I21: an advanced high-resolution resonant inelastic X-ray scattering beamline at Diamond Light Source.

The I21 beamline at Diamond Light Source is dedicated to advanced resonant inelastic X-ray scattering (RIXS) for probing charge, orbital, spin and lattice excitations in materials across condensed matter physics, applied sciences and chemistry. Both the beamline and the RIXS spectrometer employ divergent variable-line-spacing gratings covering a broad energy range of 280-3000 eV. A combined energy resolution of ∼35 meV (16 meV) is readily achieved at 930 eV (530 eV) owing to the optimized optics and the mechanics. Considerable efforts have been paid to the design of the entire beamline, particularly the implementation of the collection mirrors, to maximize the X-ray photon throughput. The continuous rotation of the spectrometer over 150° under ultra high vacuum and a cryogenic manipulator with six degrees of freedom allow accurate mappings of low-energy excitations from solid state materials in momentum space. Most importantly, the facility features a unique combination of the high energy resolution and the high photon throughput vital for advanced RIXS applications. Together with its stability and user friendliness, I21 has become one of the most sought after RIXS beamlines in the world.

The scanning four-bounce monochromator for beamline I20 at the Diamond Light Source.

A description of the technical and design details of a scanning four-bounce crystal monochromator that has recently been commissioned for the Versatile X-ray Absorption Spectroscopy (XAS) beamline at Diamond Light Source is presented. This device consists of two independent rotary axes of unique design which are synchronized using a multiple read-head encoder system. This monochromator is shown to be capable of maintaining the flux throughput of the Bragg axes without the need of any external feedback mechanism from 4 to 20 keV. The monochromator is currently equipped with cryogenically cooled crystals with the upstream axis consisting of two independent Si(111) crystals and a pair of channel-cut crystals in the downstream axis. The possibility of installing an additional Si(311) crystal-set to extend the energy range to 34 keV is incorporated into the preliminary design of the device. Experimental data are presented showing the exceptional mechanical stability and repeatability of the monochromator axes.

A modular and compact portable mini-endstation for high-precision, high-speed fixed target serial crystallography at FEL and synchrotron sources.

The design and implementation of a compact and portable sample alignment system suitable for use at both synchrotron and free-electron laser (FEL) sources and its performance are described. The system provides the ability to quickly and reliably deliver large numbers of samples using the minimum amount of sample possible, through positioning of fixed target arrays into the X-ray beam. The combination of high-precision stages, high-quality sample viewing, a fast controller and a software layer overcome many of the challenges associated with sample alignment. A straightforward interface that minimizes setup and sample changeover time as well as simplifying communication with the stages during the experiment is also described, together with an intuitive naming convention for defining, tracking and locating sample positions. The setup allows the precise delivery of samples in predefined locations to a specific position in space and time, reliably and simply.

Implementation of a beam deflection system for studies of liquid interfaces on beamline I07 at Diamond.

X-ray optics, based on a double-crystal deflection scheme, that enable reflectivity measurements from liquid surfaces/interfaces have been designed, built and commissioned on beamline I07 at Diamond Light Source. This system is able to deflect the beam onto a fixed sample position located at the centre of a five-circle diffractometer. Thus the incident angle can be easily varied without moving the sample, and the reflected beam is tracked either by a moving Pilatus 100K detector mounted on the diffractometer arm or by a stationary Pilatus 2M detector positioned appropriately for small-angle scattering. Thus the system can easily combine measurements of the reflectivity from liquid interfaces (Q(z) > 1 Å(-1)) with off-specular data collection, both in the form of grazing-incidence small-angle X-ray scattering (GISAXS) or wider-angle grazing-incidence X-ray diffraction (GIXD). The device allows operation over the energy range 10-28 keV.

Visualizing temporal brain-state changes for fMRI using t-distributed stochastic neighbor embedding.

Purpose: Currently, functional magnetic resonance imaging (fMRI) is the most commonly used technique for obtaining dynamic information about the brain. However, because of the complexity of the data, it is often difficult to directly visualize the temporal aspect of the fMRI data. Approach: We outline a t -distributed stochastic neighbor embedding (t-SNE)-based postprocessing technique that can be used for visualization of temporal information from a 4D fMRI data. Apart from visualization, we also show its utility in detection of major changes in the brain meta-states during the scan duration. Results: The t-SNE approach is able to detect brain-state changes from task to rest and vice versa for single- and multitask fMRI data. A temporal visualization can also be obtained for task and resting state fMRI data for assessing the temporal dynamics during the scan duration. Additionally, hemodynamic delay can be quantified by comparison of the detected brain-state changes with the experiment paradigm for task fMRI data. Conclusion: The t-SNE visualization can visualize help identify major brain-state changes from fMRI data. Such visualization can provide information about the degree of involvement and attentiveness of the subject during the scan and can be potentially utilized as a quality control for subject's performance during the scan.

Spatiotemporal feature extraction and classification of Alzheimer's disease using deep learning 3D-CNN for fMRI data.

Purpose: Through the last three decades, functional magnetic resonance imaging (fMRI) has provided immense quantities of information about the dynamics of the brain, functional brain mapping, and resting-state brain networks. Despite providing such rich functional information, fMRI is still not a commonly used clinical technique due to inaccuracy involved in analysis of extremely noisy data. However, ongoing developments in deep learning techniques suggest potential improvements and better performance in many different domains. Our main purpose is to utilize the potentials of deep learning techniques for fMRI data for clinical use. Approach: We present one such synergy of fMRI and deep learning, where we apply a simplified yet accurate method using a modified 3D convolutional neural networks (CNN) to resting-state fMRI data for feature extraction and classification of Alzheimer's disease (AD). The CNN is designed in such a way that it uses the fMRI data with much less preprocessing, preserving both spatial and temporal information. Results: Once trained, the network is successfully able to classify between fMRI data from healthy controls and AD subjects, including subjects in the mild cognitive impairment (MCI) stage. We have also extracted spatiotemporal features useful for classification. Conclusion: This CNN can detect and differentiate between the earlier and later stages of MCI and AD and hence, it may have potential clinical applications in both early detection and better diagnosis of Alzheimer's disease.

Digitized cervical images: problems, solutions, and potential medical impact.

OBJECTIVE: To demonstrate compression, illumination enhancement, registration, segmentation, automated classification and steganography using digitized cervical images. MATERIALS AND METHODS: The Hybrid Multi-Scale Vector Quantization algorithm developed at Texas Technological University and other automated systems were used to improve digitized cervical images. RESULTS: We demonstrated high levels of image compression, illumination enhancement, registration, automated segmentation and classification and steganography of digitized cervical images. CONCLUSIONS: Digitized cervical images can be altered to facilitate research of cervical neoplasia.

Preparing digitized cervigrams for colposcopy research and education: determination of optimal resolution and compression parameters.

OBJECTIVE: Visual assessment of digitized cervigrams through the Internet needs to be optimized. The National Cancer Institute and National Library of Medicine are involved in a large effort to improve colposcopic assessment and, in preparation, are conducting methodologic research. MATERIALS AND METHODS: We selected 50 cervigrams with diagnoses ranging from normal to cervical intraepithelial neoplasia 3 or invasive cancer. Those pictures were scanned at 5 resolution levels from 1,550 to 4,000 dots per inch (dpi) and were presented to 4 expert colposcopists to assess image quality. After the ideal resolution level was determined, pictures were compressed at 7 compression ratios from 20:1 to 80:1 to determine the optimal level of compression that permitted full assessment of key visual details. RESULTS: There were no statistically significant differences between the 3,000 and 4,000 dpi pictures. At 2,000 dpi resolution, only one colposcopist found a slightly statistically significant difference (p = 0.02) compared with the gold standard. There was a clear loss of quality of the pictures at 1,660 dpi. At compression ratio 60:1, 3 of 4 evaluators found statistically significant differences when comparing against the gold standard. CONCLUSIONS: Our results suggest that 2,000 dpi is the optimal level for digitizing cervigrams, and the optimal compression ratio is 50:1 using a novel wavelet-based technology. At these parameters, pictures have no significant differences with the gold standard.