Centimeter-scale Samples Research Articles

Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues.

Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with aberration-free 1×1×3 μm optical resolution over a large field of view (10.6×8.0 mm 2 ) and working distance (35 mm) at speeds up to 946 megavoxels/sec. Combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 250×250×750 nm optical resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and visualizing axons in human white matter.

Light-Sheet Microscopic Imaging of Whole-Mouse Vascular Network with Fluorescent Microsphere Perfusion.

Visualizing the whole vascular network system is crucial for understanding the pathogenesis of specific diseases and devising targeted therapeutic interventions. Although the combination of light sheet microscopy and tissue-clearing methods has emerged as a promising approach for investigating the blood vascular network, leveraging the spatial resolution down to the capillary level and the ability to image centimeter-scale samples remains difficult. Especially, as the resolution improves, the issue of photobleaching outside the field of view poses a challenge to image the whole vascular network of adult mice at capillary resolution. Here, we devise a fluorescent microsphere vascular perfusion method to enable labeling of the whole vascular network in adult mice, which overcomes the photobleaching limit during the imaging of large samples. Moreover, by combining the utilization of a large-scale light-sheet microscope and tissue clearing protocols for whole-mouse samples, we achieve the capillary-level imaging resolution (3.2 × 3.2 × 6.5 μm) of the whole vascular network with dimensions of 45 × 15 × 82 mm in adult mice. This method thus holds great potential to deliver mesoscopic resolution images of various tissue organs for whole-animal imaging.

A Novel Technique for Producing Three-Dimensional Data Using Serial Sectioning and Semi-Automatic Image Classification.

The three-dimensional characterization of internal features, via metrics such as orientation, porosity, and connectivity, is important to a wide variety of scientific questions. Many spatial and morphological metrics only can be measured accurately through direct in situ three-dimensional observations of large (i.e., big enough to be statistically representative) volumes. For samples that lack material contrast between phases, serial grinding and imaging—which relies solely on color and textural characteristics to differentiate features—is a viable option for extracting such information. Here, we present the Grinding, Imaging, Reconstruction Instrument (GIRI), which automatically serially grinds and photographs centimeter-scale samples at micron resolution. Although the technique is destructive, GIRI produces an archival digital image stack. This digital image stack is run through a supervised machine-learning-based image processing technique that quickly and accurately segments data into predefined classes. These classified data then can be loaded into three-dimensional visualization software for measurement. We share three case studies to illustrate how GIRI can address questions with a significant morphological component for which two-dimensional or small-volume three-dimensional measurements are inadequate. The analyzed metrics include: the morphologies of objects and pores in a granular material, the bulk mineralogy of polyminerallic solids, and measurements of the internal angles and symmetry of crystals.

Fault surface morphology as an indicator for earthquake nucleation potential

AbstractLaboratory measurements can determine the potential for geologic materials to generate unstable (seismic) slip, but a direct relation between sliding behavior in the laboratory and physical characteristics observable in the field is lacking, especially for the phyllosilicate-rich gouges that are widely observed in natural faults. We integrated laboratory friction experiments with surface topography microscopy and demonstrated a quantitative correlation between frictional slip behavior and fault surface morphology of centimeter-scale samples. Our results show that striated, smooth fault surfaces were formed in experiments that exhibited stable sliding, whereas potentially unstable sliding was associated with rougher, isotropic fault surfaces. We interpret that frictional stability and fault surface morphology are linked via the evolution of asperity contacts on localized slip surfaces. If fault surface roughness obeys a fractal relationship over a large range of length scales, then we infer that the morphological characteristics observed in the laboratory could indicate the earthquake nucleation potential on natural fault surfaces.

High contrast, isotropic, and uniform 3D-imaging of centimeter-scale scattering samples using structured illumination light-sheet microscopy with axial sweeping.

Light-sheet fluorescent microscopy (LSFM) has, in recent years, allowed for rapid 3D-imaging of cleared biomedical samples at larger and larger scale. However, even in cleared samples, multiple light scattering often degrades the imaging contrast and widens the optical sectioning. Accumulation of scattering intensifies these negative effects as light propagates inside the tissue, which accentuates the issues when imaging large samples. With axially swept light-sheet microscopy (ASLM), centimeter-scale samples can be scanned with a uniform micrometric optical sectioning. But to fully utilize these benefits for 3D-imaging in biomedical tissue samples, suppression of scattered light is needed. Here, we address this by merging ASLM with light-sheet based structured illumination into Structured Illumination Light-sheet Microscopy with Axial Sweeping (SILMAS). The SILMAS method thus enables high-contrast imaging, isotropic micrometric resolution and uniform optical sectioning in centimeter-scale scattering samples, creating isotropic 3D-volumes of e.g., whole mouse brains without the need for any computation-heavy post-processing. We demonstrate the effectiveness of the approach in agarose gel phantoms with fluorescent beads, and in an PFF injected alpha-synuclein transgenic mouse model tagged with a green fluorescent protein (SynGFP). SILMAS imaging is compared to standard ASLM imaging on the same samples and using the same optical setup, and is shown to increase contrast by as much as 370% and reduce widening of optical sectioning by 74%. With these results, we show that SILMAS improves upon the performance of current state-of-the-art light-sheet microscopes for large and imperfectly cleared tissue samples and is a valuable addition to the LSFM family.

In situ dynamic X-ray imaging of fluid-rock interactions inside tight sandstone during hydraulic fracturing: fluid flow process and fracture network growth

Hydraulic fracturing plays a fundamental role in unconventional hydrocarbon production and the development of enhanced geothermal systems. Thus, studying the fluid flow process and fracture network growth during hydraulic fracturing is necessary to provide guidance for creating and sustaining fracture networks in target reservoirs. The actual formation stress state and hydraulic fracturing process can be simulated in the laboratory for small-scale rock samples in hydraulic fracturing experiments. High-energy industrial X-ray computed tomography (CT) has been used to directly track the fracture propagation in millimeter-scale samples under triaxial stress loading. In this study, a large-scale fracture network with economic benefits for unconventional energy exploitation was the target of the experiment; therefore, centimeter-scale samples were used. A hydraulic fracturing simulation experiment was conducted on tight sandstone by applying triaxial compression and injection pressures. With the assistance of the PEEK core holder and third-generation medical X-ray CT scanner, in situ dynamic X-ray imaging of the fluid-rock interactions inside the sample was conducted for the first time. The fluid-rock interactions and fracture network growth can be dynamically observed, revealing the fluid-rock interactions during the hydraulic fracturing process and how macroscopic failure develops from the microfracture.

Hollow-grained “Voronoi foam” ceramics with high strength and thermal superinsulation up to 1400 °C

Nanostructures tend to be unstable at high temperatures due to large capillary energies, and therefore nanotechnology has not yet found many high-temperature applications at 1000 °C and above. By taking advantage of the high-temperature stability of refractory ceramics, here we develop a new approach of making hollow nano-grained materials to achieve thermal superinsulation across a wide temperature range, where the gaseous voids are mostly isolated within individual grain, with size comparable to the mean free path of air molecules to lower the thermal conduction by Knudsen effect. We have proved this general concept with hollow-grained La2Zr2O7 ceramic, and demonstrated exceptionally low thermal conductivity (0.016 W/(m⋅K)), the lowest ever reported for hard materials at or above room temperature. The centimeter-scale samples also have ultrahigh compressive strength (251 MPa), tensile strength in bending up to 100 MPa, and excellent thermal stability up to 1400 °C in air, due to monodispersity of pores that delays coarsening.

Extreme biomimetics: Preservation of molecular detail in centimeter-scale samples of biological meshes laid down by sponges.

Fabrication of biomimetic materials and scaffolds is usually a micro- or even nanoscale process; however, most testing and all manufacturing require larger-scale synthesis of nanoscale features. Here, we propose the utilization of naturally prefabricated three-dimensional (3D) spongin scaffolds that preserve molecular detail across centimeter-scale samples. The fine-scale structure of this collagenous resource is stable at temperatures of up to 1200°C and can produce up to 4 × 10-cm-large 3D microfibrous and nanoporous turbostratic graphite. Our findings highlight the fact that this turbostratic graphite is exceptional at preserving the nanostructural features typical for triple-helix collagen. The resulting carbon sponge resembles the shape and unique microarchitecture of the original spongin scaffold. Copper electroplating of the obtained composite leads to a hybrid material with excellent catalytic performance with respect to the reduction of p-nitrophenol in both freshwater and marine environments.

A High-On/Off-Ratio Floating-Gate Memristor Array on a Flexible Substrate via CVD-Grown Large-Area 2D Layer Stacking.

Memristors such as phase-change memory and resistive memory have been proposed to emulate the synaptic activities in neuromorphic systems. However, the low reliability of these types of memories is their biggest challenge for commercialization. Here, a highly reliable memristor array using floating-gate memory operated by two terminals (source and drain) using van der Waals layered materials is demonstrated. Centimeter-scale samples (1.5 cm × 1.5 cm) of MoS2 as a channel and graphene as a trap layer grown by chemical vapor deposition (CVD) are used for array fabrication with Al2 O3 as the tunneling barrier. With regard to the memory characteristics, 93% of the devices exhibit an on/off ratio of over 103 with an average ratio of 104 . The high on/off ratio and reliable endurance in the devices allow stable 6-level memory applications. The devices also exhibit excellent memory durability over 8000 cycles with a negligible shift in the threshold voltage and on-current, which is a significant improvement over other types of memristors. In addition, the devices can be strained up to 1% by fabricating on a flexible substrate. This demonstration opens a practical route for next-generation electronics with CVD-grown van der Waals layered materials.

Conceptual design of a1013-W pulsed-power accelerator for megajoule-class dynamic-material-physics experiments

We have developed a conceptual design of a next-generation pulsed-power accelerator that is optimized for megajoule-class dynamic-material-physics experiments. Sufficient electrical energy is delivered by the accelerator to a physics load to achieve—within centimeter-scale samples—material pressures as high as 1 TPa. The accelerator design is based on an architecture that is founded on three concepts: single-stage electrical-pulse compression, impedance matching, and transit-time-isolated drive circuits. The prime power source of the accelerator consists of 600 independent impedance-matched Marx generators. Each Marx comprises eight 5.8-GW bricks connected electrically in series, and generates a 100-ns 46-GW electrical-power pulse. A 450-ns-long water-insulated coaxial-transmission-line impedance transformer transports the power generated by each Marx to a system of twelve 2.5-m-radius water-insulated conical transmission lines. The conical lines are connected electrically in parallel at a 66-cm radius by a water-insulated 45-post sextuple-post-hole convolute. The convolute sums the electrical currents at the outputs of the conical lines, and delivers the combined current to a single solid-dielectric-insulated radial transmission line. The radial line in turn transmits the combined current to the load. Since much of the accelerator is water insulated, we refer to it as Neptune. Neptune is 40 m in diameter, stores 4.8 MJ of electrical energy in its Marx capacitors, and generates 28 TW of peak electrical power. Since the Marxes are transit-time isolated from each other for 900 ns, they can be triggered at different times to construct–over an interval as long as 1 μs–the specific load-current time history required for a given experiment. Neptune delivers 1 MJ and 20 MA in a 380-ns current pulse to an 18−mΩ load; hence Neptune is a megajoule-class 20-MA arbitrary waveform generator. Neptune will allow the international scientific community to conduct dynamic equation-of-state, phase-transition, mechanical-property, and other material-physics experiments with a wide variety of drive-pressure time histories.3 MoreReceived 25 January 2016DOI:https://doi.org/10.1103/PhysRevAccelBeams.19.070401This article is available under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.Published by the American Physical SocietyPhysics Subject Headings (PhySH)Physical SystemsPulsed-power acceleratorsAccelerators & Beams

Large Area Plasmonic Color Palettes with Expanded Gamut Using Colloidal Self-Assembly

Optical resonances in metallic nanostructures are promising in enabling high-resolution plasmonic color prints, color filters, and in rendering colors for plastic consumer products. However, nanostructure patterning approaches have relied on charged-particle beam lithography, with limited throughput. For the purpose of visually evaluating colors spanning a large parameter space, it is important to develop a rapid and cost-effective approach to patterning large areas. The speed at which the parameter space is explored experimentally needs to be comparable to the time it takes to run full electromagnetic simulations. Here, we used a bottom-up approach to cost-effectively create periodic nanostructures on centimeter-scale samples. Upon further processing, this approach produced more complex geometries, such as rings and domes, compared to the standard structures consisting of metal disks. By adjusting various geometric parameters, vivid colors with an expanded gamut were obtained.

High throughput multichannel fluorescence microscopy with microlens arrays.

We present a multichannel fluorescence microscopy technique for high throughput imaging applications. A microlens array with over 140,000 elements is used to image centimeter-scale samples at up to 18.1 megapixels per second. Large field-of-view multichannel fluorescent imaging is demonstrated in both sequential and parallel geometries. The extended dynamic range of this approach is also discussed.

3D imaging of fracture propagation using synchrotron X-ray microtomography

During its propagation in a rock a fracture may cross mechanical heterogeneities, which modify the stress field near the crack tip and therefore may affect the direction of propagation. Pre-existing strong (grains) and weak (pores, microcracks) defects control the final path of the fracture and the amplitude of its out-of-plane fluctuations; they may also control rupture arrest. In situ quantification of the role of heterogeneities on fracture propagation is challenging because of the technical difficulty to image the interior of a 3D medium at high spatial resolution. Here, hydraulic tension fractures were produced in 5% porosity limestone core samples, using a specially designed hydraulic cell. The 3D geometry of the centimeter-scale samples was imaged before and after fracturing, using X-ray computed synchrotron microtomography at a voxel resolution of 4.91 × 4.91 × 4.91 µm. The data show that hydraulic fractures propagated by linkage of pores, leading to a macroscopic fracture with well-developed roughness. Moreover, it was possible to estimate that the hydraulic fractures crossed up to 40% more heterogeneities (pores) than if they had propagated into the porous medium by randomly connecting these pores. This demonstrates and quantifies the strong control of local mechanical variations on rupture propagation. A statistical model of fracture propagation is proposed, involving linkage of nearest pores; this model quantitatively reproduces our experimental observation.

Permeability measurements of natural and experimental volcanic materials with a simple permeameter: Toward an understanding of magmatic degassing processes

Permeability measurement of quenched volcanic porous materials is an important approach to understand permeability development and degassing of vesicular silicic magmas. In this study, we developed a gas permeameter to measure permeability of natural samples and experimental products. The permeameter has broad measurement ranges of pressure difference (10 1–10 5 Pa) and gas-flow rate (10 − 9 –10 − 5 m 3/s). These ranges enable us to measure viscous permeability in the range of 10 − 17 –10 − 9 m 2 for 1 centimeter-scale samples, using the Forchheimer equation, which includes the inertial effect of gas flow permeating through the samples. In addition, we improved the procedure for performing permeability measurements of mm-sized products of decompression experiments. Although a previous study reported the first permeability data for vesicular silicic glass products of decompression experiments, we found an overestimation in their permeability data due to problems in sample preparation, especially for very low permeability samples. Our improved measurements give lower permeability values than those of Takeuchi et al. (2005)(Takeuchi, S., Nakashima, S., Tomiya, A., Shinohara, H., 2005. Experimental constraints on the low gas permeability of vesicular magma during decompression. Geophys. Res. Lett., 32, L10312 doi:10.1029/2005GL022491). We also evaluated the inertial effect on apparent permeability calculated using Darcy's law under the conditions of permeability measurement and magmatic degassing. The permeability measurements indicate that the apparent permeabilities of highly permeable samples (> 10 − 10 m 2 in viscous permeability) are affected considerably by the inertial effect under a high-pressure gradient (> 10 5 Pa/m) and reduced by more than 0.5 orders of magnitude from their viscous permeabilities. Also under magmatic conditions, the reduction of apparent permeability by more than 0.5–1.0 orders of magnitude may occur during the degassing of highly permeable magmas driven by a high-pressure gradient.

Compaction and dewatering processes of the oceanic sediments in the Costa Rica and Barbados subduction zones: estimates from in situ physical property measurements

During Ocean Drilling Program Legs 170 and 171A, logging-while-drilling (LWD) tools were deployed on the Costa Rica and Barbados subduction margins. High-quality density, resistivity, and natural γ-ray logs were acquired across the décollement zones on both margins. Based on a new method of ‘layer-by-layer’ correlation of the logs, changes in thickness and volume between incoming and subducted or accreted sediments are determined with 15 m resolution and 1% accuracy. The change in sediment thickness and volume generally decreases with depth, however, this change strongly depends on the lithology. Siliceous layers such as diatomaceous and radiolarian clay tend to be fluid-bearing, and the stratigraphic position of such zones is a critical factor in the fate of the subducted sediment section. On the Costa Rica Margin, the sediment section on the Cocos plate is underthrust intact beneath the toe of the Caribbean Plate with no frontal offscraping where a siliceous fluid-bearing zone is present only in the upper part of the section. On the Barbados margin, a layer of radiolarian clay exists, providing a narrow zone of mechanical weakness and anomalously high dewatering in the middle of the sediment section. This layer divides the sediments that are subducted from those that are accreted. Accreted and subducted sediments show different compaction styles. Accreted sediments are characterized by rapid compaction with vertical thickening, whereas subducted sediments are characterized by slow compaction with vertical flattening. The vertical thickening of the accreted sediments is due to horizontal tectonic compaction and contributes to the vertical thickening of the accretionary prism as a whole in the early stages of deformation. Dewatering flux is calculated by the volume change of the sediment sequences across the trench. The dewatering flux computed from the LWD data provides an estimate of the minimum fluid flux in the subduction zone and is significantly greater than the flux estimated from laboratory experiments because of meter-scale fluid conduits which influence the downhole logs but not the centimeter-scale sample measurements.