Artifact Reduction Based on Sinogram Interpolation for the 3D Reconstruction of Nanoparticles Using Electron Tomography

Electron tomography is a well‐known technique providing a 3D characterization of the morphology and chemical composition of nanoparticles. However, several reasons hamper the acquisition of tilt series with a large number of projection images, which deteriorate the quality of the 3D reconstruction. Here, an inpainting method that is based on sinogram interpolation is proposed, which enables one to reduce artifacts in the reconstruction related to a limited tilt series of projection images. The advantages of the approach will be demonstrated for the 3D characterization of nanoparticles using phantoms and several case studies.     

High-resolution time-resolved contrast-enhanced 3D MRA by combining SENSE with keyhole and SLAM strategies

Sensitivity encoding (SENSE) was combined with keyhole and selective line acquisition mode (SLAM) techniques to acquire a time series of images during contrast passage. The acquisition speed of the dynamic time frames was improved by a factor of 8 in total. The high spatial frequencies were sampled during the steady state and combined with the dynamic time frames to construct a series of high-resolution time-resolved contrast-enhanced 3D images. Filtered temporal correlation analysis was used to separate the arteries and veins.     

Position-controlled marker formation by helium ion microscope for aligning a TEM tomographic tilt series

We formed nano-dots using a helium ion microscope (HIM) equipped with a gas injection system. Because of position controllability, the nano-dot markers could be placed efficiently on a specimen using the HIM. The sizes of the dots were controlled by changing the beam radiation time. We tried for the first time to form dots on a rod-shaped specimen to use them as markers for aligning a transmission electron microscope tomographic tilt series before reconstructing 3D images.     

Quantifying heart rate dynamics using different approaches of symbolic dynamics

The analysis of symbolic dynamics applied to physiological time series is able to retrieve information about dynamical properties of the underlying system that cannot be gained with standard methods like e.g. spectral analysis. Different approaches for the transformation of the original time series to the symbolic time series have been proposed. Yet the differences between the approaches are unknown. In this study three different transformation methods are investigated: (1) symbolization according to the deviation from the average time series, (2) symbolization according to several equidistant levels between the minimum and maximum of the time series, (3) binary symbolization of the first derivative of the time series. Furthermore, permutation entropy was used to quantify the symbolic series. Each method was applied to the cardiac interbeat interval series RR _i and its difference ΔRR _I of 17 healthy subjects obtained during head-up tilt testing. The symbolic dynamics of each method is analyzed by means of the occurrence of short sequences (“words”) of length 3. The occurrence of words is grouped according to words without variations of the symbols (0V%), words with one variation (1V%), two like variations (2LV%) and two unlike variations (2UV%). Linear regression analysis showed that for method 1 0V%, 1V%, 2LV% and 2UV% changed with increasing tilt angle. For method 2 0V%, 2LV% and 2UV% changed with increasing tilt angle and method 3 showed changes for 0V% and 1V%. Furthermore, also the permutation entropy decreased with increasing tilt angle. In conclusion, all methods are capable of reflecting changes of the cardiac autonomic nervous system during head-up tilt. All methods show that even the analysis of very short symbolic sequences is capable of tracking changes of the cardiac autonomic regulation during head-up tilt testing.     

Spatially encoded NMR and the acquisition of 2D magnetic resonance images within a single scan

An approach that enables the acquisition of multidimensional NMR spectra within a single scan has been recently proposed and demonstrated. The present paper explores the applicability of such ultrafast acquisition schemes toward the collection of two-dimensional magnetic resonance imaging (2D MRI) data. It is shown that ideas enabling the application of these spatially encoded schemes within a spectroscopic setting, can be extended in a straightforward manner to pure imaging. Furthermore, the reliance of the original scheme on a spatial encoding and subsequent decoding of the evolution frequencies endows imaging applications with a greater simplicity and flexibility than their spectroscopic counterparts. The new methodology also offers the possibility of implementing the single-scan acquisition of 2D MRI images using sinusoidal gradients, without having to resort to subsequent interpolation procedures or non-linear sampling of the data. Theoretical derivations on the operational principles and imaging characteristics of a number of sequences based on these ideas are derived, and experimentally validated with a series of 2D MRI results collected on a variety of model phantom samples.     

Insight in the 3D morphology of silica-based nanotubes using electron microscopy

Amorphous silica-based nanotubes (SBNTs) were synthesized from phosphoryl triamide, OP(NH₂)₃, thiophosphoryl triamide, SP(NH₂)₃, and silicon tetrachloride, SiCl₄, at different temperatures and with varying amount of the starting material SiCl₄ using a recently developed template-free synthesis approach. Diameter and length of the SBNTs are tunable by varying the synthesis parameters. The 3D mesocrystals of the SBNTs were analyzed with focused ion beam sectioning and electron tomography in the transmission electron microscope showing the hollow tubular structure of the SBNTs. The reconstruction of a small SBNT assembly was achieved from a high-angle annular-dark field scanning transmission electron microscopy tilt series containing only thirteen images allowing analyzing beam sensitive material without altering the structure. The reconstruction revealed that the individual nanotubes are forming an interconnected array with an open channel structure.     

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介绍了一种软X射线多道能谱测量的新方法,该方法用软件实现实时采集、数据处理并通过软X射线能谱计算及时显示电子温度。和传统的脉高分析器(PHA)相比,道数和时间分辨率可用软件设定。新方法采用一台配有高速A/D采集卡的个人计算机获取原始的模拟信号,开发了专用的处理软件用来处理电子温度。新方法已经应用于HL-2A装置实验,与其它方法测到的电子温度具有较好的一致性。     

Fast EPR imaging at 300 MHz using spinning magnetic field gradients

Electron paramagnetic resonance imaging (EPRI) technology has rapidly progressed in the last decade enabling many important applications in the fields of biology and medicine. At frequencies of 300-1200 MHz a range of in vivo applications have been performed. However, the requisite imaging time duration to acquire a given number of projections, limits the use of this technique in many in vivo applications where relatively rapid kinetics occur. Therefore, there has been a great need to develop approaches to accelerate EPRI data acquisition. We report the development of a fast low-frequency EPRI technique using spinning magnetic field gradients (SMFG). Utilizing a 300 MHz CW (continuous wave) EPRI system, SMFG enabled over 10-fold accelerated acquisition of image projections. 2D images with over 200 projections could be acquired in less than 3s and with 20s acquisitions good image quality was obtained on large aqueous free radical samples. This technique should be particularly useful for in vivo studies of free radicals and their metabolism.     

Correction of spatial distortion in magnetic resonance angiography for radiosurgical treatment planning of cerebral arteriovenous malformations.

A treatment planning system based on magnetic resonance (MR) angiographic imaging data for the radiosurgery of inoperable cerebral arteriovenous malformations is reported. MR angiography was performed using a three-dimensional (3D) velocity-compensated fast imaging with steady-state precession (FISP) sequence. Depending on the individual MR system, inhomogeneities and nonlinearities induced by eddy currents during the pulse sequence can distort the images and produce spurious displacements of the stereotactic coordinates in both the x-y plane and the z axis. If necessary, these errors in position can be assessed by means of two phantoms placed within the stereotactic guidance system--a "2D-phantom" displaying "pincushion" distortion in the image, and a "3D-phantom" displaying displacement, warp, and tilt of the image plane itself. The pincushion distortion can be "corrected" (reducing displacements from 2-3 mm to 1 mm) by calculations based on modeling the distortion as a fourth order 2D polynomial. Displacement, warp, and tilt of the image plane may be corrected by adjustment of the gradient shimming currents. After correction, the accuracy of the geometric information is limited only by the pixel resolution of the image (= 1 mm). Precise definition of the target volume could be performed by the therapist either directly in the MR images or in calculated projection MR angiograms obtained by a maximum intensity projection algorithm. MR angiography provides a sensitive, noninvasive 3D method for defining target volume and critical structures, and for calculating precise dose distributions for radiosurgery of cerebral arteriovenous malformations.     

A continuous phase-modulated approach to spatial encoding in ultrafast 2D NMR spectroscopy

Ultrafast 2D NMR replaces the time-domain parametrization usually employed to monitor the indirect-domain spin evolution, with an equivalent encoding along a spatial geometry. When coupled to a gradient-assisted decoding during the acquisition, this enables the collection of complete 2D spectra within a single transient. We have presented elsewhere two strategies for carrying out the spatial encoding underlying ultrafast NMR: a discrete excitation protocol capable of imparting a phase-modulated encoding of the interactions, and a continuous protocol yielding amplitude-modulated signals. The former is general but has associated with it a number of practical complications; the latter is easier to implement but unsuitable for certain 2D NMR acquisitions. The present communication discusses a new protocol that incorporates attractive attributes from both alternatives, imparting a continuous spatial encoding of the interactions yet yielding a phase modulation of the signal. This in turn enables a number of basic experiments that have shown particularly useful in the context of in vivo 2D NMR, including 2D J-resolved and 2D H,H-COSY spectroscopies. It also provides a route to achieving sensitivity-enhanced acquisitions for other homonuclear correlation experiments, such as ultrafast 2D TOCSY. The main features underlying this new spatial encoding protocol are derived, and its potential demonstrated with a series of phase-modulated homonuclear single-scan 2D NMR examples.     

Simultaneous magnetic resonance gadolinium-enhanced 2D perfusion and 3D angiographic imaging

A method was implemented and tested that allows the simultaneous acquisition of magnetic resonance 2D slice selective perfusion and 3D angiographic data during a single bolus injection of a contrast agent. High quality contrast-enhanced perfusion images and angiograms of the lung, kidney and heart were obtained in healthy volunteers. Combined perfusion and angiography provided additional information with an acceptable increase in acquisition time. No image artifacts were attributed to the technique. The combined information may be useful in detecting, as well as characterizing, vascular abnormalities.     

Towards full-resolution inline electron holography

With the availability of fast computers, inline electron holography, a technique for reconstructing both amplitude and phase of the electron wave function as scattered by the sample from a set of differently aberrated transmission electron microscopy images, is becoming increasingly quantitative. While focal series reconstruction from transmission electron microscopy images has already been practiced for at least 3 decades, existing approaches can only recover a relatively small band of spatial frequencies. Here I present a reconstruction scheme which is capable of reconstructing the electron wave function for a very large range of spatial frequencies, demonstrating its performance using simulated as well as experimental data.     

Combination of HAADF‐STEM and ADF‐STEM Tomography for Core–Shell Hybrid Materials

Characterization of core–shell type nanoparticles in 3D by transmission electron microscopy (TEM) can be very challenging. Especially when both heavy and light elements coexist within the same nanostructure, artifacts in the 3D reconstruction are often present. A representative example would be a particle comprising an anisotropic metallic (Au) nanoparticle coated with a (mesoporous) silica shell. To obtain a reliable 3D characterization of such an object, a dose‐efficient strategy is proposed to simultaneously acquire high‐angle annular dark‐field scanning TEM and annular dark‐field tilt series for tomography. The 3D reconstruction is further improved by applying an advanced masking and interpolation approach to the acquired data. This new methodology enables us to obtain high‐quality reconstructions from which also quantitative information can be extracted. This approach is broadly applicable to investigate hybrid core–shell materials.     

Retrospective intra-scan motion correction

This paper analyzes the effects of intra-scan motion and demonstrates the possibility of correcting them directly in k-space with a new automatic retrospective method. The method is presented for series of 2D acquisitions with Cartesian sampling. Using a reference k-space acquisition (corrected for translations) within the series, intra-scan motion parameters are accurately estimated for each trajectory in k-space of each data set in the series resulting in pseudo-random sample positions. The images are reconstructed with a Bayesian estimator that can handle sparse arbitrary sampling in k-space and reduces intra-scan rotation artefacts to the noise level. The method has been assessed by means of a Monte Carlo study on axial brain images for different signal-to-noise ratios. The accuracy of motion estimates is better than 0.1 degrees for rotation, and 0.1 and 0.05 pixel, respectively, for translation along the read and phase directions for signal-to-noise ratios higher than 6 of the signals on each trajectory. An example of reconstruction from experimental data corrupted by head motion is also given.     

Width determination of SiO2-films in Si-based devices using low-loss EFTEM: image contrast as a function of sample thickness

Energy filtering transmission electron microscopy (EFTEM) has become one of the most efficient tools for specimen characterization at nanometer length scales. EFTEM imaging is most often carried out in the core-loss region but image intensity becomes more and more a limiting factor with decreasing feature size. Alternatively, it is possible to record EFTEM images in the low-loss region, where intensities are essentially higher and where in many cases the images contain material specific contrasts. In this paper we investigate the influence of the important parameters on the material contrast between silicon and silicon dioxide, e.g. specimen thickness, specimen orientation, energy-loss and energy selecting slit width. We show that sample thickness plays an important role and present two methods to calculate material contrast as a function of energy-loss and sample thicknesses. The first method uses spectra taken from both materials at different sample thickness by electron energy-loss spectroscopy, the second calculates contrast directly from a series of energy filtered images. From the results we determine the ideal acquisition parameters for the Si/SiO(2) system and demonstrate imaging at sufficient resolution below 2nm with a test sample of thin SiO(2) layers on Si.     

3D MRI of non-Gaussian (3)He gas diffusion in the rat lung

In (3)He magnetic resonance images of pulmonary air spaces, the confining architecture of the parenchymal tissue results in a non-Gaussian distribution of signal phase that non-exponentially attenuates image intensity as diffusion weighting is increased. Here, two approaches previously used for the analysis of non-Gaussian effects in the lung are compared and related using diffusion-weighted (3)He MR images of mechanically ventilated rats. One approach is model-based and was presented by Yablonskiy et al., while the other approach utilizes the second order decay contribution that is predicted from the cumulant expansion theorem. Total lung coverage is achieved using a hybrid 3D pulse sequence that combines conventional phase encoding with sparse radial sampling for efficient gas usage. This enables the acquisition of nine 3D images using a total of only approximately 1 L of hyperpolarized (3)He gas. Diffusion weighting ranges from 0 s/cm(2) to 40 s/cm(2). Results show that the non-Gaussian effects of (3)He gas diffusion in healthy rat lungs are directly attributed to the anisotropic geometry of lung microstructure as predicted by the Yablonskiy model, and that quantitative analysis over the entire lung can be reliably repeated in time-course studies of the same animal.     

Improvement of the acquisition of a large amount of MR images on a conventional whole body system

Modern whole body MR systems are equipped with echo-planar-imaging capability, which allows the measurement of a single slice in a fraction of a second or of thousands of images in few minutes. A considerable restriction to the acquisition of series containing large amounts of images in patient examinations is the time-consuming data handling time of the images at conventional systems, which includes the time to insert the images into the systems database. We propose the arrangement of several images on a new image with a large matrix size like a mosaic. The handling time depends mostly on the number of images without consideration of their matrix size. Therefore, image handling is strongly reduced by the use of such mosaic images.     

Cosmic Masers – From OH to Ho (IAU S287), edited by Roy S. Booth,Wouter H.T. Vlemmings and Elizabeth M.L. Humphreys

‘Flying Triangulation’ (FlyTri) is a recently developed principle which allows for a motion-robust optical 3D measurement of rough surfaces. It combines a simple sensor with sophisticated algorithms: a single-shot sensor acquires 2D camera images. From each camera image, a 3D profile is generated. The series of 3D profiles generated are aligned to one another by algorithms, without relying on any external tracking device. It delivers real-time feedback of the measurement process which enables an all-around measurement of objects. The principle has great potential for small-space acquisition environments, such as the measurement of the interior of a car, and motion-sensitive measurement tasks, such as the intraoral measurement of teeth. This article gives an overview of the basic ideas and applications of FlyTri. The main challenges and their solutions are discussed. Measurement examples are also given to demonstrate the potential of the measurement principle.