Generalized reverse projection method for grating-based phase tomography.

The reverse projection protocol results in fast phase-contrast imaging thanks to its compatibility with conventional computed-tomography scanning. Many researchers have proposed variants. However, all these reverse projection methods in grating-based phase-contrast imaging are built on the hypothesis of the synchronous phase of reference shifting curves in the whole field of view. The hypothesis imposes uniformity and alignment requirements on the gratings, thus the field of view is generally limited. In this paper, a generalized reverse projection method is presented analytically for the case of non-uniform reference in grating-based phase tomography. The method is demonstrated by theoretical derivation, numerical simulations and synchrotron radiation experiments. The influence of imaging position to sensitivity, and the phase-wrapping phenomenon are also discussed. The proposed method combines the advantages of the high efficiency of the reverse projection method and the universal applicability of the phase-stepping method. The authors believe that the method would be used widely in fast and dose-constrained imaging.

Quantifying redox heterogeneity in single-crystalline LiCoO2 cathode particles.

Active cathode particles are fundamental architectural units for the composite electrode of Li-ion batteries. The microstructure of the particles has a profound impact on their behavior and, consequently, on the cell-level electrochemical performance. LiCoO2 (LCO, a dominant cathode material) is often in the form of well-shaped particles, a few micrometres in size, with good crystallinity. In contrast to secondary particles (an agglomeration of many fine primary grains), which are the other common form of battery particles populated with structural and chemical defects, it is often anticipated that good particle crystallinity leads to superior mechanical robustness and suppressed charge heterogeneity. Yet, sub-particle level charge inhomogeneity in LCO particles has been widely reported in the literature, posing a frontier challenge in this field. Herein, this topic is revisited and it is demonstrated that X-ray absorption spectra on single-crystalline particles with highly anisotropic lattice structures are sensitive to the polarization configuration of the incident X-rays, causing some degree of ambiguity in analyzing the local spectroscopic fingerprint. To tackle this issue, a methodology is developed that extracts the white-line peak energy in the X-ray absorption near-edge structure spectra as a key data attribute for representing the local state of charge in the LCO crystal. This method demonstrates significantly improved accuracy and reveals the mesoscale chemical complexity in LCO particles with better fidelity. In addition to the implications on the importance of particle engineering for LCO cathodes, the method developed herein also has significant impact on spectro-microscopic studies of single-crystalline materials at synchrotron facilities, which is broadly applicable to a wide range of scientific disciplines well beyond battery research.

Precise correlative method of Cryo-SXT and Cryo-FM for organelle identification.

Cryogenic soft X-ray tomography (Cryo-SXT) is ideally suitable to image the 3D sub-cellular architecture and organization of cells with high resolution in the near-native preservation state. Cryogenic fluorescence microscopy (Cryo-FM) can determine the location of a molecule of interest that has been labeled with a fluorescent tag, thus revealing the function of the cells. To understand the relations between the sub-cellular architecture and the function of cells, correlative Cryo-SXT and Cryo-FM was applied. This method required the matching of images of different modalities, and the accuracy of the matching is important. Here, a precise correlative method of Cryo-SXT and Cryo-FM is introduced. The capability of matching images of different modalities with high resolution was verified by simulations and practical experiments, and the method was used to identify vacuoles and mitochondria.

Raman micro-spectroscopy monitoring of cytochrome c redox state in Candida utilis during cell death under low-temperature plasma-induced oxidative stress.

Oxidative stress may result in different modes of cell death, such as necrosis, apoptosis and necroptosis. Currently, researchers are still striving to develop efficient tools/methods to distinguish the cell death modes in direct and label-free ways. In this study, we attempted to employ Raman micro-spectroscopy to observe the molecular changes in Candida utilis cells under oxidative stress induced by low-temperature plasma (LTP) and explore the spectroscopic biomarkers for the modes of cell death under oxidative stress. In this research, we confirmed that LTP could impose oxidative stress on the yeast cells, and recorded the changes of Raman signals of cytochrome c in the cells under LTP oxidative stress. Subsequently, we identified the biochemical and morphological characteristic features corresponding to different modes of cell death. Interestingly, we found that LTP under certain conditions could induce oxidative stress which caused the yeast cell death mainly by means of necroptosis, which was verified by Annexin V/PI, HMGB1 location assay and immunoprecipitation assay of the RIP1/RIP3 necrosome. Correspondingly, we also showed that the LTP induced necroptosis, associated with the increase of cytoplasmic Ca2+ and mitochondrial ROS, the decrease of mitochondrial membrane potential, the release of oxidized cytochrome c from the mitochondrion to the cytoplasm, and the destruction of mitochondria in yeast cells. This work has therefore demonstrated that monitoring the redox state of cytochrome c using Raman micro-spectroscopy is very useful for distinguishing the modes of cell death and particularly may unveil the unique necroptosis process of cells under extrinsic oxidative stress.

From Cubes to Dice: Solvent-Regulated Morphology Engineering of Endohedral Fullerene Microcrystals with Anomalous Photoluminescence Enhancement.

Despite recent successes in preparing three-dimensional crystals of empty fullerenes, such as C60 and C70 , 3D endohedral fullerene crystals, and especially hollow nanostructures, have been scarcely reported. A universal approach has now been developed to prepare shape-tunable 3D crystals of several metal nitride clusterfullerenes, including cubes and dice (hollow cubes with holes at the center of each face), which can be readily switched by changing the volume ratio of good (mesitylene) and poor (isopropanol) solvents. Synchrotron-based soft X-ray nano-computed tomography was used to unambiguously identify the interior microstructure of the dice-shaped crystals of Tb3 N@C80 , and especially the depth of the hole at each face, confirming that the dice has a solid center and the holes are not interconnected. Owing to the enhanced light absorption, the dice-shaped crystals exhibit enhanced photoluminescence relative to that of the cubes.

Direct information retrieval after 3D reconstruction in grating-based X-ray phase-contrast computed tomography.

Grating-based X-ray differential phase-contrast imaging has attracted a great amount of attention and has been considered as a potential imaging method in clinical medicine because of its compatibility with the traditional X-ray tube source and the possibility of a large field of view. Moreover, phase-contrast computed tomography provides three-dimensional phase-contrast visualization. Generally, two-dimensional information retrieval performed on every projection is required prior to three-dimensional reconstruction in phase-contrast computed tomography. In this paper, a three-dimensional information retrieval method to separate absorption and phase information directly from two reconstructed images is derived. Theoretical derivations together with numerical simulations have been performed to confirm the feasibility and veracity of the proposed method. The advantages and limitations compared with the reverse projection method are also discussed. Owing to the reduced data size and the absence of a logarithm operation, the computational time for information retrieval is shortened by the proposed method. In addition, the hybrid three-dimensional images of absorption and phase information were reconstructed using an absorption reconstruction algorithm, hence the existing data pre-processing methods and iterative reconstruction algorithms in absorption reconstruction may be utilized in phase reconstruction immediately.

A modified discrete tomography for improving the reconstruction of unknown multi-gray-level material in the `missing wedge' situation.

Full angular rotational projections cannot always be acquired in tomographic reconstructions because of the limited space in the experimental setup, leading to the `missing wedge' situation. In this paper, a recovering `missing wedge' discrete algebraic reconstruction technique algorithm (rmwDART) has been proposed to solve the `missing wedge' problem and improve the quality of the three-dimensional reconstruction without prior knowledge of the material component's number or the material's values. By using oversegmentation, boundary extraction and mathematical morphological operations, `missing wedge' artifact areas can be located. Then, in the iteration process, by updating the located areas and regions, high-quality reconstructions can be obtained from the simulations, and the reconstructed images based on the rmwDART algorithm can be obtained from soft X-ray nano-computed tomography experiments. The results showed that there is the potential for discrete tomography.

Controllable long focal length microlens based on thermal expansion.

A novel method to fabricate a microlens array with a long focal length has been developed in this paper. It is based on the fabricating and heating of a microlens consisting of two materials with a great difference in coefficient of thermal expansion. A thermal expansion process leads to considerable deformation of the microlens surface and significant increase in focal length, which could be controlled by altering the processing temperature. Cylindrical polymeric microlens arrays with different focal lengths were successfully fabricated. By measuring the focal length and temperature dependence of the cylindrical microlens geometry, the formation mechanism was analyzed and validated. While the temperature is ranged from 20°C to 50°C, the focal length of the cylindrical microlens has been extended by 38.2% and the longest focal length was obtained up to 6.6 mm for the microlens with a linewidth of 240 µm.

A microfluidic surface-enhanced Raman spectroscopy approach for assessing the particle number effect of AgNPs on cytotoxicity.

Silver nanoparticles (Ag NPs) have well-known antibacterial properties and are widely applied in various medical products and general commodities. Although many studies have addressed the toxicity of Ag NPs to mammalian cells, the direct relationship between the number of Ag NPs in living cells and the corresponding cell toxicity has not yet been explicitly demonstrated. In this work, a simple and reusable microfluidic device composed of a quartz cover slip and a glass plate with etched micro-channel and micro-wells was employed for separating and trapping single living cells. The device was silanized to render the surface hydrophobic. For simplicity, HeLa cells as the model cancer cells were used in the study, which were pipette-loaded into an array of micro wells based on dead-end filling. Surface enhanced Raman spectroscopy (SERS) was then employed to examine the living cancer cells and assessed number and distribution of Ag NPs in the cells. Combined with the cell viability assay, we therefore correlated the number of Ag NPs in the cell with the toxicity to the cell directly.

Using X-ray computed tomography and micro-Raman spectrometry to measure individual particle surface area, volume, and morphology towards investigating atmospheric heterogeneous reactions.

Heterogeneous reactions on the aerosol particle surface in the atmosphere play important roles in air pollution, climate change, and global biogeochemical cycles. However, the reported uptake coefficients of heterogeneous reactions usually have large variations and may not be relevant to real atmospheric conditions. One of the major reasons for this is the use of bulk samples in laboratory experiments, while particles in the atmosphere are suspended individually. A number of technologies have been developed recently to study heterogeneous reactions on the surfaces of individual particles. Precise measurements on the reactive surface area, volume, and morphology of individual particles are necessary for calculating the uptake coefficient, quantifying reactants and products, and understanding the reaction mechanism better. In this study, for the first time we used synchrotron radiation X-ray computed tomography (XCT) and micro-Raman spectrometry to measure individual CaCO3 particle morphology, with sizes ranging from 3.5-6.5µm. Particle surface area and volume were calculated using a reconstruction method based on software three-dimensional (3-D) rendering. The XCT was first validated with high-resolution field-emission scanning electron microscopy (FE-SEM) to acquire accurate CaCO3 particle surface area and volume estimates. Our results showed an average difference of only 6.1% in surface area and 3.2% in volume measured either by micro-Raman spectrometry or X-ray tomography. X-ray tomography and FE-SEM can provide more morphological details of individual CaCO3 particles than micro-Raman spectrometry. This study demonstrated that X-ray computed tomography and micro-Raman spectrometry can precisely measure the surface area, volume, and morphology of an individual particle.

Directed Biofabrication of Nanoparticles through Regulating Extracellular Electron Transfer.

Biofabrication of nanomaterials is currently constrained by a low production efficiency and poor controllability on product quality compared to chemical synthetic routes. In this work, we show an attractive new biosynthesis system to break these limitations. A directed production of selenium-containing nanoparticles in Shewanella oneidensis MR-1 cells, with fine-tuned composition and subcellular synthetic location, was achieved by modifying the extracellular electron transfer chain. By taking advantage of its untapped intracellular detoxification and synthetic power, we obtained high-purity, uniform-sized cadmium selenide nanoparticles in the cytoplasm, with the production rates and fluorescent intensities far exceeding the state-of-the-art biosystems. These findings may fundamentally change our perception of nanomaterial biosynthesis process and lead to the development of fine-controllable nanoparticles biosynthesis technologies.

A modified equally sloped algorithm based on the total variation algorithm in computed tomography for insufficient data.

Computed tomography (CT) has become an important technique for analyzing the inner structures of material, biological and energy fields. However, there are often challenges in the practical application of CT due to insufficient data. For example, the maximum rotation angle of the sample stage is limited by sample space or image reconstruction from the limited number of views required to reduce the X-ray dose delivered to the sample. Therefore, it is difficult to acquire CT images with complete data. In this work, an iterative reconstruction algorithm based on the minimization of the image total variation (TV) has been utilized to develop equally sloped tomography (EST), and the reconstruction was carried out from limited-angle, few-view and noisy data. A synchrotron CT experiment on hydroxyapatite was also carried out to demonstrate the ability of the TV-EST algorithm. The results indicated that the new TV-EST algorithm was capable of achieving high-quality reconstructions from projections with insufficient data.

Method for extending the depth of focus in X-ray microscopy.

Transmission X-ray microscopy (TXM) is a powerful, nondestructive and three-dimensional imaging tool that has been applied in many fields. However, the ability to image large size samples using high-resolution TXM is restricted due to a limited depth of focus (DOF). In this study, a method based on multiple reconstructed slice stacks of an extended sample at different focal positions is developed to extend the DOF of TXM. The simulation and experimental results demonstrate that this novel method effectively and reliably extend the DOF of high-resolution TXM.

Nanocomputed Tomography Imaging of Bacterial Alkaline Phosphatase Activity with an Iodinated Hydrogelator.

Alkaline phosphatase (ALP) is an important enzyme, but direct imaging of ALP activity with high spatiotemporal resolution remains challenging. In this work, we rationally designed an iodinated hydrogelator precursor Nap-Phe-Phe(I)-Tyr(H2PO3)-OH (1P) which self-assembles into nanofibers to form hydrogel under the catalysis of ALP. With this property of concentrating iodine atoms at the locations of ALP, 1P was successfully applied for direct nanocomputed tomography (nano-CT) imaging of ALP activity in bacteria for the first time. We envision that, on the basis of this pioneering work, new hydrogelators containing more iodine atoms (e.g., five iodine atoms in 1P) will be designed for better nano-CT imaging of ALP activity with higher CT contrast in the near future.

A modified discrete algebraic reconstruction technique for multiple grey image reconstruction for limited angle range tomography.

The `missing wedge', which is due to a restricted rotation range, is a major challenge for quantitative analysis of an object using tomography. With prior knowledge of the grey levels, the discrete algebraic reconstruction technique (DART) is able to reconstruct objects accurately with projections in a limited angle range. However, the quality of the reconstructions declines as the number of grey levels increases. In this paper, a modified DART (MDART) was proposed, in which each independent region of homogeneous material was chosen as a research object, instead of the grey values. The grey values of each discrete region were estimated according to the solution of the linear projection equations. The iterative process of boundary pixels updating and correcting the grey values of each region was executed alternately. Simulation experiments of binary phantoms as well as multiple grey phantoms show that MDART is capable of achieving high-quality reconstructions with projections in a limited angle range. The interesting advancement of MDART is that neither prior knowledge of the grey values nor the number of grey levels is necessary.

Wafer scale fabrication of highly dense and uniform array of sub-5 nm nanogaps for surface enhanced Raman scatting substrates.

Metallic nanogap is very important for a verity of applications in plasmonics. Although several fabrication techniques have been proposed in the last decades, it is still a challenge to produce uniform nanogaps with a few nanometers gap distance and high throughput. Here we present a simple, yet robust method based on the atomic layer deposition (ALD) and lift-off technique for patterning ultranarrow nanogaps array. The ability to accurately control the thickness of the ALD spacer layer enables us to precisely define the gap size, down to sub-5 nm scale. Moreover, this new method allows to fabricate uniform nanogaps array along different directions densely arranged on the wafer-scale substrate. It is demonstrated that the fabricated array can be used as an excellent substrate for surface enhanced Raman scatting (SERS) measurements of molecules, even on flexible substrates. This uniform nanogaps array would also find its applications for the trace detection and biosensors.

Ultralong focal length microlens array fabricated based on SU-8 photoresist.

In this paper, a novel method to fabricate ultralong focal length microlens arrays has been proposed. The microlens arrays were fabricated based on surface tension when heating temperature is over a glass transition temperature of SU-8 photoresist. An ultralong focal length was achieved by the large radius of curvature of a photoresist surface. Microlenses of widths from 30 to 210 µm were successfully fabricated. The longest focal length was up to 4.4 mm from the microlens of 210 µm width. The formation mechanism was also studied and validated by simulation based on the finite element method.

Dual-mode harvest solar energy for photothermal Cu2-xSe biomineralization and seawater desalination by biotic-abiotic hybrid.

Biotic-abiotic hybrid photocatalytic system is an innovative strategy to capture solar energy. Diversifying solar energy conversion products and balancing photoelectron generation and transduction are critical to unravel the potential of hybrid photocatalysis. Here, we harvest solar energy in a dual mode for Cu2-xSe nanoparticles biomineralization and seawater desalination by integrating the merits of Shewanella oneidensis MR-1 and biogenic nanoparticles. Photoelectrons generated by extracellular Se0 nanoparticles power Cu2-xSe synthesis through two pathways that either cross the outer membrane to activate periplasmic Cu(II) reduction or are directly delivered into the extracellular space for Cu(I) evolution. Meanwhile, photoelectrons drive periplasmic Cu(II) reduction by reversing MtrABC complexes in S. oneidensis. Moreover, the unique photothermal feature of the as-prepared Cu2-xSe nanoparticles, the natural hydrophilicity, and the linking properties of bacterium offer a convenient way to tailor photothermal membranes for solar water production. This study provides a paradigm for balancing the source and sink of photoelectrons and diversifying solar energy conversion products in biotic-abiotic hybrid platforms.

Near-Native Imaging of Label-Free Silver Nanoparticles-Triggered 3D Subcellular Ultrastructural Reorganization in Microalgae.

Understanding the spatial orientation of nanoparticles and the corresponding subcellular architecture events favors uncovering fundamental toxic mechanisms and predicting response pathways of organisms toward environmental stressors. Herein, we map the spatial location of label-free citrate-coated Ag nanoparticles (Cit-AgNPs) and the corresponding subcellular reorganization in microalgae by a noninvasive 3D imaging approach, cryo-soft X-ray tomography (cryo-SXT). Cryo-SXT near-natively displays the 3D maps of Cit-AgNPs presenting in rarely identified sites, namely, extracellular polymeric substances (EPS) and the cytoplasm. By comparative 3D morphological assay, we observe that Cit-AgNPs disrupt the cellular ultrastructural homeostasis, triggering a severe malformation of cytoplasmic organelles with energy-producing and stress-regulating functions. AgNPs exposure causes evident disruption of the chloroplast membrane, significant attenuation of the pyrenoid matrix and starch sheath, extreme swelling of starch granules and lipid droplets, and shrinkage of the nucleolus. In accompaniment, the number and volume occupancy of starch granules are significantly increased. Meanwhile, the spatial topology of starch granules extends from the chloroplast to the cytoplasm with a dispersed distribution. Linking the dynamics of the internal structure and the alteration of physiological properties, we derive a comprehensive cytotoxic and response pathway of microalgae exposed to AgNPs. This work provides a perspective for assessing the toxicity at subcellular scales to achieve label-free nanoparticle-caused ultrastructure remodeling of phytoplankton.

Detection of early pulmonary emphysema by multi-contrast x-ray Talbot-Lau interferometer.

BACKGROUND: Pulmonary emphysema is a part of chronic obstructive pulmonary disease, which is an irreversible chronic respiratory disease. In order to avoid further damage to lung tissue, early diagnosis and treatment of pulmonary emphysema is essential. PURPOSE: Early pulmonary emphysema diagnosis is difficult with conventional radiographic imaging. Recently, x-ray phase contrast imaging has proved to be an effective and promising imaging strategy for soft tissue, due to its high sensitivity and multi-contrast. The aim of this study is to diagnose pulmonary emphysema early utilizing an x-ray Talbot-Lau interferometer (TLI). METHODS: We successfully established the mouse model of emphysema by porcine pancreatic elastase treatment, and then used the established x-ray TLI to perform imaging experiments on the mice with different treatment time. The traditional absorption CT and phase contrast CT were obtained simultaneously through TLI. The CT results and histopathology of mice lung in different treatment time were quantitatively analyzed. RESULTS: By imaging mice lungs, it can be found that phase contrast has higher sensitivity than absorption contrast in early pulmonary emphysema. The results show that the phase contrast signal could distinguish the pulmonary emphysema earlier than the conventional attenuation signal, which can be consistent with histological images. Through the quantitative analysis of pathological section and phase contrast CT, it can be found that there is a strong linear correlation. CONCLUSIONS: In this study, we quantitatively analyze mean linear intercept of histological sections and CT values of mice. The results show that the phase contrast signal has higher imaging sensitivity than the attenuation signal. X-ray TLI multi-contrast imaging is proved as a potential diagnostic method for early pulmonary emphysema in mice.