Registration of phase contrast images in propagation-based X-ray phase tomography

International audienceX-ray phase tomography aims at reconstructing the 3D electron density distribution of an object. It offers enhanced sensitivity compared to attenuation-based X-ray absorption tomography. In propagation-based methods, phase contrast is achieved by letting the beam propagate after interaction with the object. The phase shift is then retrieved at each projection angle, and subsequently used in tomographic reconstruction to obtain the refractive index decrement distribution, which is proportional to the electron density. Accurate phase retrieval is achieved by combining images at different propagation distances. For reconstructions of good quality, the phase-contrast images recorded at different distances need to be accurately aligned. In this work, we characterise the artefacts related to misalignment of the phase-contrast images, and investigate the use of different registration algorithms for aligning in-line phase-contrast images. The characterisation of artefacts is done by a simulation study and comparison with experimental data. Loss in resolution due to vibrations is found to be comparable to attenuation-based computed tomography. Further, it is shown that registration of phase-contrast images is nontrivial due to the difference in contrast between the different images, and the often periodical artefacts present in the phase-contrast images if multilayer X-ray optics are used. To address this, we compared two registration algorithms for aligning phase-contrast images acquired by magnified X-ray nanotomography: one based on cross-correlation and one based on mutual information. We found that the mutual information-based registration algorithm was more robust than a correlation-based method

Reconstruction tomographique itérative de phase

Phase contrast imaging has been of growing interest in the biomedical field, since it provides an enhanced contrast compared to attenuation-based imaging. Actually, the phase shift of the incoming X-ray beam induced by an object can be up to three orders of magnitude higher than its attenuation, particularly for soft tissues in the imaging energy range. Phase contrast can be, among others existing techniques, achieved by letting a coherent X-ray beam freely propagate after the sample. In this case, the obtained and recorded signals can be modeled as Fresnel diffraction patterns. The challenge of quantitative phase imaging is to retrieve, from these diffraction patterns, both the attenuation and the phase information of the imaged object, quantities that are non-linearly entangled in the recorded signal. In this work we consider developments and applications of X-ray phase micro and nano-CT. First, we investigated the reconstruction of seeded bone scaffolds using sed multiple distance phase acquisitions. Phase retrieval is here performed using the mixed approach, based on a linearization of the contrast model, and followed by filtered-back projection. We implemented an automatic version of the phase reconstruction process, to allow for the reconstruction of large sets of samples. The method was applied to bone scaffold data in order to study the influence of different bone cells cultures on bone formation. Then, human bone samples were imaged using phase nano-CT, and the potential of phase nano-imaging to analyze the morphology of the lacuno-canalicular network is shown. We applied existing tools to further characterize the mineralization and the collagen orientation of these samples. Phase retrieval, however, is an ill-posed inverse problem. A general reconstruction method does not exist. Existing methods are either sensitive to low frequency noise, or put stringent requirements on the imaged object. Therefore, we considered the joint inverse problem of combining both phase retrieval and tomographic reconstruction. We proposed an innovative algorithm for this problem, which combines phase retrieval and tomographic reconstruction into a single iterative regularized loop, where a linear phase contrast model is coupled with an algebraic tomographic reconstruction algorithm. This algorithm is applied to numerical simulated data.L’imagerie par contraste de phase suscite un intérêt croissant dans le domaine biomédical, puisqu’il offre un contraste amélioré par rapport à l’imagerie d’atténuation conventionnelle. En effet, le décalage en phase induit par les tissus mous, dans la gamme d’énergie utilisée en imagerie, est environ mille fois plus important que leur atténuation. Le contraste de phase peut être obtenu, entre autres, en laissant un faisceau de rayons X cohérent se propager librement après avoir traversé un échantillon. Dans ce cas, les signaux obtenus peuvent être modélisés par la diffraction de Fresnel. Le défi de l’imagerie de phase quantitative est de retrouver l’atténuation et l’information de phase de l’objet observé, à partir des motifs diffractés enregistrés à une ou plusieurs distances. Ces deux quantités d’atténuation et de phase, sont entremêlées de manière non-linéaire dans le signal acquis. Dans ces travaux, nous considérons les développements et les applications de la micro- et nanotomographie de phase. D’abord, nous nous sommes intéressés à la reconstruction quantitative de biomatériaux à partir d’une acquisition multi-distance. L’estimation de la phase a été effectuée via une approche mixte, basée sur la linéarisation du modèle de contraste. Elle a été suivie d’une étape de reconstruction tomographique. Nous avons automatisé le processus de reconstruction de phase, permettant ainsi l’analyse d’un grand nombre d’échantillons. Cette méthode a été utilisée pour étudier l’influence de différentes cellules osseuses sur la croissance de l’os. Ensuite, des échantillons d’os humains ont été observés en nanotomographie de phase. Nous avons montré le potentiel d’une telle technique sur l’observation et l’analyse du réseau lacuno-canaliculaire de l’os. Nous avons appliqué des outils existants pour caractériser de manière plus approfondie la minéralisation et les l’orientation des fibres de collagènes de certains échantillons. L’estimation de phase, est, néanmoins, un problème inverse mal posé. Il n’existe pas de méthode de reconstruction générale. Les méthodes existantes sont soit sensibles au bruit basse fréquence, soit exigent des conditions strictes sur l’objet observé. Ainsi, nous considérons le problème inverse joint, qui combine l’estimation de phase et la reconstruction tomographique en une seule étape. Nous avons proposé des algorithmes itératifs innovants qui couplent ces deux étapes dans une seule boucle régularisée. Nous avons considéré un modèle de contraste linéarisé, couplé à un algorithme algébrique de reconstruction tomographique. Ces algorithmes sont testés sur des données simulées

Refractive index retrieval by combining the contrast transfer function and SART in X-ray in-line phase tomography

International audienceThis work presents a new iterative algorithm for synchrotron radiation micro-tomography, using multidistance propagation-based phase contrast imaging. Up to now, phase retrieval and tomographic reconstruction were processed as two separated problems. Here, we combine these two parts into a single step algorithm (CTF-SART). A linearized version of the contrast model (known as the contrast transfer function, CTF) was used for phase retrieval, and the simultaneous algebraic reconstruction technique (SART) for the tomographic reconstruction. We present the theoretical framework of the method and the first tests on simulated data.Ce travail présente un algorithme itératif innovant pour la reconstruction en micro-tomographie X de phase par rayonnement synchrotron. La technique d’acquisition est basée sur la propagation multi-distance (holotomographie). Jusqu’à présent, les étapes d’estimation de phase et de reconstruction tomographique étaient traitées indépendamment. Ici, nous proposons un nouvel algorithme (CTF-SART) qui combine ces deux étapes en une seule. Il utilise d’une part un modèle linéaire du contraste (appelé Fonction de Transfert du Contraste) pour l’estimation de la phase, et d’autre part l’algorithme itératif SART pour la reconstruction tomographique. Nous décrivons le formalisme de la méthode et présentons les premiers résultats sur données simulées

Regularized phase retrieval algorithms for X-ray phase tomography of 3D bone cell culture analysis

International audienceRegenerative medicine is receiving increased interest. In the field of bone tissue engineering, a recurrent problem is to select efficient association of scaffolds and bone cells to maximize bone formation. Sensitive imaging modalities are required to quantify both cells and mineralized tissue. Tothis aim, X-ray phase contrast imaging is an attractive modality since it offers three orders of magnitude higher sensitivity than conventional radiology. In-line phase contrast imaging consists in letting a spatially coherent beam propagate after passing through a sample [1]. Projections areacquired at several angles, for several sample-to-detector distances. The phase can be extracted from projections using a so-called phase retrieval algorithm. A tomographic reconstruction algorithm is then applied to these phase projections to obtain a 3D-map of the refractive index in the object.In this work, we compare several phase retrieval methods based on different priors [3, 4, 5] in porous bone scaffolds seeded with bone forming cells. These algorithms not only enable to discriminate bone cells, newly formed bone and scaffolds, but quantify the volume and density of the calcified fraction, as well as the volume of extra-cellular matrix generated by the bone cells, by thresholding the refractive index maps. Further, the use of heterogeneous object algorithms enabled quantification of the refractive index of the soft tissue compartment, as well as segmentation of osteoblasts trapped in the pre-bone matrix, which was not possible using standard μCT

Combining SART and CTF for 3D phase retrieval in X-ray in-line phase tomography

International audienceThis paper presents a new iterative algorithm for X-ray in-line phase tomography. It combines the phase retrieval and the tomographic reconstruction, previously regarded and solved as two distinct problems, in a single step. The Contrast Transfer Function (CTF), a linear phase contrast model, is coupled to the simultaneous algebraic reconstruction technique. The aim is to reduce the a priori assumptions about the imaged sample used in conventional approaches. We have derived an analytical expression for this framework for two different types of samples: pure phase objects and weakly absorbing objects. In a first step, the resulting algorithm has been tested on simulated data

Synchrotron X-Ray Phase Nanotomography for Bone Tissue Characterization

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In-line phase nano-tomography of human femoral bone in osteoporosis and osteoarthritis

International audienceX-ray in-line phase contrast tomography has been of growing interest in biology and medicine, since it enables non-destructive, quantitative 3D imaging of samples with very high sensitivity and spatial resolution. This is mainly enabled by the relatively large propagation distances of a highly spatially coherent beam that increase phase contrast interference fringes and also the use of cutting-edge detectors. Combined with tomographic reconstruction, it gives access to the refractive index distribution in the sample [1].Here, we used magnified in-line phase nano-tomography [2] to image human bone at the cellular level. This nano-imaging technique is similar to propagation-based phase contrast, except that the beam is focused using reflective X-ray optics. The sample is placed after the focal spot, so that the beam divergence and different propagation distances induce different magnification factors.Four human femoral cortical bone samples, one healthy, one suffering from osteoporosis (OP) and two suffering from osteoarthritis (OA), were imaged at the ID22 beamline at 60 nm pixel size. This resolution gives access to 3D imaging of the lacuno-canicular network (LCN) and matrix properties such as collagen fibril orientation and sub-micrometric mineralization. The field of view at this pixel size is ~120 μm, yielding a relatively large analysed volume compared to other 3D nano-tomographic techniques ([5], [6]).Quantitative analysis will be performed to determine relevant characteristics of the LCN, as well as collagen fibril orientation [3], and mineralization of the bone matrix [4]. We will investigate changes of these cell and matrix properties in OP and OA. This methodology can be applied in other studies, providing better understanding of the link between different pathologies and bone properties on the cellular length scale.[1] P. Cloetens, W. Ludwig, J. Baruchel, D. Van Dyck, J. Van Landuyt, J. P. Guigay, and M. Schlenker, Appl. Phys. Lett.,p. 2912, 1999.[2] M. Langer, A. Pacureanu, H. Suhonen, Q. Grimal, P. Cloetens, and F. Peyrin, PLoS One, p. e35691, 2012.[3] P. Varga, A. Pacureanu, M. Langer, H. Suhonen, B. Hesse, Q. Grimal, P. Cloetens, K. Raum, and F. Peyrin, EuropeanSociety of Biomechanics, 2013.[4] B. Hesse, M. Langer, P. Varga, A. Pacureanu, P. Dong, S. Schrof, N. Männicke, H. Suhonen, C. Olivier, P. Maurer, G.J. Kazakia, K. Raum, and F. Peyrin, Plos one, p. e88481, 2014.[5] M. Dierolf, A. Menzel, P. Thibault, P. Schneider, C. M. Kewish, R. Wepf, O. Bunk, and F. Pfeiffer, Nature, pp. 436–9,2010.[6] J. C. Andrews, E. Almeida, M. C. H. van der Meulen, J. S. Alwood, C. Lee, Y. Liu, J. Chen, F. Meirer, M. Feser, J. Gelb,J. Rudati, A. Tkachuk, W. Yun, and P. Pianetta, Microsc. Microanal., pp. 327–36, 2010

Phase retrieval in 3D X-ray magnified phase nano CT: Imaging bone tissue at the nanoscale

International audienceX-ray phase computed tomography (CT) offers higher sensitivity than conventional X-ray CT. A new phase-CT instrument producing a nano-focused beam has been developed at the ESRF (European Synchrotron Radiation Facility) for nano-imaging. In order to obtain final images, a suited phase retrieval algorithm is necessary, which is attracting broader interest recently. In this paper, we explicit the 3D phase CT image reconstruction problem, including the stage of phase retrieval prior to 3D CT reconstruction. The phase retrieval problem is solved by extending the single distance Paganin method to multi-distance acquisitions, followed by an iterative non-linear conjugate gradient descent optimization method. The method is evaluated on bone tissue samples imaged at voxel sizes of 120 nm. The results obtained from acquisition at 1 and 4 distances, with and without the iterative refinement are compared. The results show that this method yields improved images compared to other methods

Evaluation of phase retrieval approaches in magnified X-ray phase nano computerized tomography applied to bone tissue

International audienceX-ray phase contrast imaging offers higher sensitivity compared to conventional X-ray attenuation imaging and can be simply implemented by propagation when using a partially coherent synchrotron beam. We address the phase retrieval in in-line phase nano-CT using multiple propagation distances. We derive a method which extends Paganin's single distance method and compare it to the contrast transfer function (CTF) approach in the case of a homogeneous object. The methods are applied to phase nano-CT data acquired at the voxel size of 30 nm (ID16A, ESRF, Grenoble, France). Our results show a gain in image quality in terms of the signal-to-noise ratio and spatial resolution when using four distances instead of one. The extended Paganin's method followed by an iterative refinement step provides the best reconstructions while the homogeneous CTF method delivers quasi comparable results for our data, even without refinement step

SYNCHROTRON RADIATION PHASE CT FOR THE INVESTIGATION OF NANO PROPERTIES IN FEMORAL HUMAN BONE

International audienceThe mechanisms of bone fragility in relation to diseases such as osteoporosis remain only partially understood. Extensive attention has been devoted to the osteocyte cell network, which plays a central role in bone remodeling, but for which observation remains challenging. To assess bone nano-structure, we propose to use a new 3D X-ray phase nano-CT setup developed at the ESRF (European Synchrotron Radiation Facility) in Grenoble, which targets to reach isotropic spatial resolution up to 20 nm. Images of cortical bone samples with isotropic voxel size of 120nm, 50nm and 30nm are presented