Molecular X-ray computed tomography of myelin in a rat brain

X-ray scattering based scanning tomography for imaging and structural characterization of cellulose in plants

X-ray and neutron scattering have long been used for structural characterization of cellulose in plants. Due to averaging over the illuminated sample volume, these measurements traditionally overlooked the compositional and morphological heterogeneity within the sample. Here, a scanning tomographic imaging method is described, using contrast derived from the X-ray scattering intensity, for virtually sectioning the sample to reveal its internal structure at a resolution of a few micrometres. This method provides a means for retrieving the local scattering signal that corresponds to any voxel within the virtual section, enabling characterization of the local structure using traditional data-analysis methods. This is accomplished through tomographic reconstruction of the spatial distribution of a handful of mathematical components identified by non-negative matrix factorization from the large dataset of X-ray scattering intensity. Joint analysis of multiple datasets, to find similarity between voxels by clustering of the decomposed data, could help elucidate systematic differences between samples, such as those expected from genetic modifications, chemical treatments or fungal decay. The spatial distribution of the microfibril angle can also be analyzed, based on the tomographically reconstructed scattering intensity as a function of the azimuthal angle.

A step towards 6D WAXD tensor tomography

X-ray scattering/diffraction tensor tomography techniques are promising methods to acquire the 3D texture information of heterogeneous biological tissues at micrometre resolution. However, the methods suffer from a long overall acquisition time due to multi-dimensional scanning across real and reciprocal space. Here, a new approach is introduced to obtain 3D reciprocal information of each illuminated scanning volume using mathematic modeling, which is equivalent to a physical scanning procedure for collecting the full reciprocal information required for voxel reconstruction. The virtual reciprocal scanning scheme was validated by a simulated 6D wide-angle X-ray diffraction tomography experiment. The theoretical validation of the method represents an important technological advancement for 6D diffraction tensor tomography and a crucial step towards pervasive applications in the characterization of heterogeneous materials.

Multimodal 2D and 3D microscopic mapping of growth cartilage by computational imaging techniques - a short review including new research

Being able to image the microstructure of growth cartilage is important for understanding the onset and progression of diseases such as osteochondrosis and osteoarthritis, as well as for developing new treatments and implants. Studies of cartilage using conventional optical brightfield microscopy rely heavily on histological staining, where the added chemicals provide tissue-specific colours. Other microscopy contrast mechanisms include polarization, phase- and scattering contrast, enabling non-stained or 'label-free' imaging that significantly simplifies the sample preparation, thereby also reducing the risk of artefacts. Traditional high-performance microscopes tend to be both bulky and expensive.Computational imagingdenotes a range of techniques where computers with dedicated algorithms are used as an integral part of the image formation process. Computational imaging offers many advantages like 3D measurements, aberration correction and quantitative phase contrast, often combined with comparably cheap and compact hardware. X-ray microscopy is also progressing rapidly, in certain ways trailing the development of optical microscopy. In this study, we first briefly review the structures of growth cartilage and relevant microscopy characterization techniques, with an emphasis on Fourier ptychographic microscopy (FPM) and advanced x-ray microscopies. We next demonstrate with our own results computational imaging through FPM and compare the images with hematoxylin eosin and saffron (HES)-stained histology. Zernike phase contrast, and the nonlinear optical microscopy techniques of second harmonic generation (SHG) and two-photon excitation fluorescence (TPEF) are explored. Furthermore, X-ray attenuation-, phase- and diffraction-contrast computed tomography (CT) images of the very same sample are presented for comparisons. Future perspectives on the links to artificial intelligence, dynamic studies andin vivopossibilities conclude the article.

The new small-angle X-ray scattering beamline for materials research at PETRA III: SAXSMAT beamline P62

The SAXSMAT beamline P62 (Small-Angle X-ray Scattering beamline for Materials Research) is a new beamline at the high-energy storage ring PETRA III at DESY. This beamline is dedicated to combined small- and wide-angle X-ray scattering (SAXS/WAXS) techniques for both soft and hard condensed matter systems. It works mainly in transmission geometry. The beamline covers an energy range from 3.5 keV to 35.0 keV, which fulfills the requirements of the user community to perform anomalous scattering experiments. Mirrors are used to reduce the intensity of higher harmonics. Furthermore, the mirrors and 2D compound refracting lenses can focus the beam down to a few micrometres at the sample position. This option with the high photon flux enables also SAXS/WAXS tensor tomography experiments to be performed at this new beamline in a relatively short time. The first SAXS/WAXS pattern was collected in August 2021, while the first user experiment was carried out two months later. Since January 2022 the beamline has been in regular user operation mode. In this paper the beamline optics and the SAXS/WAXS instrument are described and two examples are briefly shown.

Small-angle scattering tensor tomography algorithm for robust reconstruction of complex textures

The development of small-angle scattering tensor tomography has enabled the study of anisotropic nanostructures in a volume-resolved manner. It is of great value to have reconstruction methods that can handle many different nanostructural symmetries. For such a method to be employed by researchers from a wide range of backgrounds, it is crucial that its reliance on prior knowledge about the system is minimized, and that it is robust under various conditions. Here, a method is presented that employs band-limited spherical functions to enable the reconstruction of reciprocal-space maps of a wide variety of nanostructures. This method has been thoroughly tested and compared with existing methods in its ability to retrieve known reciprocal-space maps, as well as its robustness to changes in initial conditions, using both simulations and experimental data. It has also been evaluated for its computational performance. The anchoring of this method in a framework of integral geometry and linear algebra highlights its possibilities and limitations.

Recent developments in X-ray diffraction/scattering computed tomography for materials science

X-ray diffraction/scattering computed tomography (XDS-CT) methods are a non-destructive class of chemical imaging techniques that have the capacity to provide reconstructions of sample cross-sections with spatially resolved chemical information. While X-ray diffraction CT (XRD-CT) is the most well-established method, recent advances in instrumentation and data reconstruction have seen greater use of related techniques like small angle X-ray scattering CT and pair distribution function CT. Additionally, the adoption of machine learning techniques for tomographic reconstruction and data analysis are fundamentally disrupting how XDS-CT data is processed. The following narrative review highlights recent developments and applications of XDS-CT with a focus on studies in the last five years. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

A multiscale tissue assessment in a rat model of mild traumatic brain injury

Diffusion tensor imaging (DTI) has demonstrated the potential to assess the pathophysiology of mild traumatic brain injury (mTBI) but correlations of DTI findings and pathological changes in mTBI are unclear. We evaluated the potential of ex vivo DTI to detect tissue damage in a mild mTBI rat model by exploiting multiscale imaging methods, histology and scanning micro-X-ray diffraction (SμXRD) 35 days after sham-operation (n = 2) or mTBI (n = 3). There were changes in DTI parameters rostral to the injury site. When examined by histology and SμXRD, there was evidence of axonal damage, reduced myelin density, gliosis, and ultrastructural alterations in myelin that were ongoing at the experimental time point of 35 days postinjury. We assessed the relationship between the 3 imaging modalities by multiple linear regression analysis. In this analysis, DTI and histological parameters were moderately related, whereas SμXRD parameters correlated weakly with DTI and histology. These findings suggest that while DTI appears to distinguish tissue changes at the microstructural level related to the loss of myelinated axons and gliosis, its ability to visualize alterations in myelin ultrastructure is limited. The use of several imaging techniques represents a novel approach to reveal tissue damage and provides new insights into mTBI detection.

Scanning structural mapping at the Life Science X-ray Scattering Beamline

This work describes the instrumentation and software for microbeam scattering and structural mapping at the Life Science X-ray Scattering (LiX) beamline at NSLS-II. Using a two-stage focusing scheme, an adjustable beam size between a few micrometres and a fraction of a millimetre is produced at the sample position. Scattering data at small and wide angles are collected simultaneously on multiple Pilatus detectors. A recent addition of an in-vacuum Pilatus 900k detector, with the detector modules arranged in a C-shaped configuration, has improved the azimuthal angle coverage in the wide-angle data. As an option, fluorescence data can be collected simultaneously. Fly scans have been implemented to minimize the time interval between scattering patterns and to avoid unnecessary radiation damage to the sample. For weakly scattering samples, an in-vacuum sample environment has been developed here to minimize background scattering. Data processing for these measurements is highly sample-specific. To establish a generalized data process workflow, first the data are reduced to reciprocal coordinates at the time of data collection. The users can then quantify features of their choosing from these intermediate data and construct structural maps. As examples, results from in-vacuum mapping of onion epidermal cell walls and 2D tomographic sectioning of an intact poplar stem are presented.

Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled in-line (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid- β (A β ) plaques.

Three-dimensional virtual histology of the cerebral cortex based on phase-contrast X-ray tomography

In this work, we optimize the setups and experimental parameters of X-ray phase-contrast computed-tomography for the three-dimensional imaging of the cyto- and myeloarchitecture of cerebral cortex, including both human and murine tissue. We present examples for different optical configurations using state-of-the art synchrotron instruments for holographic tomography, as well as compact laboratory setups for phase-contrast tomography in the direct contrast (edge-enhancement) regime. Apart from unstained and paraffin-embedded tissue, we tested hydrated tissue, as well as heavy metal stained and resin-embedded tissue using two different protocols. Further, we show that the image quality achieved allows to assess the neuropathology of multiple sclerosis in a biopsy sample collected during surgery.

Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue

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.

Small-angle X-ray scattering (SAXS) combines the high tissue penetration of X-rays with specificity to periodic nanostructures. The authors use SAXS tensor tomography (SAXS-TT) on intact mouse and human brain tissue samples, to quantify myelin levels and determine myelin integrity, myelinated axon orientation, and fibre tracts non-destructively.

Feasibility of imaging amyloid in the brain using small-angle x-ray scattering

Small-angle x-ray scattering (SAXS) imaging may have the potential to imageβ-amyloid plaquesin vivoin the brain without tracers for assessment of Alzheimer's disease (AD). We use a laboratory SAXS system for planar imaging of AD model and control mouse brains slices to detect regions with high density of amyloid plaques. These regions were validated with histology methods. Using Monte Carlo techniques, we simulate SAXS computed tomography (SAXS-CT) system to study the potential of selectively differentiating amyloid targets in mouse and human head phantoms with detailed anatomy. We found contrast between amyloid and brain tissue at smallq(below 0.8 nm^-1) in the neocortex region of the transgenic brain slices as supported by histology. We observed similar behavior through planar SAXS imaging of an amyloid-like fibril deposit with a 0.8 mm diameter at a known location on a wild type mouse brain. In our SAXS-CT simulations, we found that 33-keV x rays provide increase plaque visibility in the mouse head for targets of at least 0.1 mm in diameter, while in the human head, 70-keV x rays were capable of detecting plaques as small as 2 mm. To increase radiation efficiency, we used a weighted-sum image visualization approach allowing the dose deposited by 70-keV x rays per SAXS-CT slice of the human head to be reduced by a factor of 10 to 71 mGy for gray matter and 63 mGy for white matter. The findings suggest that a dedicated SAXS-CT system forin vivoamyloid imaging in small animals and humans can be successfully developed with further system optimization to detect regions with amyloid plaques in the brain with a safe level of radiation dose.

Feasibility of a label-free X-ray method to estimate brain amyloid load in small animals

BACKGROUND

Amyloid plaque in the brain is associated with a wide range of neurodegenerative diseases such as Alzheimer's and Parkinson's and defined as aggregates of amyloid fibrils rich in β-sheet structures.

NEW METHOD

We report a label-free method based on small-angle X-ray scattering (SAXS) to estimate amyloid load in an intact mouse head with skull. The method is based on recording and analyzing the X rays elastically scattered from the β-sheets of amyloid plaques in a mouse head at angles smaller than 10° and energies between 30 and 45 keV. The method is demonstrated by acquiring the spectral SAXS data of an amyloid model and an excised head from a wild-type mouse for 600 s.

RESULTS

We captured the distinct scattering peaks of the amyloid plaques at momentum transfer (q) of 6 and 13 nm^-1 associated with β-sheet structure. We first show linear correlation between the mass fraction of the amyloid target and the area under the peak (AUP) of the scattering curve. We report results for estimating amyloid load in a fixed mouse head by recovering the characteristic scattering signal from the amyloid target situated at various locations. The coefficient of variation in the amyloid load estimate is found to be less than 10%.

COMPARISON WITH EXISTING METHODS

There are no previously described label-free X-ray methods for the estimation of amyloid load in an intact head.

CONCLUSIONS

We demonstrated the feasibility of a label-free method based on SAXS to potentially estimate brain amyloid in small animals.

Validation study of small-angle X-ray scattering tensor tomography

Small-angle scattering tensor tomography (SASTT) is a recently developed technique able to tomographically reconstruct the 3D reciprocal space from voxels within a bulk volume. SASTT extends the concept of X-ray computed tomography, which typically reconstructs scalar values, by reconstructing a tensor per voxel, which represents the local nanostructure 3D organization. In this study, the nanostructure orientation in a human trabecular-bone sample obtained by SASTT was validated by sectioning the sample and using 3D scanning small-angle X-ray scattering (3D sSAXS) to measure and analyze the orientation from single voxels within each thin section. Besides the presence of cutting artefacts from the slicing process, the nanostructure orientations obtained with the two independent methods were in good agreement, as quantified with the absolute value of the dot product calculated between the nanostructure main orientations obtained in each voxel. The average dot product per voxel over the full sample containing over 10 000 voxels was 0.84, and in six slices, in which fewer cutting artefacts were observed, the dot product increased to 0.91. In addition, SAXS tensor tomography not only yields orientation information but can also reconstruct the full 3D reciprocal-space map. It is shown that the measured anisotropic scattering for individual voxels was reproduced from the SASTT reconstruction in each voxel of the 3D sample. The scattering curves along different 3D directions are validated with data from single voxels, demonstrating SASTT's potential for a separate analysis of nanostructure orientation and structural information from the angle-dependent intensity distribution.

Retrieving neuronal orientations using 3D scanning SAXS and comparison with diffusion MRI

While diffusion MRI (dMRI) is currently the method of choice to non-invasively probe tissue microstructure and study structural connectivity in the brain, its spatial resolution is limited and its results need structural validation. Current ex vivo methods employed to provide 3D fiber orientations have limitations, including tissue-distorting sample preparation, small field of view or inability to quantify 3D fiber orientation distributions. 3D fiber orientation in tissue sections can be obtained from 3D scanning small-angle X-ray scattering (3D sSAXS) by analyzing the anisotropy of scattering signals. Here we adapt the 3D sSAXS method for use in brain tissue, exploiting the high sensitivity of the SAXS signal to the ordered molecular structure of myelin. We extend the characterization of anisotropy from vectors to tensors, employ the Funk-Radon-Transform for converting scattering information to real space fiber orientations, and demonstrate the feasibility of the method in thin sections of mouse brain with minimal sample preparation. We obtain a second rank tensor representing the fiber orientation distribution function (fODF) for every voxel, thereby generating fODF maps. Finally, we illustrate the potential of 3D sSAXS by comparing the result with diffusion MRI fiber orientations in the same mouse brain. We show a remarkably good correspondence, considering the orthogonality of the two methods, i.e. the different physical processes underlying the two signals. 3D sSAXS can serve as validation method for microstructural MRI, and can provide novel microstructural insights for the nervous system, given the method's orthogonality to dMRI, high sensitivity to myelin sheath's orientation and abundance, and the possibility to extract myelin-specific signal and to perform micrometer-resolution scanning.

High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm

The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349-352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.

Hard X-Ray Nanoholotomography: Large-Scale, Label-Free, 3D Neuroimaging beyond Optical Limit

There have been great efforts on the nanoscale 3D probing of brain tissues to image subcellular morphologies. However, limitations in terms of tissue coverage, anisotropic resolution, stain dependence, and complex sample preparation all hinder achieving a better understanding of the human brain functioning in the subcellular context. Herein, X-ray nanoholotomography is introduced as an emerging synchrotron radiation-based technology for large-scale, label-free, direct imaging with isotropic voxel sizes down to 25 nm, exhibiting a spatial resolution down to 88 nm. The procedure is nondestructive as it does not require physical slicing. Hence, it allows subsequent imaging by complementary techniques, including histology. The feasibility of this 3D imaging approach is demonstrated on human cerebellum and neocortex specimens derived from paraffin-embedded tissue blocks. The obtained results are compared to hematoxylin and eosin stained histological sections and showcase the ability for rapid hierarchical neuroimaging and automatic rebuilding of the neuronal architecture at the level of a single cell nucleolus. The findings indicate that nanoholotomography can complement microscopy not only by large isotropic volumetric data but also by morphological details on the sub-100 nm level, addressing many of the present challenges in brain tissue characterization and probably becoming an important tool in nanoanatomy.

Micro-imaging of Brain Cancer Radiation Therapy Using Phase-contrast Computed Tomography

PURPOSE

Experimental neuroimaging provides a wide range of methods for the visualization of brain anatomic morphology down to subcellular detail. Still, each technique-specific detection mechanism presents compromises among the achievable field-of-view size, spatial resolution, and nervous tissue sensitivity, leading to partial sample coverage, unresolved morphologic structures, or sparse labeling of neuronal populations and often also to obligatory sample dissection or other sample invasive manipulations. X-ray phase-contrast imaging computed tomography (PCI-CT) is an experimental imaging method that simultaneously provides micrometric spatial resolution, high soft-tissue sensitivity, and ex vivo full organ rodent brain coverage without any need for sample dissection, staining or labeling, or contrast agent injection. In the present study, we explored the benefits and limitations of PCI-CT use for in vitro imaging of normal and cancerous brain neuromorphology after in vivo treatment with synchrotron-generated x-ray microbeam radiation therapy (MRT), a spatially fractionated experimental high-dose radiosurgery. The goals were visualization of the MRT effects on nervous tissue and a qualitative comparison of the results to the histologic and high-field magnetic resonance imaging findings.

METHODS AND MATERIALS

MRT was administered in vivo to the brain of both healthy and cancer-bearing rats. At 45 days after treatment, the brain was dissected out and imaged ex vivo using propagation-based PCI-CT.

RESULTS

PCI-CT visualizes the brain anatomy and microvasculature in 3 dimensions and distinguishes cancerous tissue morphology, necrosis, and intratumor accumulation of iron and calcium deposits. Moreover, PCI-CT detects the effects of MRT throughout the treatment target areas (eg, the formation of micrometer-thick radiation-induced tissue ablation). The observed neurostructures were confirmed by histologic and immunohistochemistry examination and related to the micro-magnetic resonance imaging data.

CONCLUSIONS

PCI-CT enabled a unique 3D neuroimaging approach for ex vivo studies on small animal models in that it concurrently delivers high-resolution insight of local brain tissue morphology in both normal and cancerous micro-milieu, localizes radiosurgical damage, and highlights the deep microvasculature. This method could assist experimental small animal neurology studies in the postmortem evaluation of neuropathology or treatment effects.

Scanning X-ray diffraction on cardiac tissue: automatized data analysis and processing

A scanning X-ray diffraction study of cardiac tissue has been performed, covering the entire cross section of a mouse heart slice. To this end, moderate focusing by compound refractive lenses to micrometer spot size, continuous scanning, data acquisition by a fast single-photon-counting pixel detector, and fully automated analysis scripts have been combined. It was shown that a surprising amount of structural data can be harvested from such a scan, evaluating the local scattering intensity, interfilament spacing of the muscle tissue, the filament orientation, and the degree of anisotropy. The workflow of data analysis is described and a data analysis toolbox with example data for general use is provided. Since many cardiomyopathies rely on the structural integrity of the sarcomere, the contractile unit of cardiac muscle cells, the present study can be easily extended to characterize tissue from a diseased heart.

Small-angle X-ray scattering characteristics of mouse brain: Planar imaging measurements and tomographic imaging simulations

Small-angle x-ray scattering (SAXS) imaging can differentiate tissue types based on their nanoscale molecular structure. However, characterization of the coherent scattering cross-section profile of relevant tissues is needed to optimally design SAXS imaging techniques for a variety of biomedical applications. Reported measured nervous tissue x-ray scattering cross sections under a synchrotron source have had limited agreement. We report a set of x-ray cross-section measurements obtained from planar SAXS imaging of 1 mm thick mouse brain (APP/PS1 wild-type) coronal slices using an 8 keV laboratory x-ray source. Two characteristic peaks were found at 0.96 and 1.60 nm-1 attributed to myelin. The peak intensities varied by location in the slice. We found that regions of gray matter, white matter, and corpus callosum could be segmented by their increasing intensities of myelin peaks respectively. Measured small-angle x-ray scattering cross sections were then used to define brain tissue scattering properties in a GPU-accelerated Monte Carlo simulation of SAXS computed tomography (CT) using a higher monochromatic x-ray energy (20 keV) to study design trade-offs for noninvasive in vivo SAXS imaging on a small-animal head including radiation dose, signal-to-noise ratio (SNR), and the effect of skull presence on the previous two metrics. Simulation results show the estimated total dose to the mouse head for a single SAXS-CT slice was 149.4 mGy. The pixel SNR was approximately 30.8 for white matter material whether or not a skull was present. In this early-stage proof-of-principle work, we have demonstrated our brain cross-section data and simulation tools can be used to assess optimal instrument parameters for dedicated small-animal SAXS-CT prototypes.

Improving the efficiency of small-angle x-ray scattering computed tomography using the OSEM algorithm

Small-angle x-ray scattering computed tomography (SAXS-CT) is a nondestructive method for the nanostructure analysis of heterogeneous materials. However, the limits of a long data acquisition time and vast amounts of data prevent SAXS-CT from becoming a routine experimental method in the applications of synchrotron radiation. In this study, the ordered subsets expectation maximization (OSEM) algorithm is introduced to improve the efficiency of SAXS-CT. To demonstrate the practicability of this method, a systematic simulation and experiments were carried out. The simulation results on a numerical phantom show that the OSEM-based SAXS-CT can effectively eliminate streaking artifacts and improve the efficiency of data acquisition by at least 3 times compared with the filter backprojection algorithm. By compromising the reconstruction speed and image quality, the optimal reconstruction parameters are also given for the image reconstruction in the OSEM-based SAXS-CT experiments. An experiment on a bamboo sample verified the validity of the proposed method with limited projection data. A further experiment on polyethylene demonstrated that the OSEM-based SAXS-CT is able to reveal the local nanoscale information about the crystalline structure and distributional difference inside the sample. In conclusion, the OSEM-based SAXS-CT can significantly improve experimental efficiency, which may promote SAXS-CT becoming a conventional method.

Techniques to assess bone ultrastructure organization: orientation and arrangement of mineralized collagen fibrils

Bone's remarkable mechanical properties are a result of its hierarchical structure. The mineralized collagen fibrils, made up of collagen fibrils and crystal platelets, are bone's building blocks at an ultrastructural level. The organization of bone's ultrastructure with respect to the orientation and arrangement of mineralized collagen fibrils has been the matter of numerous studies based on a variety of imaging techniques in the past decades. These techniques either exploit physical principles, such as polarization, diffraction or scattering to examine bone ultrastructure orientation and arrangement, or directly image the fibrils at the sub-micrometre scale. They make use of diverse probes such as visible light, X-rays and electrons at different scales, from centimetres down to nanometres. They allow imaging of bone sections or surfaces in two dimensions or investigating bone tissue truly in three dimensions, in vivo or ex vivo, and sometimes in combination with in situ mechanical experiments. The purpose of this review is to summarize and discuss this broad range of imaging techniques and the different modalities of their use, in order to discuss their advantages and limitations for the assessment of bone ultrastructure organization with respect to the orientation and arrangement of mineralized collagen fibrils.

Imaging of neuronal tissues by x-ray diffraction and x-ray fluorescence microscopy: evaluation of contrast and biomarkers for neurodegenerative diseases

We have used scanning X-ray diffraction (XRD) and X-ray fluorescence (XRF) with micro-focused synchrotron radiation to study histological sections from human substantia nigra (SN). Both XRF and XRD mappings visualize tissue properties, which are inaccessible by conventional microscopy and histology. We propose to use these advanced tools to characterize neuronal tissue in neurodegeneration, in particular in Parkinson's disease (PD). To this end, we take advantage of the recent experimental progress in x-ray focusing, detection, and use automated data analysis scripts to enable quantitative analysis of large field of views. XRD signals are recorded and analyzed both in the regime of small-angle (SAXS) and wide-angle x-ray scattering (WAXS). The SAXS signal was analyzed in view of the local myelin structure, while WAXS was used to identify crystalline deposits. PD tissue scans exhibited increased amounts of crystallized cholesterol. The XRF analysis showed increased amounts of iron and decreased amounts of copper in the PD tissue compared to the control.

Imaging of Biological Materials and Cells by X-ray Scattering and Diffraction

Cells and biological materials are large objects in comparison to the size of internal components such as organelles and proteins. An understanding of the functions of these nanoscale elements is key to elucidating cellular function. In this review, we describe the advances in X-ray scattering and diffraction techniques for imaging biological systems at the nanoscale. We present a number of principal technological advances in X-ray optics and development of sample environments. We identify radiation damage as one of the most severe challenges in the field, thus rendering the dose an important parameter when putting different X-ray methods in perspective. Furthermore, we describe different successful approaches, including scanning and full-field techniques, along with prominent examples. Finally, we present a few recent studies that combined several techniques in one experiment in order to collect highly complementary data for a multidimensional sample characterization.

Retrieving the spatially resolved preferred orientation of embedded anisotropic particles by small-angle X-ray scattering tomography

Experimental nondestructive methods for probing the spatially varying arrangement and orientation of ultrastructures in hierarchical materials are in high demand. While conventional computed tomography (CT) is the method of choice for nondestructively imaging the interior of objects in three dimensions, it retrieves only scalar density fields. In addition to the traditional absorption contrast, other contrast mechanisms for image formation based on scattering and refraction are increasingly used in combination with CT methods, improving both the spatial resolution and the ability to distinguish materials of similar density. Being able to obtain vectorial information, like local growth directions and crystallite orientations, in addition to scalar density fields, is a longstanding scientific desire. In this work, it is demonstrated that, under certain conditions, the spatially varying preferred orientation of anisotropic particles embedded in a homogeneous matrix can be retrieved using CT with small-angle X-ray scattering as the contrast mechanism. Specifically, orientation maps of filler talc particles in injection-moulded isotactic polypropylene are obtained nondestructively under the key assumptions that the preferred orientation varies slowly in space and that the orientation of the flake-shaped talc particles is confined to a plane. It is expected that the method will find application inin situstudies of the mechanical deformation of composites and other materials with hierarchical structures over a range of length scales.

X-rays Reveal the Internal Structure of Keratin Bundles in Whole Cells

In recent years, X-ray imaging of biological cells has emerged as a complementary alternative to fluorescence and electron microscopy. Different techniques were established and successfully applied to macromolecular assemblies and structures in cells. However, while the resolution is reaching the nanometer scale, the dose is increasing. It is essential to develop strategies to overcome or reduce radiation damage. Here we approach this intrinsic problem by combing two different X-ray techniques, namely ptychography and nanodiffraction, in one experiment and on the same sample. We acquire low dose ptychography overview images of whole cells at a resolution of 65 nm. We subsequently record high-resolution nanodiffraction data from regions of interest. By comparing images from the two modalities, we can exclude strong effects of radiation damage on the specimen. From the diffraction data we retrieve quantitative structural information from intracellular bundles of keratin intermediate filaments such as a filament radius of 5 nm, hexagonal geometric arrangement with an interfilament distance of 14 nm and bundle diameters on the order of 70 nm. Thus, we present an appealing combined approach to answer a broad range of questions in soft-matter physics, biophysics and biology.

Monte Carlo X-ray transport simulation of small-angle X-ray scattering instruments using measured sample cross sections

Small-angle X-ray scattering (SAXS) has recently been proposed as a novel noninvasivein vivomolecular imaging technique to characterize molecular interactions deep within the body using high-contrast probes. This article describes a detailed Monte Carlo X-ray transport simulation technique that utilizes user-provided cross sections to describe X-ray interaction in virtual samples and explore SAXS instrument design choices. The accuracy of the simulation code is validated with sample material cross sections derived from analytical models and empirical measurements of a homogeneous spherical gold nanoparticle (GNP) monomer, a dimer and heterogeneous mixtures of the two in aqueous solution. Analytical and measured scattering profiles from these samples were converted to cross sections using an absolute water standard. Our Monte Carlo estimates of the fraction of dimers from analytically derived and empirically derived cross sections are strongly correlated, with less than 1.5 and 16% error, respectively, to the expected concentration of monomer and dimer species. In addition, a variety of monoenergetic X-ray beams were simulated to investigate coherent scatteringversusradiation dose for a range of sample sizes. For GNP spheres in aqueous solution, the energy range that produces the most coherent scattering at the detector per deposited energy was between 31 and 49 keV for a sample thickness of 1 mm to 10 cm. The method described here for the detailed simulation of SAXS using measured and modeled cross sections will enable instrumentation optimization forin vivomolecular imaging applications.

Six-dimensional real and reciprocal space small-angle X-ray scattering tomography

When used in combination with raster scanning, small-angle X-ray scattering (SAXS) has proven to be a valuable imaging technique of the nanoscale, for example of bone, teeth and brain matter. Although two-dimensional projection imaging has been used to characterize various materials successfully, its three-dimensional extension, SAXS computed tomography, poses substantial challenges, which have yet to be overcome. Previous work using SAXS computed tomography was unable to preserve oriented SAXS signals during reconstruction. Here we present a solution to this problem and obtain a complete SAXS computed tomography, which preserves oriented scattering information. By introducing virtual tomography axes, we take advantage of the two-dimensional SAXS information recorded on an area detector and use it to reconstruct the full three-dimensional scattering distribution in reciprocal space for each voxel of the three-dimensional object in real space. The presented method could be of interest for a combined six-dimensional real and reciprocal space characterization of mesoscopic materials with hierarchically structured features with length scales ranging from a few nanometres to a few millimetres--for example, biomaterials such as bone or teeth, or functional materials such as fuel-cell or battery components.

Nanostructure surveys of macroscopic specimens by small-angle scattering tensor tomography

The mechanical properties of many materials are based on the macroscopic arrangement and orientation of their nanostructure. This nanostructure can be ordered over a range of length scales. In biology, the principle of hierarchical ordering is often used to maximize functionality, such as strength and robustness of the material, while minimizing weight and energy cost. Methods for nanoscale imaging provide direct visual access to the ultrastructure (nanoscale structure that is too small to be imaged using light microscopy), but the field of view is limited and does not easily allow a full correlative study of changes in the ultrastructure over a macroscopic sample. Other methods of probing ultrastructure ordering, such as small-angle scattering of X-rays or neutrons, can be applied to macroscopic samples; however, these scattering methods remain constrained to two-dimensional specimens or to isotropically oriented ultrastructures. These constraints limit the use of these methods for studying nanostructures with more complex orientation patterns, which are abundant in nature and materials science. Here, we introduce an imaging method that combines small-angle scattering with tensor tomography to probe nanoscale structures in three-dimensional macroscopic samples in a non-destructive way. We demonstrate the method by measuring the main orientation and the degree of orientation of nanoscale mineralized collagen fibrils in a human trabecula bone sample with a spatial resolution of 25 micrometres. Symmetries within the sample, such as the cylindrical symmetry commonly observed for mineralized collagen fibrils in bone, allow for tractable sampling requirements and numerical efficiency. Small-angle scattering tensor tomography is applicable to both biological and materials science specimens, and may be useful for understanding and characterizing smart or bio-inspired materials. Moreover, because the method is non-destructive, it is appropriate for in situ measurements and allows, for example, the role of ultrastructure in the mechanical response of a biological tissue or manufactured material to be studied.

Diffraction scattering computed tomography: a window into the structures of complex nanomaterials

Modern functional nanomaterials and devices are increasingly composed of multiple phases arranged in three dimensions over several length scales. Therefore there is a pressing demand for improved methods for structural characterization of such complex materials. An excellent emerging technique that addresses this problem is diffraction/scattering computed tomography (DSCT). DSCT combines the merits of diffraction and/or small angle scattering with computed tomography to allow imaging the interior of materials based on the diffraction or small angle scattering signals. This allows, e.g., one to distinguish the distributions of polymorphs in complex mixtures. Here we review this technique and give examples of how it can shed light on modern nanoscale materials.

Myelinated mouse nerves studied by X-ray phase contrast zoom tomography

We have used X-ray phase contrast tomography to resolve the structure of uncut, entire myelinated optic, saphenous and sciatic mouse nerves. Intrinsic electron density contrast suffices to identify axonal structures. Specific myelin labeling by an osmium tetroxide stain enables distinction between axon and surrounding myelin sheath. Utilization of spherical wave illumination enables zooming capabilities which enable imaging of entire sciatic internodes as well as identification of sub-structures such as nodes of Ranvier and Schmidt-Lanterman incisures.

Evolution of myelin ultrastructure and the major structural myelin proteins

Myelin sheaths, as the specialized tissue wrapping the nerve fibers in the central and peripheral nervous systems (CNS and PNS), are responsible for rapid conduction of electrical signals in these fibers. We compare the nerve myelin sheaths of different phylogenetic origins-including mammal, rodent, bird, reptile, amphibian, lungfish, teleost, and elasmobranch-with respect to periodicities and inter-membrane separations at their cytoplasmic and extracellular appositions, and correlate these structural parameters with biochemical composition. P0 glycoprotein and P0-like proteins are present in PNS of terrestrial species or land vertebrates (Tetrapod) and in CNS and PNS of aquatic species. Proteolipid protein (PLP) is a major component only in the CNS myelin of terrestrial species and is involved in compaction of the extracellular apposition. The myelin structures of aquatic garfish and lungfish, which contain P0-like protein both in CNS and PNS, are similar to those of terrestrial species, indicating that they may be transitional organisms between water and land species. This article is part of a Special Issue entitled SI: Myelin Evolution.

Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept

Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species.

Laboratory implementation of X-ray diffraction/scattering computed tomography

This article demonstrates the possibility to perform X-ray diffraction/scattering computed tomography experiments with a laboratory diffraction setup. This technique is useful to characterize samples with inhomogeneities on a length scale of a couple of hundred micrometres. Furthermore, the method can be applied to preliminary phase-selective imaging prior to higher-resolution characterization using synchrotron radiation. This article presents the results of test experiments carried out on a rhombohedral C60sample previously studied at the ESRF.

Aging of a Pt/Al2O3 exhaust gas catalyst monitored by quasi in situ X-ray micro computed tomography

Catalyst aging effects are analyzed using X-ray absorption micro-computed tomography in combination with conventional characterization methods on various length scales ranging from nm to μm to gain insight into deactivation mechanisms.

Changes of statistical structural fluctuations unveils an early compacted degraded stage of PNS myelin

Degradation of the myelin sheath is a common pathology underlying demyelinating neurological diseases from Multiple Sclerosis to Leukodistrophies. Although large malformations of myelin ultrastructure in the advanced stages of Wallerian degradation is known, its subtle structural variations at early stages of demyelination remains poorly characterized. This is partly due to the lack of suitable and non-invasive experimental probes possessing sufficient resolution to detect the degradation. Here we report the feasibility of the application of an innovative non-invasive local structure experimental approach for imaging the changes of statistical structural fluctuations in the first stage of myelin degeneration. Scanning micro X-ray diffraction, using advances in synchrotron x-ray beam focusing, fast data collection, paired with spatial statistical analysis, has been used to unveil temporal changes in the myelin structure of dissected nerves following extraction of the Xenopus laevis sciatic nerve. The early myelin degeneration is a specific ordered compacted phase preceding the swollen myelin phase of Wallerian degradation. Our demonstration of the feasibility of the statistical analysis of SµXRD measurements using biological tissue paves the way for further structural investigations of degradation and death of neurons and other cells and tissues in diverse pathological states where nanoscale structural changes may be uncovered.

A computational model coupling mechanics and electrophysiology in spinal cord injury

Traumatic brain injury and spinal cord injury have recently been put under the spotlight as major causes of death and disability in the developed world. Despite the important ongoing experimental and modeling campaigns aimed at understanding the mechanics of tissue and cell damage typically observed in such events, the differentiated roles of strain, stress and their corresponding loading rates on the damage level itself remain unclear. More specifically, the direct relations between brain and spinal cord tissue or cell damage, and electrophysiological functions are still to be unraveled. Whereas mechanical modeling efforts are focusing mainly on stress distribution and mechanistic-based damage criteria, simulated function-based damage criteria are still missing. Here, we propose a new multiscale model of myelinated axon associating electrophysiological impairment to structural damage as a function of strain and strain rate. This multiscale approach provides a new framework for damage evaluation directly relating neuron mechanics and electrophysiological properties, thus providing a link between mechanical trauma and subsequent functional deficits.

Investigation of the three-dimensional orientation of mineralized collagen fibrils in human lamellar bone using synchrotron X-ray phase nano-tomography

We investigate the three-dimensional (3-D) organization of mineralized collagen fibrils in human cortical bone based on synchrotron X-ray phase nano-tomography images. In lamellar bone the collagen fibrils are assumed to have a plywood-like arrangement, but due to experimental limitations the 3-D fibril structure has only been deduced from section surfaces so far and the findings have been controversial. Breakthroughs in synchrotron tomographic imaging have given access to direct 3-D information on the bone structure at the nanoscale level. Using an autocorrelation-based orientation measure we confirm that the fibrils are unidirectional in quasi-planes of sub-lamellae and find two specific dominant patterns, oscillating and twisted plywoods coexisting in a single osteon. Both patterns exhibit smooth orientation changes between adjacent quasi-planes. Moreover, we find that the periodic changes in collagen fibril orientation are independent of fluctuations in local mass density. These data improve our understanding of the lamellar arrangement in bone and allow more detailed investigations of structure-function relationships at this scale, providing templates for bio-inspired materials. The presented methodology can be applied to non-destructive 3-D characterization of the sub-micron scale structure of other natural and artificial mineralized biomaterials.

Biochemical label-free tissue imaging with subcellular-resolution synchrotron FTIR with focal plane array detector

The critical questions into the cause of neural degeneration, in Alzheimer disease and other neurodegenerative disorders, are closely related to the question of why certain neurons survive. Answers require detailed understanding of biochemical changes in single cells. Fourier transform infrared microspectroscopy is an excellent tool for biomolecular imaging in situ, but resolution is limited. The mid-infrared beamline IRENI (InfraRed ENvironmental Imaging) at the Synchrotron Radiation Center, University of Wisconsin-Madison, enables label-free subcellular imaging and biochemical analysis of neurons with an increase of two orders of magnitude in pixel spacing over current systems. With IRENI's capabilities, it is now possible to study changes in individual neurons in situ, and to characterize their surroundings, using only the biochemical signatures of naturally-occurring components in unstained, unfixed tissue. We present examples of analyses of brain from two transgenic mouse models of Alzheimer disease (TgCRND8 and 3xTg) that exhibit different features of pathogenesis. Data processing on spectral features for nuclei reveals individual hippocampal neurons, and neurons located in the proximity of amyloid plaque in TgCRND8 mouse. Elevated lipids are detected surrounding and, for the first time, within the dense core of amyloid plaques, offering support for inflammatory and aggregation roles. Analysis of saturated and unsaturated fatty acid ester content in retina allows characterization of neuronal layers. IRENI images also reveal spatially-resolved data with unprecedented clarity and distinct spectral variation, from sub-regions including photoreceptors, neuronal cell bodies and synapses in sections of mouse retina. Biochemical composition of retinal layers can be used to study changes related to disease processes and dietary modification.