Robotic pendant drop: containerless liquid for µs-resolved, AI-executable XPCS.

The dynamics and structure of mixed phases in a complex fluid can significantly impact its material properties, such as viscoelasticity. Small-angle X-ray Photon Correlation Spectroscopy (SA-XPCS) can probe the spontaneous spatial fluctuations of the mixed phases under various in situ environments over wide spatiotemporal ranges (10-6-103 s /10-10-10-6 m). Tailored material design, however, requires searching through a massive number of sample compositions and experimental parameters, which is beyond the bandwidth of the current coherent X-ray beamline. Using 3.7-µs-resolved XPCS synchronized with the clock frequency at the Advanced Photon Source, we demonstrated the consistency between the Brownian dynamics of ~100 nm diameter colloidal silica nanoparticles measured from an enclosed pendant drop and a sealed capillary. The electronic pipette can also be mounted on a robotic arm to access different stock solutions and create complex fluids with highly-repeatable and precisely controlled composition profiles. This closed-loop, AI-executable protocol is applicable to light scattering techniques regardless of the light wavelength and optical coherence, and is a first step towards high-throughput, autonomous material discovery.

Linking scientific instruments and computation: Patterns, technologies, and experiences.

Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Thus, methods are required for configuring and running distributed computing pipelines-what we call flows-that link instruments, computers (e.g., for analysis, simulation, artificial intelligence [AI] model training), edge computing (e.g., for analysis), data stores, metadata catalogs, and high-speed networks. We review common patterns associated with such flows and describe methods for instantiating these patterns. We present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages powerful computers for data inversion,model training, or other purposes. We also discuss implications of such methods for operators and users of scientific facilities.

Fixed-target serial crystallography at the Structural Biology Center.

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two ß-lactamases: a class D serine ß-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-ß-lactamase from Stenotrophomonas maltophilia K279a.

Materials Engineering of Violin Soundboards by Stradivari and Guarneri.

We investigated the material properties of Cremonese soundboards using a wide range of spectroscopic, microscopic, and chemical techniques. We found similar types of spruce in Cremonese soundboards as in modern instruments, but Cremonese spruces exhibit unnatural elemental compositions and oxidation patterns that suggest artificial manipulation. Combining analytical data and historical information, we may deduce the minerals being added and their potential functions-borax and metal sulfates for fungal suppression, table salt for moisture control, alum for molecular crosslinking, and potash or quicklime for alkaline treatment. The overall purpose may have been wood preservation or acoustic tuning. Hemicellulose fragmentation and altered cellulose nanostructures are observed in heavily treated Stradivari specimens, which show diminished second-harmonic generation signals. Guarneri's practice of crosslinking wood fibers via aluminum coordination may also affect mechanical and acoustic properties. Our data suggest that old masters undertook materials engineering experiments to produce soundboards with unique properties.

A three-dimensional thalamocortical dataset for characterizing brain heterogeneity.

Neural microarchitecture is heterogeneous, varying both across and within brain regions. The consistent identification of regions of interest is one of the most critical aspects in examining neurocircuitry, as these structures serve as the vital landmarks with which to map brain pathways. Access to continuous, three-dimensional volumes that span multiple brain areas not only provides richer context for identifying such landmarks, but also enables a deeper probing of the microstructures within. Here, we describe a three-dimensional X-ray microtomography imaging dataset of a well-known and validated thalamocortical sample, encompassing a range of cortical and subcortical structures from the mouse brain . In doing so, we provide the field with access to a micron-scale anatomical imaging dataset ideal for studying heterogeneity of neural structure.

Publisher Correction: Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

X-ray tomography of extended objects: a comparison of data acquisition approaches.

The penetration power of x rays allows one to image large objects, while their short wavelength allows for high spatial resolution. As a result, with synchrotron sources, one has the potential to obtain tomographic images of centimeter-sized specimens with sub-micrometer pixel sizes. However, limitations on beam and detector size make it difficult to acquire such data of this sort in a single take, necessitating strategies for combining data from multiple regions. One strategy is to acquire a tiled set of local tomograms by rotating the specimen around each of the local tomogram center positions. Another strategy, sinogram oriented acquisition, involves the collection of projections at multiple offset positions from the rotation axis followed by data merging and reconstruction. We have carried out a simulation study to compare these two approaches in terms of radiation dose applied to the specimen, and reconstructed image quality. Local tomography acquisition involves an easier data alignment problem, and immediate viewing of subregions before the entire dataset has been acquired. Sinogram oriented acquisition involves a more difficult data assembly and alignment procedure, and it is more sensitive to accumulative registration error. However, sinogram oriented acquisition is more dose efficient, involves fewer translation motions of the object, and avoids certain artifacts of local tomography.

Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.

Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (µCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline's reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.

Tomosaic: efficient acquisition and reconstruction of teravoxel tomography data using limited-size synchrotron X-ray beams.

X-rays offer high penetration with the potential for tomography of centimetre-sized specimens, but synchrotron beamlines often provide illumination that is only millimetres wide. Here an approach is demonstrated termed Tomosaic for tomographic imaging of large samples that extend beyond the illumination field of view of an X-ray imaging system. This includes software modules for image stitching and calibration, while making use of existing modules available in other packages for alignment and reconstruction. The approach is compatible with conventional beamline hardware, while providing a dose-efficient method of data acquisition. By using parallelization on a distributed computing system, it provides a solution for handling teravoxel-sized or larger datasets that cannot be processed on a single workstation in a reasonable time. Using experimental data, the package is shown to provide good quality three-dimensional reconstruction for centimetre-sized samples with sub-micrometre pixel size.

A versatile x-ray microtomography station for biomedical imaging and materials research.

An x-ray microtomography station implemented at the X-ray Applied Crystallography Laboratory of the State University of Campinas is described. The station is based on a propagation based phase contrast imaging setup with a microfocus source and digital x-ray area detectors. Due to its simplicity, this setup is ideal for fast, high resolution imaging and microtomography of small biological specimens and materials research samples. It can also be coupled to gratings to use and develop new techniques as the harmonic spatial coherent imaging, which allow scattering contrast imaging. Details of the experimental setup, equipment, and software integration are described. Test microtomography for setup commissioning and characterization is shown. We conclude that phase contrast enhanced x-ray imaging and microtomography with resolution below 5 µm voxel size are possible and data sets as wide as 2000 × 2000 × 2000 voxels are obtained with this instrumentation.