Small Angle-X-ray Scattering Tensor Tomography (SAS-TT) is a relatively new but powerful technique for studying the multiscale architecture of hierarchical structures particularly relevant to life science applications. Currently, the technique is very demanding on synchrotron beamtime, which limits its applications, especially for cases requiring a statistically relevant number of samples. This study reports the first SAS-TT measurement at a macromolecular X-ray crystallography beamline, PX-I at the Swiss Light Source (SLS), with an improvement in acquisition time from 96 h/Mvoxel in the pilot experiments to 6 h/Mvoxel with comparable sampling, defining a new standard for fast SAS-TT with a micrometer beam size and allowing to record a full tomogram in 1.2 h. Measurements are performed on the long and lenticular process of the incus bone, one of the three human auditory ossicles. The main orientation and degree of alignment of the mineralised collagen fibrils are characterised, as well as the size and shape of the mineral particles which show relevant variations in different tissue locations. The study reveals three distinct regions of high fibril alignment, most likely important pathways of sound throughout the ossicular chain, and highlights the technique's potential to aid in future developments in middle ear reconstructive surgery.

Microcalcifications (MC) are observed in various tissues and in relation to several diseases. For breast cancer, recent studies have reported differences in the nature of the MC and correlations to the degree of malignancy of the neoplasm. Here, investigations of benign, ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) breast MC using X-ray fluorescence, X-ray absorption spectroscopy and wide-angle X-ray scattering are reported. While Mg has been observed in all MC, only for the benign MC has a rim of crystalline whitlockite been identified as a minor crystalline phase in addition to the major hy-droxy-apatite (HAP) one. MC in DCIS and IDC tissue exhibit a higher abundance of a high-crystallinity HAP phase in comparison with the less well ordered MC in the benign tissue. Moreover, the distribution of other trace elements in the MC, such as Na, S, Cl, Sr and Y, is observed. For the quantitative analysis of the elemental maps, the experimentally determined sample thickness in each pixel has been incorporated as an additional parameter in the fitting process to account for sample roughness.

Maps of biological tissues at subcellular detail are key for understanding how organs function. X-ray nanotomography is a promising alternative to volume electron microscopy: it has the potential to nondestructively image millimeter-sized samples at ultrastructural resolution within a few days. A fundamental barrier is that the intense X-rays required for imaging also deform and disintegrate the tissue samples. Here we show a combination of solutions that overcome this barrier: We used a cryogenic and stable sample stage, tailored nonrigid tomographic reconstruction algorithms and an epoxy resin developed for the nuclear and aerospace industry. Tissue samples were resistant to radiation doses exceeding 1.15 × 1010 Gy, and sub-40 nm isotropic resolution allowed identifying axon bundles, dendrites and synapses in mouse brain tissue without physical sectioning. Using volume electron microscopy, we demonstrate that tissue ultrastructure remains intact after X-ray imaging. Together, this unlocks the potential of X-ray tomography for high-resolution tissue imaging. Optimizations of X-ray nanotomography including the choice of resin allows high-resolution imaging of mouse brain tissue, approaching the resolution of volume electron microscopy. Since it does not require slicing the tissue, this technology may become an attractive alternative to current standard methods for connectomics.

Dear Editor, Microcalcifications (MCs) are common findings in mammography and can be indicative of different degrees of malignancy, thus requiring multiple stereotaxis vacuumassisted biopsies under mammography to identify and characterize breast cancer [1, 2]. In many cases, however, the presence of MCs is not associated with the presence of a tumor. Therefore, a better understanding of the physical-chemical properties ofMCs is needed to assess the relationship between their presence and breast cancer. It is known that MCs are mostly composed of hydroxyapatite (HAp), a particular form of calcium phosphate, regardless of the clinical characteristics of the surrounding tissue. However, crystal features of HAp are altered in breast cancer [3]. In addition, other forms of calcium have been more recently identified in breast MCs [4], but their role is yet to be understood. Whitlockite (Whit) is a magnesium (Mg)-substituted form of calcium phosphate [5], whose presence in breast MCs was suggested as a possible marker of benignity [4] or a marker of invasiveness [6, 7]. In this work, we aimed to determine the relationship between the presence of Whit and the histological and crystal features of MCs and investigate its spatial distribution in breast MCs. To assess Whit presence in breast MCs, we first performed a correlative mapping study in representative biopsies: one from a healthy tissue (benign), one from ductal carcinoma in-situ (DCIS), and one from an invasive ductal carcinoma (IDC) (Supplementary Figure S1). X-ray fluorescence (XRF) and wide-angle X-ray scattering

Type I collagen physiological scaffold for tissue regeneration is considered one of the widely used biomaterials for tissue engineering and medical applications. It is hierarchically organized: five laterally staggered molecules are packed within fibrils, arranged into fascicles and bundles. The structural organization is correlated to the direction and intensity of the forces which can be loaded onto the tissue. For a tissue-specific regeneration, the required macro- and microstructure of a suitable biomaterial has been largely investigated. Conversely, the function of multiscale structural integrity has been much less explored but is crucial for scaffold design and application. In this work, collagen was extracted from different animal sources with protocols that alter its structure. Collagen of tendon shreds excised from cattle, horse, sheep and pig was structurally investigated by wide- and small-angle X-ray scattering techniques, at both molecular and supramolecular scales, and thermo-mechanically with thermal and load-bearing tests. Tendons were selected because of their resistance to chemical degradation and mechanical stresses. The multiscale structural integrity of tendons' collagen was studied in relation to the animal source, anatomic location and source for collagen extraction.

The purpose of this study is to use a multi-technique approach to detect the effects of spatially fractionated X-ray Microbeam (MRT) and Minibeam Radiation Therapy (MB) and to compare them to seamless Broad Beam (BB) irradiation. Healthy- and Glioblastoma (GBM)-bearing male Fischer rats were irradiated in-vivo on the right brain hemisphere with MRT, MB and BB delivering three different doses for each irradiation geometry. Brains were analyzed post mortem by multi-scale X-ray Phase Contrast Imaging-Computed Tomography (XPCI-CT), histology, immunohistochemistry, X-ray Fluorescence (XRF), Small- and Wide-Angle X-ray Scattering (SAXS/WAXS). XPCI-CT discriminates with high sensitivity the effects of MRT, MB and BB irradiations on both healthy and GBM-bearing brains producing a first-time 3D visualization and morphological analysis of the radio-induced lesions, MRT and MB induced tissue ablations, the presence of hyperdense deposits within specific areas of the brain and tumor evolution or regression with respect to the evaluation made few days post-irradiation with an in-vivo magnetic resonance imaging session. Histology, immunohistochemistry, SAXS/WAXS and XRF allowed identification and classification of these deposits as hydroxyapatite crystals with the coexistence of Ca, P and Fe mineralization, and the multi-technique approach enabled the realization, for the first time, of the map of the differential radiosensitivity of the different brain areas treated with MRT and MB. 3D XPCI-CT datasets enabled also the quantification of tumor volumes and Ca/Fe deposits and their full-organ visualization. The multi-scale and multi-technique approach enabled a detailed visualization and classification in 3D of the radio-induced effects on brain tissues bringing new essential information towards the clinical implementation of the MRT and MB radiation therapy techniques.

Myelin insulates neuronal axons and enables fast signal transmission, constituting a key component of brain development, aging and disease. Yet, myelin-specific imaging of macroscopic samples remains a challenge. Here, we exploit myelin's nanostructural periodicity, and use small-angle X-ray scattering tensor tomography (SAXS-TT) to simultaneously quantify myelin levels, nanostructural integrity and axon orientations in nervous tissue. Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples. Outcomes are validated by 2D/3D histology and compared to MRI measurements sensitive to myelin and axon orientations. Specificity to nanostructure is exemplified by concomitantly imaging different myelin types with distinct periodicities. Finally, we illustrate the method's sensitivity towards myelin-related diseases by quantifying myelin alterations in dysmyelinated mouse brain. This non-destructive, stain-free molecular imaging approach enables quantitative studies of myelination within and across samples during development, aging, disease and treatment, and is applicable to other ordered biomolecules or nanostructures.

Diseases like widespread diabetes or rare galactosemia may lead to high sugar concentrations in the human body, thereby promoting the formation of glycoconjugates. Glycation of collagen, i.e. the formation of glucose bridges, is nonenzymatic and therefore cannot be prevented in any other way than keeping the sugar level low. It relates to secondary diseases, abundantly occurring in aging populations and diabetics. However, little is known about the effects of glycation of collagen on the molecular level. We studied in vitro the effect of glycation, with d-glucose and d-galactose as well as d-ribose, on the structure of type 1 collagen by preparing decellularized matrices of bovine pericardia soaked in different sugar solutions, at increasing concentrations (0, 2.5, 5, 10, 20 and 40 mg ml−1), and incubated at 37°C for 3, 14, 30 and 90 days. The tissue samples were analyzed with small- and wide-angle X-ray scattering in scanning mode. We found that glucose and galactose produce similar changes in collagen, i.e. they mainly affect the lateral packing between macromolecules. However, ribose is much faster in glycation, provoking a larger effect on the lateral packing, but also seems to cause qualitatively different effects on the collagen structure.

Glycosylation is the process of combining one or more glucose molecules (or other monosaccharides) with molecules of a different nature (which are therefore glycosylated). In biochemistry, glycosylation is catalyzed by several specific enzymes, and assumes considerable importance since it occurs mainly at the expense of proteins and phospholipids which are thus transformed into glycoproteins and glycolipids. Conversely, in diabetes and aging, glycation of proteins is a phenomenon of non-enzymatic nature and thus not easily controlled. Glycation of collagen distorts its structure, renders the extracellular matrix stiff and brittle and at the same time lowers the degradation susceptibility thereby preventing renewal. Based on models detailed in this paper and with parameters determined from experimental data, we describe the glycation of type 1 collagen in bovine pericardium derived bio-tissues, upon incubation in glucose and ribose. With arginine and lysine/hydroxylysine amino acids as the primary sites of glycation and assuming that the topological polar surface area of the sugar molecules determines the glycation rates, we modelled the glycation as a function of time and determined the glycation rate and thus the progression of glycation as well as the resulting volume increase.

Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.

In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU with 10 Mpixel at 2.2 kHz in the future. In this context, we highlight the challenges for computer architecture and how these challenges can be addressed with innovative hardware including IBM POWER9 servers and field-programmable gate arrays. We discuss also data science challenges, showing the effect of rounding and lossy compression schemes on the MX JUNGFRAU detector images.

Abstract Breast microcalcifications are a common mammographic finding. Microcalcifications are considered suspicious signs of breast cancer and a breast biopsy is required, however, cancer is diagnosed in only a few patients. Reducing unnecessary biopsies and rapid characterization of breast microcalcifications are unmet clinical needs. In this study, 473 microcalcifications detected on breast biopsy specimens from 56 patients were characterized entirely by Raman mapping and confirmed by X-ray scattering. Microcalcifications from malignant samples were generally more homogeneous, more crystalline, and characterized by a less substituted crystal lattice compared with benign samples. There were significant differences in Raman features corresponding to the phosphate and carbonate bands between the benign and malignant groups. In addition to the heterogeneous composition, the presence of whitlockite specifically emerged as marker of benignity in benign microcalcifications. The whole Raman signature of each microcalcification was then used to build a classification model that distinguishes microcalcifications according to their overall biochemical composition. After validation, microcalcifications found in benign and malignant samples were correctly recognized with 93.5% sensitivity and 80.6% specificity. Finally, microcalcifications identified in malignant biopsies, but located outside the lesion, reported malignant features in 65% of in situ and 98% of invasive cancer cases, respectively, suggesting that the local microenvironment influences microcalcification features. This study confirms that the composition and structural features of microcalcifications correlate with breast pathology and indicates new diagnostic potentialities based on microcalcifications assessment. Significance: Raman spectroscopy could be a quick and accurate diagnostic tool to precisely characterize and distinguish benign from malignant breast microcalcifications detected on mammography.

Across all branches of science, medicine and engineering, high-resolution microscopy is required to understand functionality. Although optical methods have been developed to `defeat' the diffraction limit and produce 3D images, and electrons have proven ever more useful in creating pictures of small objects or thin sections, so far there is no substitute for X-ray microscopy in providing multiscale 3D images of objects with a single instrument and minimal labeling and preparation. A powerful technique proven to continuously access length scales from 10 nm to 10 µm is ptychographic X-ray computed tomography, which, on account of the orthogonality of the tomographic rotation axis to the illuminating beam, still has the limitation of necessitating pillar-shaped samples of small (ca 10 µm) diameter. Large-area planar samples are common in science and engineering, and it is therefore highly desirable to create an X-ray microscope that can examine such samples without the extraction of pillars. Computed laminography, where the axis of rotation is not perpendicular to the illumination direction, solves this problem. This entailed the development of a new instrument, LamNI, dedicated to high-resolution 3D scanning X-ray microscopy via hard X-ray ptychographic laminography. Scanning precision is achieved by a dedicated interferometry scheme and the instrument covers a scan range of 12 mm × 12 mm with a position stability of 2 nm and positioning errors below 5 nm. A new feature of LamNI is a pair of counter-rotating stages carrying the sample and interferometric mirrors, respectively.

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers ( Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T 2 R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

The imaging of integrated circuits across different length scales is required for failure analysis, design validation and quality control. At present, such inspection is accomplished using a hierarchy of different probes, from optical microscopy on the millimetre length scale to electron microscopy on the nanometre scale. Here we show that ptychographic X-ray laminography can provide non-destructive, three-dimensional views of integrated circuits, yielding both images of an entire chip volume and high-resolution images of arbitrarily chosen subregions. We demonstrate the approach using chips produced with 16 nm fin field-effect transistor technology, achieving a reconstruction resolution of 18.9 nm, and compare our results with photolithographic mask layout files and more conventional imaging approaches such as scanning electron microscopy. The technique should also be applicable to other branches of science and engineering where three-dimensional X-ray images of planar samples are required.

Blood glucose supplies energy to cells and is critical for the human brain. Glycation of collagen, the nonenzymatic formation of glucose-bridges, relates to diseases of aging populations and diabetics. This chemical reaction, together with its biomechanical effects, has been well studied employing animal models. However, the direct impact of glycation on collagen nano-structure is largely overlooked, and there is a lack of ex vivo model systems. Here, we present the impact of glucose on collagen nanostructure in a model system based on abundantly available connective tissue of farm animals. By combining ex vivo small and wide-angle X-ray scattering (SAXS/WAXS) imaging, we characterize intra- and inter-molecular parameters of collagen in decellularized bovine pericardium with picometer precision. We observe three distinct regimes according to glucose concentration. Such a study opens new avenues for inspecting the effects of diabetes mellitus on connective tissues and the influence of therapies on the resulting secondary disorders.

Abdominal aortic and popliteal artery aneurysms are vascular diseases which show massive degeneration, weakening of the vascular wall and loss of the vascular tissue functionality. They are driven by inflammatory, hemodynamical factors and biological alterations that may lead, in the case of an abdominal aortic aneurysm, to sudden and dangerous ruptures of the arteries. Here, human aortic and popliteal aneurysm tissues were obtained during surgical repair, and studied by synchrotron radiation X-ray scanning microdiffraction and small-angle scattering, to investigate the microcalcifications present in the tissues. Data collected during the experiments were transformed into quantitative microscopy images through the combination of statistical approaches and crystallographic methods. As a result of this multi-step analysis, microcalcifications, which are markers of the pathology, were classified in terms of chemical and structural content. This analysis helped to identify the presence of nanocrystalline hy-droxy-apatite and microcrystalline cholesterol, embedded in myofilament, and elastin-containing tissue with low collagen content in predominantly nanocrystalline areas. The generality of the approach allows it to be transferred to other types of tissue and other pathologies affected by microcalcifications, such as thyroid carcinoma, breast cancer, testicular microli-thia-sis or glioblastoma.