[en] In this paper we present a filtered backprojection reconstruction algorithm for Compton Camera detectors of particles. Compared to iterative methods, widely used for the reconstruction of images from Compton camera data, analytical methods are fast, easy to implement and avoid convergence issues. The method we propose is exact for an idealized Compton camera composed of two parallel plates of infinite dimension. We show that it copes well with low number of detected photons simulated from a realistic device. Images reconstructed from both synthetic data and realistic ones obtained with Monte Carlo simulations demonstrate the efficiency of the algorithm. (orig.)

[en] Three-dimensional numerical simulations of ultrasound transmission were performed through 31 trabecular bone samples measured by synchrotron microtomography. The synchrotron microtomography provided high resolution 3D mappings of bone structures, which were used as the input geometry in the simulation software developed in our laboratory. While absorption (i.e. the absorption of ultrasound through dissipative mechanisms) was not taken into account in the algorithm, the simulations reproduced major phenomena observed in real through-transmission experiments in trabecular bone. The simulated attenuation (i.e. the decrease of the transmitted ultrasonic energy) varies linearly with frequency in the MHz frequency range. Both the speed of sound (SOS) and the slope of the normalized frequency-dependent attenuation (nBUA) increase with the bone volume fraction. Twenty-five out of the thirty-one samples exhibited negative velocity dispersion. One sample was rotated to align the main orientation of the trabecular structure with the direction of ultrasonic propagation, leading to the observation of a fast and a slow wave. Coupling numerical simulation with real bone architecture therefore provides a powerful tool to investigate the physics of ultrasound propagation in trabecular structures. As an illustration, comparison between results obtained on bone modelled either as a fluid or a solid structure suggested the major role of mode conversion of the incident acoustic wave to shear waves in bone to explain the large contribution of scattering to the overall attenuation

[en] The availability of three-dimensional measuring techniques coupled to specific image processing methods opens new opportunities for the analysis of bone structure. In particular, synchrotron radiation microtomography may provide three-dimensional images with spatial resolution as high as one micrometer. Moreover, the use of a monoenergetic synchrotron beam, which avoids beam-hardening effects, allows quantitative measurements of the degree of mineralization in bone samples. Indeed, the reconstructed gray levels of tomographic images correspond directly to a map of the linear attenuation coefficient within the sample. Since the absorption depends on the amount of mineral content, we proposed a calibration method to evaluate the three-dimensional distribution of the degree of mineralization within the sample. First a theoretical linear relationship modeling the linear attenuation coefficient as a function of the hydroxyapatite concentrations was derived. Then, an experimental validation on phantoms confirmed both the accuracy of the image processing tools and the experimental setup used. Finally, the analysis of the degree of mineralization in four iliac crest bone biopsy samples was reported. Our method was compared to the reference microradiography technique, currently used for this quantification in two dimensions. The concentration values of the degree of mineralization were found with both techniques in the range 0.5-1.6 g of mineral per cubic centimeter of bone, both in cortical and in trabecular region. The mean difference between the two techniques was around 4.7%, and was slightly higher in trabecular region than in cortical bone

[en] Microcomputed tomography (μCT) produces three-dimensional (3D) images of trabecular bone. We compared conventional μCT (CμCT) with a polychromatic x-ray cone beam to synchrotron radiation (SR) μCT with a monochromatic parallel beam for assessing trabecular bone microarchitecture of 14 subchondral femoral head specimens from patients with osteoarthritis (n=10) or osteoporosis (n=4). SRμCT images with a voxel size of 10.13 μm were reconstructed from 900 2D radiographic projections (angular step, 0.2 deg. ). CμCT images with a voxel size of 10.77 μm were reconstructed from 205, 413, and 825 projections obtained using angular steps of 0.9 deg., 0.45 deg., and 0.23 deg., respectively. A single threshold was used to binarize the images. We computed bone volume/tissue volume (BV/TV), bone surface/bone volume (BS/BV), trabecular number (Tb.N), trabecular thickness (Tb.Th and Tb.Th*), trabecular spacing (Tb.Sp), degree of anisotropy (DA), and Euler density. With the 0.9 deg. angular step, all CμCT values were significantly different from SRμCT values. With the 0.23 deg. and 0.45 deg. rotation steps, BV/TV, Tb.Th, and BS/BV by CμCT differed significantly from the values by SRμCT. The error due to slice matching (visual site matching ±10 slices) was within 1% for most parameters. Compared to SRμCT, BV/TV, Tb.Sp, and Tb.Th by CμCT were underestimated, whereas Tb.N and Tb.Th* were overestimated. A Bland and Altman plot showed no bias for Tb.N or DA. Bias was -0.8±1.0%, +5.0±1.1 μm, -5.9±6.3 μm, and -5.7±29.1 μm for BV/TV, Tb.Th*, Tb.Th, and Tb.Sp, respectively, and the differences did not vary over the range of values. Although systematic differences were noted between SRμCT and CμCT values, correlations between the techniques were high and the differences would probably not change the discrimination between study groups. CμCT provides a reliable 3D assessment of human defatted bone when working at the 0.23 deg. or 0.45 deg. rotation step; the 0.9 deg. rotation step may be insufficiently accurate for morphological bone analysis

[en] A well-known problem in x-ray microcomputed tomography is low sensitivity. Phase contrast imaging offers an increase of sensitivity of up to a factor of 10³ in the hard x-ray region, which makes it possible to image soft tissue and small density variations. If a sufficiently coherent x-ray beam, such as that obtained from a third generation synchrotron, is used, phase contrast can be obtained by simply moving the detector downstream of the imaged object. This setup is known as in-line or propagation based phase contrast imaging. A quantitative relationship exists between the phase shift induced by the object and the recorded intensity and inversion of this relationship is called phase retrieval. Since the phase shift is proportional to projections through the three-dimensional refractive index distribution in the object, once the phase is retrieved, the refractive index can be reconstructed by using the phase as input to a tomographic reconstruction algorithm. A comparison between four phase retrieval algorithms is presented. The algorithms are based on the transport of intensity equation (TIE), transport of intensity equation for weak absorption, the contrast transfer function (CTF), and a mixed approach between the CTF and TIE, respectively. The compared methods all rely on linearization of the relationship between phase shift and recorded intensity to yield fast phase retrieval algorithms. The phase retrieval algorithms are compared using both simulated and experimental data, acquired at the European Synchrotron Radiation Facility third generation synchrotron light source. The algorithms are evaluated in terms of two different reconstruction error metrics. While being slightly less computationally effective, the mixed approach shows the best performance in terms of the chosen criteria.

[en] The SOLEIL synchrotron is organizing, with the next annual SOLEIL Users' Meeting (18-19 January 2012) gathering about 350 international scientists each year, a satellite workshop entitled: 'Biology and medicine: from fundamental research ta diagnosis'. The workshop aims to bring together medical doctors, bio-physicists/-chemists, structural and cell biologists as well as synchrotron scientists. The participants in biology will highlight recent studies that combine complementary methods in order to understand the complexity of living organisms and their functional mechanisms, from atomic resolution macromolecular structures to cell and tissue imaging. In medicine, synchrotron radiation related techniques are now used in cutting edge investigations for diagnosis and fundamental understandings of diseases. Recent advances in medical applications of SOLEIL synchrotron radiation related techniques to the study of various diseases such as urolithiasis, liver pathologies or endocarditis will be presented. This book gathers the abstracts of 22 talks and 11 posters: Application of Synchrotron Based FTIR Spectroscopy in Medicine - Is There a Niche? Calcifications in Human Osteoarthritic Articular Cartilage: Ex Vivo Assessment of Calcium Compounds Using Xanes Spectroscopy. Synchrotron Infrared and Fluorescence Microspectroscopies to Assess the Diffusion and Effects of Antibacterial Agents in Bacterial Communities. Quantitative Imaging of Regional lung Function Using Synchrotron Radiation Computed Tomography: Present Status, Future Orientations. When the Sun Highlights the Randall's Plaques and Kidney Concretions. Influence of Green Tea on Oxalate Kidney Stones: an ex vivo Investigation of the Ultrastructure. Qualitative and Quantitative Assessment of Liver Steatosis Using infrared Microspectroscopy. Chemical Analysis of Thyroid Microcalcifications: Can it Have an Impact on Thyroid Diseases Care? Micro-tomography Using Synchrotron Radiation: New Developments at the Microscopic Level to Study Bone. Investigation of the Bone Osteocyte Network from Synchrotron Nano-CT. Synchrotron Radiation Therapy, Preparation of a Clinical Trial. Structures of Two Lactococcal Phage Baseplates - Their Mechanism of Activation Deciphered Using Hybrid Methods. Integrative Structural Analysis of Transcription and Translation Complexes. Structural Study of Telomeres Molecular Architecture. Regulatory Mechanisms in Toxin-Antitoxin Modules. Scanning Hard X-ray Nano-imaging in Biology and Life Sciences: Tissular and Subcellular Topography, and Speciation of Trace Elements, Transition Metals. Coherent X-ray Tomography at the Synchrotron: Multimodal 3D imaging with High Resolution and Sensitivity. From the Fibrinogen Structure to the Mechanism of Fibrin Polymerization: HPLC-SAXS and Stopped-Flow/MALLS/SAXS at the SOLEIL SWING Beamline. Structure of Inclusions of Huntington Disease Brain Revealed by Synchrotron infrared Microspectroscopy. Analyzing Metal Binding Sites in Proteins Using (far) Infrared Spectroscopy: Why and How? Multi-Drug Resistance in Bacteria: Study of the Antibiotics Uptake in Resistant Bacterial Strains by DUV Fluorescence Microspectroscopy. Titanium Dioxide Nanoparticle Uptake and Impact on Gastro-Intestinal and Lung Models. Zn(II) Coordination to Human and Murine Amyloid-β Peptides involved in Alzheimer's Disease. Molecular mechanisms of PGC-1 α Coactivator Recognition by Estrogen-Related Receptors. Role of a Hydrophobic Cavity in Urate Oxidase Enzymatic Activity Revealed by X-ray Crystallography and Enzymatic Assay under High Hydrostatic Pressure and Under inert Gas Moderate Pressure. Analysis of Liver Steatosis Using Infrared Microspectroscopy on Tissue Sections. Structure-Photophysics Relationships at Acidic pH of the Cyan Fluorescent Protein. Yeast Lipid Bodies Under Sunlights Dynamic and Structural Studies Using SMIS and DISCO Beamlines. Nanoassemblies of Nucleoside Analogues Coupled to Terpenoids: Structural Analysis. Need for New imaging Tools to Study the internalization and the Localization of Nanoparticles into Cells. Structural basis for the functional versatility of β-Thymosin/WH2 Domains in Actin Assembly. Nanotoxicity of Nanodrugs Using SRCD (SOLEIL): Tests on Human Proteins. DISCO: Synchrotron Radiation Circular Dichroism at SOLEIL

[en] This paper addresses the inverse problem of time-resolved (fluorescence) diffuse optical tomography from temporal moments of the measurements. A methodology that enables one to provide fairly comparable reconstructions is presented. The proposed reconstruction methodology is applied to infinite medium synthetic phantoms in the transmission geometry. Reconstructions are performed for moment orders increasing from 0 to 3. The reconstruction quality is shown to be increasing when higher moment orders are added. However, the value of the highest useful moments order strongly depends on the number of photons that can be acquired. In particular, it can be considered that the benefit of using higher order moments vanishes when fewer than 10⁸ photons are detected. The evolution of the reconstruction quality with respect to the optical properties of the medium and fluorescence lifetime is also shown.

[en] The problem of fluorescence diffuse optical tomography consists in localizing fluorescent markers from near-infrared light measurements. Among the different available acquisition modalities, the time-resolved modality is expected to provide measurements of richer information content. To extract this information, the moments of the time-resolved measurements are often considered. In this paper, a theoretical analysis of the moments of the forward problem in fluorescence diffuse optical tomography is proposed for the infinite medium geometry. The moments are expressed as a function of the source, detector and markers positions as well as the optical properties of the medium and markers. Here, for the first time, an analytical expression holding for any moments order is mathematically derived. In addition, analytical expressions of the mean, variance and covariance of the moments in the presence of noise are given. These expressions are used to demonstrate the increasing sensitivity of moments to noise. Finally, the newly derived expressions are illustrated by means of sensitivity maps. The physical interpretation of the analytical formulae in conjunction with their map representations could provide new insights into the analysis of the information content provided by moments.

[en] The ESRF synchrotron beamline ID19, dedicated to full-field parallel-beam imaging techniques such as phase-contrast and absorption microtomography and X-ray topography, is one of the most versatile instruments of its kind. This paper presents key characteristics of ID19 in its present form, names examples for research and development performed on the beamline, and outlines the plans for an upgrade on the beamline in coming years, to adapt to the growing needs of the user community. The technical goals envisioned include an increase in available beam size and maximum photon energy, and a substantial increase in flux density for applications using beams of small and intermediate size.

[en] Purpose: Trabecular bone microarchitecture is made of a complex network of plate and rod structures evolving with age and disease. The purpose of this article is to propose a new 3D local analysis method for the quantitative assessment of parameters related to the geometry of trabecular bone microarchitecture. Methods: The method is based on the topologic classification of the medial axis of the 3D image into branches, rods, and plates. Thanks to the reversibility of the medial axis, the classification is next extended to the whole 3D image. Finally, the percentages of rods and plates as well as their mean thicknesses are calculated. The method was applied both to simulated test images and 3D micro-CT images of human trabecular bone. Results: The classification of simulated phantoms made of plates and rods shows that the maximum error in the quantitative percentages of plate and rods is less than 6% and smaller than with the structure model index (SMI). Micro-CT images of human femoral bone taken in osteoporosis and early or advanced osteoarthritis were analyzed. Despite the large physiological variability, the present method avoids the underestimation of rods observed with other local methods. The relative percentages of rods and plates were not significantly different between osteoarthritis and osteoporotic groups, whereas their absolute percentages were in relation to an increase of rod and plate thicknesses in advanced osteoarthritis with also higher relative and absolute number of nodes. Conclusions: The proposed method is model-independent, robust to surface irregularities, and enables geometrical characterization of not only skeletal structures but entire 3D images. Its application provided more accurate results than the standard SMI on simple simulated phantoms, but the discrepancy observed on the advanced osteoarthritis group raises questions that will require further investigations. The systematic use of such a local method in the characterization of trabecular bone samples could provide new insight in bone microarchitecture changes related to bone diseases or to those induced by drugs or therapy.