Emmanuel Brun

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.

High-resolution, low-dose phase contrast X-ray tomography for 3D diagnosis of human breast cancers

Mammography is the primary imaging tool for screening and diagnosis of human breast cancers, but ∼10–20% of palpable tumors are not detectable on mammograms and only about 40% of biopsied lesions are malignant. Here we report a high-resolution, low-dose phase contrast X-ray tomographic method for 3D diagnosis of human breast cancers. By combining phase contrast X-ray imaging with an image reconstruction method known as equally sloped tomography, we imaged a human breast in three dimensions and identified a malignant cancer with a pixel size of 92 μm and a radiation dose less than that of dual-view mammography. According to a blind evaluation by five independent radiologists, our method can reduce the radiation dose and acquisition time by ∼74% relative to conventional phase contrast X-ray tomography, while maintaining high image resolution and image contrast. These results demonstrate that high-resolution 3D diagnostic imaging of human breast cancers can, in principle, be performed at clinical compatible doses.

Synchrotron microbeam radiation therapy induces hypoxia in intracerebral gliosarcoma but not in the normal brain

PURPOSE Synchrotron microbeam radiation therapy (MRT) is an innovative irradiation modality based on spatial fractionation of a high-dose X-ray beam into lattices of microbeams. The increase in lifespan of brain tumor-bearing rats is associated with vascular damage but the physiological consequences of MRT on blood vessels have not been described. In this manuscript, we evaluate the oxygenation changes induced by MRT in an intracerebral 9L gliosarcoma model. METHODS Tissue responses to MRT (two orthogonal arrays (2 × 400Gy)) were studied using magnetic resonance-based measurements of local blood oxygen saturation (MR_SO2) and quantitative immunohistology of RECA-1, Type-IV collagen and GLUT-1, marker of hypoxia. RESULTS In tumors, MR_SO2 decreased by a factor of 2 in tumor between day 8 and day 45 after MRT. This correlated with tumor vascular remodeling, i.e. decrease in vessel density, increases in half-vessel distances (×5) and GLUT-1 immunoreactivity. Conversely, MRT did not change normal brain MR_SO2, although vessel inter-distances increased slightly. CONCLUSION We provide new evidence for the differential effect of MRT on tumor vasculature, an effect that leads to tumor hypoxia. As hypothesized formerly, the vasculature of the normal brain exposed to MRT remains sufficiently perfused to prevent any hypoxia.

Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging

Hundreds of papyrus rolls, buried by the eruption of Mount Vesuvius in 79 AD and belonging to the only library passed on from Antiquity, were discovered 260 years ago at Herculaneum. These carbonized papyri are extremely fragile and are inevitably damaged or destroyed in the process of trying to open them to read their contents. In recent years, new imaging techniques have been developed to read the texts without unwrapping the rolls. Until now, specialists have been unable to view the carbon-based ink of these papyri, even when they could penetrate the different layers of their spiral structure. Here for the first time, we show that X-ray phase-contrast tomography can reveal various letters hidden inside the precious papyri without unrolling them. This attempt opens up new opportunities to read many Herculaneum papyri, which are still rolled up, thus enhancing our knowledge of ancient Greek literature and philosophy.

Cartilage and soft tissue imaging using X-rays: propagation-based phase-contrast computed tomography of the human knee in comparison with clinical imaging techniques and histology.

ObjectivesThis study evaluates high-resolution tomographic x-ray phase-contrast imaging in whole human knee joints for the depiction of soft tissue with emphasis on hyaline cartilage. The method is compared with conventional computed tomography (CT), synchrotron radiation absorption-based CT, and magnetic resonance imaging (MRI). Material and MethodsAfter approval of the institutional review board, 2 cadaveric human knees were examined at an synchrotron institution using a monochromatic x-ray beam of 60 keV, a detector with a 90-mm2 field of view, and a pixel size of 46 × 46 &mgr;m2. Images of phase-contrast imaging CT were reconstructed with the filtered back projection algorithm and the equally sloped tomography method. Image quality and tissue contrast were evaluated and compared in all modalities and with histology. ResultsPhase-contrast imaging provides visualization of altered cartilage regions invisible in absorption CT with simultaneous high detail of the underlying bony abnormalities. The delineation of surface changes is similar to 3-T MRI using cartilage-dedicated sequences. Phase-contrast imaging CT presents soft tissue contrast surpassing that of conventional CT with a clear discrimination of ligamentous, muscular, neural, and vascular structures. In addition, phase-contrast imaging images show cartilage and meniscal calcifications that are not perceptible on conventional CT or on MRI. ConclusionsPhase-contrast imaging CT may facilitate a more complete evaluation of the human knee joint by providing concurrent comprehensive information about cartilage, the underlying subchondral bone, and their changes in osteoarthritic conditions.

Single-image phase retrieval using an edge illumination X-ray phase-contrast imaging setup

A method enabling the retrieval of thickness or projected electron density of a sample from a single input image is derived theoretically and successfully demonstrated on experimental data.

High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography

Acellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds’ internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation, and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory.

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.

An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy.

Medical imaging and radiation therapy are widely used synchrotron-based techniques which have one thing in common: a significant dose delivery to typically biological samples. Among the ways to provide the experimenters with image guidance techniques indicating optimization strategies, Monte Carlo simulation has become the gold standard for accurately predicting radiation dose levels under specific irradiation conditions. A highly important hampering factor of this method is, however, its slow statistical convergence. A track length estimator (TLE) module has been coded and implemented for the first time in the open-source Monte Carlo code GATE/Geant4. Results obtained with the module and the procedures used to validate them are presented. A database of energy-absorption coefficients was also generated, which is used by the TLE calculations and is now also included in GATE/Geant4. The validation was carried out by comparing the TLE-simulated doses with experimental data in a synchrotron radiation computed tomography experiment. The TLE technique shows good agreement versus both experimental measurements and the results of a classical Monte Carlo simulation. Compared with the latter, it is possible to reach a pre-defined statistical uncertainty in about two to three orders of magnitude less time for complex geometries without loss of accuracy.

The ID21 X-ray and infrared microscopy beamline at the ESRF: status and recent applications to artistic materials

The ID21 beamline (European Synchrotron Radiation facility, France) is a multi micro-analytical platform combining X-ray and infrared micro-probes, for characterization of elements, species, molecular groups and crystalline structures in complex materials. Applications are mainly in the fields of cultural heritage, life science, environmental and earth sciences, materials sciences. Here, we first present the status of instruments: (i) the scanning micro-spectroscopy end-station, operating from 2.0 to 9.2 keV, under vacuum and offering cryo conditions, for the acquisition of 2D micro X-ray fluorescence (μXRF) maps, single point micro X-ray Absorption Near Edge Structure (μXANES) spectra and speciation maps with sub-micrometric resolution; (ii) the XANES full-field end-station, operating in the same vacuum and energy conditions, for the acquisition of hyper-spectral radiographs of thin concentrated samples, resulting in speciation maps with micrometric resolution and millimetric field of view; (iii) the scanning micro-X-ray diffraction (μXRD)/μXRF end-station, operating at 8.5 keV, in air, for the acquisition of 2D crystalline phase maps, with micrometric resolution; and (iv) the scanning infrared microscope, operating in the mid-infrared range for the acquisition of molecular maps and some structural maps with micrometric resolution. Recent hardware and software developments are presented, as well as new protocols for improved sample preparation of thin sections. Secondly, a review of recent applications for the study of cultural heritage is presented, illustrated by various examples: determination of the origin of the color in blue Chinese porcelains and in brown Sevres porcelains; detection of lead in ink on Herculaneum papyri; identification and degradation of modeling materials used by Auguste Rodin and of chrome yellow pigments used by Vincent van Gogh. Cryo capabilities are illustrated by the analysis of plants exposed to chromate solutions. These examples show the variety of materials analyzed, of questions tackled, and particularly the multiple advantages of the ID21 analytical platform for the analysis of ancient and artistic materials.