interest from knowledge of truncated phase-contrast projection data.

Quantitative in-line phase-contrast imaging methods seek to reconstruct separate images that depict an object's absorption and real-valued refractive index distributions. An understanding of the statistical properties of images in planar and tomographic implementations of X-ray phase-contrast imaging is required for optimizing system and algorithm designs using task-based measures of image quality. In this work, the statistical properties of phase-contrast imaging are investigated by use of analytical and computer-simulation methods.

X-ray phase-contrast tomographic microimaging is a powerful tool to reveal the internal structure of opaque soft-matter objects that are not easily seen in standard absorption contrast. In such low Z materials, the phase shift of X-rays transmitted can be important as compared to the absorption. An easy experimental set up that exploits refractive contrast formation can deliver images that are providing detailed structural information. Applications are abundant in fields including polymer science and engineering, biology, biomedical engineering, life sciences, zoology, water treatment and filtration, membrane science, and micro/nanomanufacturing. However, available software for absorptive contrast tomography cannot be simply used for structure retrieval as the contrast forming effect is different. In response, CSIRO has developed a reconstruction code for phase-contrast imaging. Here, we present a quantitative comparison of a micro phantom manufactured at SSLS with the object reconstructed by the code using X-ray images taken at SSLS. The phantom is a 500 μm thick 800 μm diameter cylindrical disk of SU-8 resist having various eccentric cylindrical bores with diameters ranging from 350 μm to 40 μm. Comparison of these parameters that are well known from design and post-manufacturing measurements with reconstructed ones gives encouraging results.

We report advances and complementary results concerning a recently developed method for high-sensitivity grating-based hard x-ray phase tomography. We demonstrate how the soft tissue sensitivity of the technique can be used to obtain in-vitro tomographic images of a tumor bearing rat brain specimen, without use of contrast agents. In particular, we demonstrate that brain tumors and the white and gray brain matter structure in a rat's cerebellum can be resolved by this approach. The findings are potentially interesting from a clinical point of view, since a similar approach using three transmission gratings can be implemented with more readily available x-ray sources, such as standard x-ray tubes. Moreover, open the results the way to in-vivo experiments in the near future.

X-ray imaging is of paramount importance for clinical and pre-clinical applications but it is fundamentally restricted by the attenuation-based contrast mechanism, which has remained essentially the same since Roentgen's discovery a century ago. Recently, based on the Talbot effect, groundbreaking work was reported using 1D gratings for x-ray phase-contrast imaging with a hospital-grade x-ray tube instead of a synchrotron or micro-focused source. In this paper, we report an extension of our earlier 2D-grating-based work to the case of Gaussian beams. This 2D-grating-based approach has the potential to reduce the imaging time, increase the spatial coherence, and enhance the accuracy and robustness compared to current 1D-grating-based phase-contrast imaging techniques.

Phase-contrast imaging using grating interferometers has been developed over the last few years for x-ray energies of up to 28 keV. We have now developed a grating interferometer for phase-contrast imaging that operates at 60 keV x-ray energy. Here, we show first phase-contrast projection and CT images recorded with this interferometer using an x-ray tube source operated at 100 kV acceleration voltage. By comparison of the CT data with theoretical values, we find that our measured phase images represent the refractive index decrement at 60 keV in good agreement with the theoretically expected values. The extension of phase-contrast imaging to this significantly higher x-ray energy opens up many new applications of the technique in industry, medicine, and research.

We are developing and exploring the imaging performance of, an in vivo, in-line holography, x-ray phase-contrast, micro-CT system with an ultrafast laser-based x-ray (ULX) source. By testing and refining our system, and by performing computer simulations, we plan to improve system performance in terms of contrast resolution and multi-energy imaging to a level beyond what can be obtained using a conventional microfocal x-ray tube. Initial CT projection sets at single energy (Mo K_α and K_β lines) were acquired in the Fresnel regime and reconstructed for phantoms and a euthanized mouse. We also performed computer simulations of phase-contrast micro-CT scans for low-contrast, soft-tissue, tumor imaging. We determined that, in order to perform a phase-contrast, complete micro-CT scan using ULX, the following conditions must be met: (i) the x-ray source needs to be stable during the scan; (ii) the laser focal spot size needs to be less than 10 μm for source-to-object distance greater than 30 cm; (iii) the laser light intensity on the target needs to be in the range of 5 × 10¹⁷ to 5 × 10¹⁹ W/cm²; (iv) the ablation protection system needs to allow uninterrupted scans; (v) the laser light focusing on the target needs to remain accurate during the entire scan; (vi) a fresh surface of the target must be exposed to consecutive laser shots during the entire scan; (vii) the effective detector element size must be less than 12 μm. Based on the results obtained in this research project, we anticipate that the new 10 Hz, 200 TW laser with 50W average power that is being commissioned at ALLS will allow us practical implementation of in vivo x-ray phase-contrast micro-CT.

We discuss theoretical, experimental and numerical aspects of several new techniques for quantitative phase-contrast tomography using, for example, unfiltered radiation from a polychromatic X-ray microfocus source. The proposed algorithms allow one to reconstruct the three-dimensional distribution of complex refractive index in a sample consisting of one or more constituent materials, given one or more projection images per view angle. If the sample is weakly absorbing or consists predominantly of a single material, these reconstruction algorithms can be simplified and fewer projections may be required for an unambiguous quantitative reconstruction of the spatial distribution of the refractive index. In the case of weakly absorbing samples, the reconstruction algorithm is shown to be achromatic and stable with respect to high-spatial-frequency noise, in contrast to conventional tomography. A variation of the algorithm exploits the natural combination of binary tomography with a phase-retrieval method that makes explicit use of the single-material nature of the sample. Such consistent use of a priori knowledge dramatically reduces the number of required projections, implying significantly reduced dose and scanning time when compared to most alternative phase-contrast tomography methods. Experimental demonstrations are also given, using data from a point-projection X-ray microscope. The refractive index distribution, in test samples of both a polymer fibre scaffold and an adult mouse, is accurately reconstructed from polychromatic phase-contrast data. Applications of the new techniques to rapid non-destructive testing in materials science and biomedical imaging are considered.

Accurate models that describe the propagation of partially coherent wave fields and their interaction with refractive index inhomogeneities within a sample are required to optimally design X-ray phase-contrast imaging systems. Several methods have been proposed for the direct propagation of the second-order statistical properties of a wave field. One method, which has been demonstrated for x-ray microscopy, employs a single eikonal for propagation, approximating the phase by an average over the temporal Fourier components of the field. We have revisited this method by use of a coherent mode model from classic coherence theory. Our analysis produces a variant of the transport of intensity equation for partially coherent wave fields.

Micro-CT and especially nano-CT scanning requires very high mechanical precision and stability of object manipulator, which is difficult to reach. Several other problems, such as drift of emission point inside an X-ray source, thermal expansion in different parts of the scanner, mechanical vibrations, and object movement or shrinkage during long scans, can also contribute to geometrical inaccuracies. All these inaccuracies result in artifacts which reduce achievable spatial resolution. Linear distortions can be partially compensated by rigid X/Y shifts in projection images. More complicated object movement and shrinkage will require non-linear transforms. This paper investigates techniques to compensate geometrical inaccuracies by linear transformation only. We have developed two methods to estimate individual X/Y shifts in each measured projection. The first method aligns measured projections with forward-projected projections iteratively to reach an optimal X/Y shift estimation. It is more suitable for mechanical inaccuracies caused by random and jittery movement. The second method uses a very short reference scan acquired immediately after a main scan to obtain estimates of X/Y shifts. This method is rather effective for mechanical inaccuracies caused by slow and coherent mechanical drifts. Both methods have been implemented and evaluated on multiple scanners. Significant improvements in image quality have been observed.

During the last few years microtomography using synchrotron radiation (SR) has become a standard technique to characterize samples 3-dimensionally in the fields of biology, medicine and materials science. The GKSS Research Center Geesthacht, Germany, is responsible for developing and running the microtomography experiments at the SR-facility DESY, Hamburg, Germany. The application of SRμCT using attenuation-contrast at the beamlines W2/HARWI-II and BW2 of the storage ring DORIS III results in high throughput investigations. For achieving tomograms showing not only high spatial resolution but also high density resolution special emphasis was given to the stability of the used monochromators and the calibration of the total system. The influence of the photon statistic from the measurement to the tomograms is simulated and the achieved high density resolution is demonstrated showing selected results.

Beam hardening in X-ray tomography is often corrected using an arbitrary polynomial whose coefficients are subjectively selected. A better approach is to model X-ray generation, transmission and detection and to use step wedge transmission measurements to fit the model parameters. This allows for extrapolation of linearization curves beyond the range of the step wedge and it allows this curve to be adjusted according to the specimen composition without changing the composition of the step wedge. This paper presents the principles behind beam-hardening and the model used for correction. Initial tests of this method have shown very good results where a priori knowledge of the specimen composition is available.

Over the last years computed tomography (CT) with conventional x-ray sources has evolved from imaging method in medicine to a well established technology for industrial applications in the field of material science, microelectronics, geology, etc. By using modern microfocus and nanofocus® X-ray tubes, parts can be scanned with sub-micrometer resolutions. Currently, micro-CT is used more and more as a technology for metrological applications. Especially if complex parts with hidden or difficult accessible surfaces have to be measured, CT offers big advantages comparing with conventional tactile or optical coordinate measuring machines (CMMs): high density of measurement points and fast capturing of the complete sample's geometry. When using this modern technology the question arises how precise a CT based CMM can measure in comparison to conventional CMMs? To characterize the metrological capabilities of a tactile or optical CMM, internationally standardized characteristics like length measurement error and probing error are used. To increase the acceptance of CT as a metrological method, the definition and usage of these parameters is important. In this paper, an overview of the process chain in CT based metrology will be given and metrological characteristics will be described. With the help of a special material standard designed and calibrated by PTB-National Metrology Institute of Germany-the influence of methods for beam hardening correction and for surface extraction on the metrological characteristics will be analyzed. It will be shown that with modern micro-CT systems length measurement error of less than 1μm for an object diameter of 20 mm can be reached.

Knowledge on the geometry of pore networks of intra-aggregate soil pore spaces are of great value for many soil environmental processes. Advances in non-invasive 3D imaging techniques such as synchrotron-radiation-based microtomography offer an excellent opportunity to study the interrelationship of the pore network geometry with physical processes at a spatial resolution of a few micrometers. This paper presents results of a quantitative 3D pore space geometry analysis of small scale (~5mm across) soil aggregates from contrasting soil management systems. Soil aggregates have been scanned at the SR-μCT facility operated by the GKSS Research Center at HASYLAB / DESY (Hamburger Synchrotron Strahlungslabor / Deutsches Elektronen Synchrotron) in Hamburg/Germany. The achieved isotropic voxel resolution of the scans ranged from 2.4 to 5.4 μm. Three-dimensional reconstructions of the soil aggregates were analysed for various pore space features using a suite of algorithms based on mathematical morphology. Results have shown expected differences in distributions of pore size, throat size, channel length and width as well as tortuosity and connectivity of the intra-aggregate pores with potential implications for soil functions. Underlying image transformations and methods of visualization and quantification of soil pore networks will be discussed in view of their robustness and possible application of such information in soil related research fields.

A better understanding of micro deformation and damage processes that the microstructure of particle reinforced metal matrix composites (MMC_p) undergoes at microscale before macroscopical failure gives the right direction for the microstructural design of these materials. To this end, a μCT-based analysis was performed that combines μCT-experiments and FE simulations: The gauge length of tiny tensile specimens (cross-section A = 2 x 1 mm²) consisting of the MMC_p systems Cobalt/Diamond and Al/B₄C was imaged by tomography at different stages of deformation. 3D strain tensor fields and displacement vector fields were determined by digital image correlation of the reconstructed tomograms. Based on tomograms of the analyzed volume at the undeformed state, FE meshes were generated that model the microstructure close to reality. Using these meshes and the displacement vector fields measured at the volume boundaries, FE simulations of the deformation and damage behavior were carried out. In both composites volume strains below 1% have been found experimentally. The spatial resolution of deformation fields is limited by the characteristic microstructural length which depends on the particle diameter and the particle spacing. The results of the experiments and the simulations are compared on the basis of 3D-strain fields sampled within the analyzed microstructural region. Additionally, the impact of microstructural features on the localization of strain, the initiation of localized damage and the successive failure of the composite materials is discussed.

X-ray microtomography was applied for in-situ study of void coalescence during high-temperature creep of a brass alloy. Using image correlation techniques the movement of single slices and cavities connected to these images were monitored during deformation. Coalescence of voids was detected using ancestors analysis and independently checked with a geometrical parameter describing the distorted cavity shape. The analysis of in situ results suggests the existence of a critical volume fraction, as well as critical value of the ligament size between cavities at the onset of coalescence. The maximum number of primary coalescence events takes place in the tertiary stage of creep.

High-angular-resolution Fraunhofer diffraction data were collected from several samples with interfaces between dissimilar metals and an artificial crack in a metal foil using synchrotron x-radiation. The refractive index profile in the vicinity of the interface and crack of each sample was reconstructed with spatial resolution of about 40-60 nm by the Phase Retrieval X-Ray Diffractometry technique, using only limited a priori knowledge of the sample. These studies have demonstrated the viability of the technique as an in-situ nondestructive method of characterization of internal interfaces within multiphase materials and crack developing under external force.

The radio-contrast agent Angiofil has recently been developed to be predominantely applied in forensic medicine. Angiofil is a liquid radio-contrast agent based on iodine. Its viscosity is easy to adjust by the choice and the concentration of the solvent. Therefore, it is well suited for penetrating vessels of different diameters. The liquid Angiofil avoids the sedimentation of suspensions containing radio-opaque materials such as barium sulfate. The injection of Angiofil into the vascular system of mice post-mortem results in remarkable data showing the vascular trees of tissues and entire organs. Penetration into the surrounding tissue was not observed. Consequently, Angiofil has the potential to reach the performance of the established casting agent Microfil.

A system for high-resolution X-ray diagnostics is presented. It consists of a microfocus X-ray source with spot size of 5 μm that is operated in the 10-90 kV range. The detector is a Ce:YAG crystal coupled to a CCD camera with 5μm pixel size and 1392x1040 format. The magnification of the optical coupling is chosen in the 1 to 4 range, giving a spatial resolving element of 5 to 20 μm. The sample to be acquired is mounted on a motorized rototranslation stage for the automatic acquisition of the X-tay views both for tomography and phase-contrast imaging. The sample is positioned half-way between the source and the detector. X-ray images show very high contrast due to phase effects in addition to absorption. Some images of biological specimens are presented to assess the capability of revealing very low differences in density due to the presence of phase contrast. A complete high-resolution tomography of a drosophila is presented.

Reconstruction theory requires that an object should be fully inside the field of view (FOV) of the scanning geometry. This implies that the number of pixels in the detector determines the smallest resolvable details for a given FOV size. Many commercially available micro-CT scanners use a 1-megapixel cameras with 1K pixels in horizontal direction, which can resolve features of 1/1000 of the FOV size. Using a large format detector and a few offset positions will increase imaging resolution, but will also dramatically reduces number of X-ray photons collected per pixel. To improve acquisition efficiency without compromising scanning time, we developed and implemented in commercially produced SkyScan-1172 scanners an adaptive geometry approach. To achieve a chosen magnification, the distances between x-ray source, detector and object are adjusted automatically to most compact geometry with maximum use of X-ray. This adaptive geometry improves significantly the acquisition speed for a large range of magnifications and allows using 10+ megapixels detectors instead of detectors with 1-2 megapixels. Flexible acquisition geometry also opens possibility to use phase-contrast enhancement for improvement in spatial resolution.

Many detection systems for acquiring two-dimensional projections in emission tomography (like SPECT, micro-SPECT, micro-XRF) are based on pinhole optics and a photon counting array detector. Practically all such detection systems use a standard round pinhole with cone-shaped openings on both sides to improve efficiency for inclined beams. Theoretical analysis shows that a square pinhole with pyramidal openings can improve sensitivity and efficiency of photon detection of such detectors. Replacing a round/cone pinhole by a square/pyramidal one increases the number of counted photons in the central part of the image by 25% and even more in the sides and in the corners of the imaging area. In the case of multi-pinhole optics, square pinhole shape allows better filling of used detector area without overlaps of partial images. Experimental comparison between round and square pinholes has been done on a micro-XRF setup. The imaging geometry parameters are identical in both cases. Performance is evaluated on efficiency and spatial resolution. The tests show significant efficiency improvement in the case of using a camera with a square pinhole shape.

It has been shown that coherently scattered x-rays can be used to discriminate and identify specific components in a mixture of materials. To assess the feasibility of using coherent x-ray scatter (CXS) to characterize the material components within tissue scaffolds, we studied the CXS properties of the bio-compatible materials of polymers (polypropylene fumarate, polycaprolactone, epoxy, etc.), sugar and salt solutions at different concentration, and complex materials consisting of more than one polymer. We also investigated the effects of x-ray spectra on the CXS functions of polymers by measuring them with different x-ray source anodes. It is shown that the synthesized polymers with different portions of base polymers can be characterized with CXS. The polymerization process does not significantly change the CXS characteristics of the measured polymers. When protein is denatured, no substantial change in scatter was detected. Solutions of different concentration can be characterized and quantified by the CXS features corresponding to the solutes. The difference among CXS of solutions of different concentration makes it possible to image and trace fluids and their concentration changes in tissues or scaffolds. Our results show that CXS of complex specimens can be decomposed with the scatter functions of the component materials. By simulating a tissue scaffold with a phantom with several bio-compatible materials, we demonstrated that significant contrast can be achieved at proper scatter angles by measuring the coherent x-ray scatter, despite the low attenuation-based contrast between them. We conclude that use of x-ray scatter makes it possible to track and map the fate (e.g., its breakdown and/or removal) of specific components within tissue scaffolds.

There are surprisingly few experimental models of neural growth and cranial integration. This and the dearth of information regarding fetal brain development detract from a mechanistic understanding of cranial integration and its relevance to the patterning of skull form, specifically the role of encephalization on basicranial flexion. To address this shortcoming, our research uses transgenic mice expressing a stabilized form of β-catenin to isolate the effects of relative brain size on craniofacial development. These mice develop highly enlarged brains due to an increase in neural precursors, and differences between transgenic and wild-type mice are predicted to result solely from variation in brain size. Comparisons of wild-type and transgenic mice at several prenatal ages were performed using microCT (Scanco Medical MicroCT 40) and microMRI (Avance 600 WB MR spectrometer). Statistical analyses show that the larger brain of the transgenic mice is associated with a larger neurocranium and an altered basicranial morphology. However, body size and postcranial ossification do not seem to be affected by the transgene. Comparisons of the rate of postcranial and cranial ossification using microCT also point to an unexpected effect of neural growth on skull development: increased fetal encephalization may result in a compensatory decrease in the level of cranial ossification. Therefore, if other life history factors are held constant, the ontogeny of a metabolically costly structure such as a brain may occur at the expense of other cranial structures. These analyses indicate the benefits of a multifactorial approach to cranial integration using a mouse model.

The use of new technologies, especially computer-based three dimensional reconstructions and micro-computer tomography (μ-CT) have greatly improved and facilitated the detailed investigation of insect anatomy. Optimal results in morphological work aiming at phylogenetic reconstruction can be obtained with a combined application of different techniques such as histology, scanning electron microscopy, and μ-CT. The use of μ-CT greatly enhances the efficiency of the acquisition of detailed anatomical data and allows a broad taxon sampling in phylogenetic studies partly or entirely based on morphological characters. A disadvantage of phase contrasted μ-CT images is the poor differentiation of different tissue types. This problem can be overcome by the use of stable low energy photon beams as available at the beamline BW2 of the Deutsches Elektronen-Synchrotron in Hamburg (DESY). Synchrotron-radiation-based μ-CT data (SR μ-CT) obtained with this approach are an ideal basis for highly efficient three dimensional reconstructions of high quality.

Using laser welding in fabrication of metallic airframes reduces the weight and hence fuel consumption. Currently only limited parts of the airframes are welded. To increase laser beam welded parts, there is the need for a better understanding of crack propagation and crack-pore interaction within the welds. Laser beam welded Al-alloys may contain isolated small process pores and their role and interaction with growing crack need to be investigated. The present paper presents the first results of a crack propagation study in laser beam welded (LBW) Al-alloy T-joints using synchrotron radiation based micro computed tomography (SRμCT). A region-of-interest technique was used, since the specimens exceeded the field of view of the X-ray detector. As imaging with high density resolution at high photon energies is very challenging, a feasibility measurement on a small laser weld, cut cylindrically from the welded region of a T-joint, was done before starting the crack-propagation study. This measurement was performed at the beamline HARWI-II at DESY to demonstrate the potential of the SRμCT as non-destructive testing method. The result has shown a high density resolution, hence, the different Al alloys used in the T-joint and the weld itself were clearly separated. The quantitative image analysis of the 3D data sets allows visualizing non-destructively and calculating the pore size distribution.

Zoological sciences widely rely on morphological data to reconstruct and understand body structures of animals. The best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR μCT became widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SRμCT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR μCT must not be present. As a consequence, to allow biological sciences to fully exploit the power of SR μCT further increase of density resolution in absorption contrast methods is desirable.

Recently the importance of the third dimension in cell biology has been better understood, resulting in a re-orientation towards three-dimensional (3D) cultivation. Yet adequate tools for their morphological characterization have to be established. Synchrotron radiation-based micro computed tomography (SRμCT) allows visualizing such biological systems with almost isotropic micrometer resolution, non-destructively. We have applied SRμCT for studying the internal morphology of human osteoblast-derived, scaffold-free 3D cultures, termed histoids. Primary human osteoblasts, isolated from femoral neck spongy bone, were grown as 2D culture in non-mineralizing osteogenic medium until a rather thick, multi-cellular membrane was formed. This delicate system was intentionally released to randomly fold itself. The folded cell cultures were grown to histoids of cubic milli- or centimeter size in various combinations of mineralizing and non-mineralizing osteogenic medium for a total period of minimum 56 weeks. The SRμCT-measurements were performed in the absorption contrast mode at the beamlines BW 2 and W 2 (HASYLAB at DESY, Hamburg, Germany), operated by the GKSS-Research Center. To investigate the entire volume of interest several scans were performed under identical conditions and registered to obtain one single dataset of each sample. The histoids grown under different conditions exhibit similar external morphology of globular or ovoid shape. The SRμCT-examination revealed the distinctly different morphological structures inside the histoids. One obtains details of the histoids that permit to identify and select the most promising slices for subsequent histological characterization.

Synchrotron-based X-ray Tomographic Microscopy is a powerful technique for fast, non-destructive, high resolution quantitative volumetric investigations on diverse samples. At the TOMCAT (TOmographic Microscopy and Coherent radiology experimenTs) beamline at the Swiss Light Source (SLS), synchrotron light is delivered by a 2.9 T superbend. The main optical component, a Double Crystal Multilayer Monochromator, covers an energy range between 8 and 45 keV. The standard TOMCAT detector offers field of views ranging from 0.75x0.75 mm² up to 12.1x12.1mm² with a theoretical resolution of 0.37 μm and 5.92 μm, respectively. The beamline design and flexible endstation setup make a large range of investigations possible. In addition to routine measurements, which exploit the absorption contrast, the high coherence of the source also enables phase contrast tomography, implemented with two complementary techniques. Differential Phase Contrast (DPC) imaging has been fully integrated in terms of fast acquisition and data reconstruction. Scans of samples within an aqueous environment are also feasible. The second phase contrast method is a Modified Transport of Intensity approach that yields a good approximation of the 3D phase distribution of a weakly absorbing object from a single tomographic dataset. Typical acquisition times for a tomogram are in the order of few minutes, ensuring high throughput and allowing for semi-dynamical investigations and in-situ experiments. Raw data are automatically post-processed online and full reconstructed volumes are available shortly after a scan with minimal user intervention. In addition to a beamline overview, a selection of high-impact tomographic applications will be presented.