Alessandro Mirone

The PyHST2 hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities

We present the PyHST2 code which is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the 3rd generation synchrotron facilities (10 terabytes per experiment) by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a priori knowledge. These latter are used to improve the reconstruction quality or in order to reduce the required data volume or the deposited dose to the sample and reach a given quality goal. The implemented a priori knowledge techniques are based on the total variation penalization and a new recently found convex functional which is based on overlapping patches. We give details of the different methods and discuss how they are implemented in the PyHST2 code, which is distributed under free license. We provide methods for estimating, in the absence of ground-truth data, the optimal parameters values for a priori techniques.

Three-dimensional synchrotron virtual paleohistology: A new insight into the world of fossil bone microstructures

The recent developments of phase-contrast synchrotron imaging techniques have been of great interest for paleontologists, providing three-dimensional (3D) tomographic images of anatomical structures, thereby leading to new paleobiological insights and the discovery of new species. However, until now, it has not been used on features smaller than 5-7 μm voxel size in fossil bones. Because much information is contained within the 3D histological architecture of bone, including an ontogenetic record, crucial for understanding the paleobiology of fossil species, the application of phase-contrast synchrotron tomography to bone at higher resolutions is potentially of great interest. Here we use this technique to provide new 3D insights into the submicron-scale histology of fossil and recent bones, based on the development of new pink-beam configurations, data acquisition strategies, and improved processing tools. Not only do the scans reveal by nondestructive means all of the major features of the histology at a resolution comparable to that of optical microscopy, they provide 3D information that cannot be obtained by any other method.

Photoinduced Melting of Antiferromagnetic Order in La0.5Sr1.5MnO4 Measured Using Ultrafast Resonant Soft X-Ray Diffraction

We used ultrafast resonant soft x-ray diffraction to probe the picosecond dynamics of spin and orbital order in La(0.5)Sr(1.5)MnO(4) after photoexcitation with a femtosecond pulse of 1.5 eV radiation. Complete melting of antiferromagnetic spin order is evidenced by the disappearance of a (1/4,1/4,1/2) diffraction peak. On the other hand, the (1/4,1/4,0) diffraction peak, reflecting orbital order, is only partially reduced. We interpret the results as evidence of destabilization in the short-range exchange pattern with no significant relaxation of the long-range Jahn-Teller distortions. Cluster calculations are used to analyze different possible magnetically ordered states in the long-lived metastable phase. Nonthermal coupling between light and magnetism emerges as a primary aspect of photoinduced phase transitions in manganites.

A GPU-based architecture for real-time data assessment at synchrotron experiments

Current imaging experiments at synchrotron beam lines often lack a real-time data assessment. X-ray imaging cameras installed at synchrotron facilities like ANKA provide millions of pixels, each with a resolution of 12 bits or more, and take up to several thousand frames per second. A given experiment can produce data sets of multiple gigabytes in a few seconds. Up to now the data is stored in local memory, transferred to mass storage, and then processed and analyzed off-line. The data quality and thus the success of the experiment, can, therefore, only be judged with a substantial delay, which makes an immediate monitoring of the results impossible. To optimize the usage of the micro-tomography beam-line at ANKA we have ported the reconstruction software to modern graphic adapters which offer an enormous amount of calculation power. We were able to reduce the reconstruction time from multiple hours to just a few minutes with a sample dataset of 20 GB. Using the new reconstruction software it is possible to provide a near real-time visualization and significantly reduce the time needed for the first evaluation of the reconstructed sample. The main paradigm of our approach is 100% utilization of all system resources. The compute intensive parts are offloaded to the GPU. While the GPU is reconstructing one slice, the CPUs are used to prepare the next one. A special attention is devoted to minimize data transfers between the host and GPU memory and to execute I/O operations in parallel with the computations. It could be shown that for our application not the computational part but the data transfers are now limiting the speed of the reconstruction. Several changes in the architecture of the DAQ system are proposed to overcome this second bottleneck. The article will introduce the system architecture, describe the hardware platform in details, and analyze performance gains during the first half year of operation.

Planning, performing and analyzing X-ray Raman scattering experiments

A summarising review of data treatment for non-resonant inelastic X-ray scattering data from modern synchrotron-based multi-analyzer spectrometers.

Determination of the single-ion anisotropy energy in a S=5/2 kagome antiferromagnet using x-ray absorption spectroscopy

We report x-ray absorption and x-ray linear dichroism measurements at the Fe L-2,L-3 edges of the geometrically frustrated systems of potassium and hydronium iron jarosite. Comparison with simulated spectra, involving ligand-field multiplet calculations modeling the 3d-2p hybridization between the iron ion and the oxygen ligands, has yielded accurate estimates for the ligand metal-ion hybridization and the resulting single-ion crystal-field anisotropy energy. Using this method we provide an experimentally verified scenario for the appearance of a single-ion anisotropy in this nominally high-spin 3d(5) orbital singlet S-6 system, which accounts for features of the spin-wave dispersion in the long-range-ordered ground state of potassium iron jarosite.

Anomalous dispersion of longitudinal optical phonons in Nd(1.86)Ce(0.14)CuO(4+delta) determined by inelastic x-ray scattering.

The phonon dispersions of Nd(1.86)Ce(0.14)CuO(4+delta) along the [xi,0,0] direction have been determined by inelastic x-ray scattering. Compared to the undoped parent compound, the two highest longitudinal phonon branches, associated with the Cu-O bond stretching and out-of-plane oxygen vibration, are shifted to lower energies. Moreover, an anomalous softening of the bond-stretching band is observed at about q = (0.2,0,0). These signatures provide evidence for strong electron-phonon coupling in this electron-doped high-temperature superconductor.

Magnetic and electronic Co states in the layered cobaltate GdBaCo2O5.5−x

We have performed nonresonant x-ray diffraction, resonant soft and hard x-ray magnetic diffraction, soft x-ray absorption, and x-ray magnetic circular dichroism measurements to clarify the electronic and magnetic high-spin (HS) state at the states of the Co3+, ions in GdBaCo2O5.5. Our data are consistent with a Co-Py(3+) pyramidal sites and a Co-Oc(3+), low-spin (LS) state at the octahedral sites. The structural distortion with a doubling of the a axis (2a(p)X2a(p)X2a(p) cell) shows alternating elongations and contractions of the pyramids, and indicates that the metal-insulator transition is associated with orbital order in the t(2g) orbitals of the Co-Py(3+) HS state. This distortion corresponds to an alternating ordering of xz and yz orbitals along the a and c axes for the Co-Py(3+). The orbital ordering and pyramidal distortion lead to deformation of the octahedra but the Co-Oc(3+) LS state does not allow an orbital order to occur for the Co-Oc(3+), ions. The soft x-ray magnetic diffraction results indicate that the magnetic moments are aligned in the ab plane but are not parallel to the crystallographic a or b axes. The orbital order and the doubling of the magnetic unit cell along the c axis support a noncollinear magnetic structure. The x-ray magnetic circular dichroism data indicate that there is a large orbital magnetic contribution to the total ordered Co moment.

Tomographic reconstruction of the refractive index with hard X-rays: an efficient method based on the gradient vector-field approach.

The refractive-index gradient vector field approach establishes a connection between a tomographic data set of differential phase contrast images and the distribution of the partial spatial derivatives of the refractive index in an object. The reconstruction of the refractive index in a plane requires the integration of its gradient field. This work shows how this integration can be efficiently performed by converting the problem to the Poisson equation, which can be accurately solved even in the case of noisy and large datasets. The performance of the suggested method is discussed and demonstrated experimentally by computing the refractive index distribution in both a simple plastic phantom and a complex biological sample. The quality of the reconstruction is evaluated through the direct comparison with other commonly used methods. To this end, the refractive index is retrieved from the same data set using also (1) the filtered backprojection algorithm for gradient projections, and (2) the regularized phase-retrieval procedure. Results show that the gradient vector field approach combined with the developed integration technique provides a very accurate depiction of the sample internal structure. Contrary to the two other techniques, the considered method does not require a preliminary phase-retrieval and can be implemented with any advanced computer tomography algorithm. In this work, analyzer-based phase contrast images are used for demonstration. Results, however, are generally valid and can be applied for processing differential phase-contrast tomographic data sets obtained with other phase-contrast imaging techniques.

A dictionary learning approach with overlap for the low dose computed tomography reconstruction and its vectorial application to differential phase tomography.

X-ray based Phase-Contrast Imaging (PCI) techniques have been demonstrated to enhance the visualization of soft tissues in comparison to conventional imaging methods. Nevertheless the delivered dose as reported in the literature of biomedical PCI applications often equals or exceeds the limits prescribed in clinical diagnostics. The optimization of new computed tomography strategies which include the development and implementation of advanced image reconstruction procedures is thus a key aspect. In this scenario, we implemented a dictionary learning method with a new form of convex functional. This functional contains in addition to the usual sparsity inducing and fidelity terms, a new term which forces similarity between overlapping patches in the superimposed regions. The functional depends on two free regularization parameters: a coefficient multiplying the sparsity-inducing norm of the patch basis functions coefficients, and a coefficient multiplying the norm of the differences between patches in the overlapping regions. The solution is found by applying the iterative proximal gradient descent method with FISTA acceleration. The gradient is computed by calculating projection of the solution and its error backprojection at each iterative step. We study the quality of the solution, as a function of the regularization parameters and noise, on synthetic data for which the solution is a-priori known. We apply the method on experimental data in the case of Differential Phase Tomography. For this case we use an original approach which consists in using vectorial patches, each patch having two components: one per each gradient component. The resulting algorithm, implemented in the European Synchrotron Radiation Facility tomography reconstruction code PyHST, has proven to be efficient and well-adapted to strongly reduce the required dose and the number of projections in medical tomography.