The discriminative bilateral filter: An enhanced denoising filter for electron microscopy data

Advances in three-dimensional (313) electron microscopy (EM) and image processing are providing considerable improvements in the resolution of subcellular volumes, macromolecular assemblies and individual proteins. However, the recovery of high-frequency information from biological samples is hindered by specimen sensitivity to beam damage. Low dose electron cryo-microscopy conditions afford reduced beam damage but typically yield images with reduced contrast and low signal-to-noise ratios (SNRs). Here, we describe the properties of a new discriminative bilateral (DBL) filter that is based upon the bilateral filter implementation of Jiang et al. (Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chin, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struc. Biol. 128, 82-97.). In contrast to the latter, the DBL filter can distinguish between object edges and high-frequency noise pixels through the use of an additional photometric exclusion function. As a result, high frequency noise pixels are smoothed, yet object edge detail is preserved. In the present study, we show that the DBL filter effectively reduces noise in low SNR single particle data as well as cellular tomograms of stained plastic sections. The properties of the DBL filter are discussed in terms of its usefulness for single particle analysis and for pre-processing cellular tomograms ahead of image segmentation. (c) 2006 Elsevier Inc. All rights reserved.

Mining information from atom probe data

Whilst atom probe tomography (APT) is a powerful technique with the capacity to gather information containing hundreds of millions of atoms from a single specimen, the ability to effectively use this information creates significant challenges. The main technological bottleneck lies in handling the extremely large amounts of data on spatial-chemical correlations, as well as developing new quantitative computational foundations for image reconstruction that target critical and transformative problems in materials science. The power to explore materials at the atomic scale with the extraordinary level of sensitivity of detection offered by atom probe tomography has not been not fully harnessed due to the challenges of dealing with missing, sparse and often noisy data. Hence there is a profound need to couple the analytical tools to deal with the data challenges with the experimental issues associated with this instrument. In this paper we provide a summary of some key issues associated with the challenges, and solutions to extract or "mine" fundamental materials science information from that data.

Micas in experimentally shocked gneiss

Biotites and muscovites from a gneiss have been experimentally shocked between 18 and 70 GPa using powder-propellant guns at NASA Johnson Space Center and at the California Institute of Technology. This study shows that shock in biotite and muscovite can produce homogeneous and devolatilized glasses within microseconds. Shock-deformed micas display fracturing, kinking, and complex extinction patterns over the entire pressure range investigated. However, these deformation features are not a sensitive pressure indicator. Localized melting of micas begins at 33 GPa and goes to completion at 70 GPa. Melted biotite and muscovite are optically opaque, but show extensive microvesiculation and flow when observed with the SEM. Electron diffraction confirms that biotite and muscovite have transformed to a glass. The distribution of vesicles in shock-vitrified mica shows escape of volatiles within the short duration of the shock experiment. Experimentally shocked biotite and muscovite undergo congruent melting. Compositions of the glasses are similar to the unshocked micas except for volatiles (H2O loss and K loss). These unusual glasses derived from mica may be quenched by rapid cooling conditions during the shock experiment. Based on these results, the extremely low H2O content of tektites may be reconciled with a terrestrial origin by impact. Release of volatiles in shock-melted micas affects the melting behavior of coexisting dry silicates during the short duration of the shock experiment. Transportation and escape of volatiles released from shock-melted micas may provide plausible mechanisms for the origin of protoatmospheres on terrestrial planets, hydrothermal activity on phyllosilicate-rich meteorite parent bodies, and fluid entrapment in meteorites.

Mineralogy of chondritic interplanetary dust particles

From a mineralogical survey of approximately 30 chondritic micrometeorites collected from the lower stratosphere and studied in detail using current electron microscopy techniques, it is concluded that these particles represent a unique group of extraterrestrial materials. These micrometeorites differ significantly in form and texture from components of carbonaceous chondrites and contain some mineral assemblages which do not occur in any meteorite class. Electron microscope investigations of chondritic micrometeorites have established that these materials (1) are extraterrestrial in origin, (2) existed in space as small objects, (3) endured minimal alteration by planetary processes since formation, and (4) can suffer minimal pulse heating (<600°C) on entering earth's atmosphere. The probable sources for chondritic interplanetary dust particles (IDPs) are cometary and asteroidal debris and, perhaps to a lesser extent, interstellar regions. These sources have not been conclusively linked to any specific mineralogical subset of IDP, although the chondritic porous (CP) aggregate is considered of likely cometary origin. Chondritic IDPs occur in two predominant mineral assemblages: (1) carbonaceous phases and phyllosilicates and (2) carbonaceous phases and nesosilicates or inosilicates, although particles with both types of silicate assemblages are observed. Olivines, pyroxenes, layer silicates, and carbon-rich phases are the most commonly occurring minerals in many chondritic IDPs. Other phases often observed in variable proportions include sulphides, spinels, metals, metal carbides, carbonates, and minor amounts of sulphates and phosphates. Individual mineral grain sizes range from micrometers (primarily pyroxenes and olivines) to nanometers, with the predominant size for all phases less than 100 nm. Specific mineral characteristics for particular chondritic IDPs provide an indication of processes which may have occurred prior to collection in the earth's stratosphere. For example, pyroxene mineralogy in some chondritic aggregates is consistent with condensation from a vapor phase and, we consider, with condensation in a turbulent solar nebula at relatively low temperatures (<1000°C). Carbonaceous phases present in other CP aggregates have been used to imply low-temperature formation processes such as Fischer-Tropsch synthesis (∼530°C) or carbonization and graphitization (∼315°C). Alteration processes have been implicated in the formation of some layer silicates in CP aggregates and may have involved hydrocryogenic alteration at <0°C. In general, interpretations of transformation processes on submicrometer-size minerals in chondritic IDPs are consistent with formation at a radius equivalent to the asteroid belt or greater during the later stages of solar nebula evolution using currently available models.

The Langmuir probe as a diagnostic of the electron component within low temperature laser ablated plasma plumes

A Langmuir probe has been used as a diagnostic of the temporally evolving electron component within a laser ablated Cu plasma expanding into vacuum, for an incident laser power density on target similar to that used for the pulsed laser deposition of thin films. Electron temperature data were obtained from the retarding region of the probe current/voltage (I/V) characteristic, which was also used to calculate an associated electron number density. Additionally, electron number density data were obtained from the saturation electron current region of the probe (I/V) characteristic. Electron number density data, extracted by the two different techniques, were observed to show the same temporal form, with measured absolute values agreeing to within a factor of 2. The Langmuir probe, in the saturation current region, has been shown for the first time to be a convenient diagnostic of the electron component within relatively low temperature laser ablated plasma plumes. (C) 1999 American Institute of Physics. [S0034-6748(99)01503-8].

Grain boundary segregation in Fe-Mn-C twinning-induced plasticity steels studied by correlative electron backscatter diffraction and atom probe tomography

We report on the characterization of grain boundary (GB) segregation in an Fe-28Mn-0.3C (wt.%) twinning-induced plasticity (TWIP) steel. After recrystallization of this steel for 24 h at 700 °C, ∼50% general grain boundaries (GBs) and ∼35% Σ3 annealing twin boundaries were observed (others were high-order Σ and low-angle GBs). The segregation of B, C and P and traces of Si and Cu were detected at the general GB by atom probe tomography (APT) and quantified using ladder diagrams. In the case of the Σ3 coherent annealing twin, it was necessary to first locate the position of the boundary by density analysis of the atom probe data, then small amounts of B, Si and P segregation and, surprisingly, depletion of C were detected. The concentration of Mn was constant across the interface for both boundary types. The depletion of C at the annealing twin is explained by a local change in the stacking sequence at the boundary, creating a local hexagonal close-packed structure with low C solubility. This finding raises the question of whether segregation/depletion also occurs at Σ3 deformation twin boundaries in high-Mn TWIP steels. Consequently, a previously published APT dataset of the Fe-22Mn-0.6C alloy system, containing a high density of deformation twins due to 30% tensile deformation at room temperature, was reinvestigated using the same analysis routine as for the annealing twin. Although crystallographically identical to the annealing twin, no evidence of segregation or depletion was found at the deformation twins, owing to the lack of mobility of solutes during twin formation at room temperature.

Heterostructure intervalley transferred electron effects

A Gunn active layer is used as an X electron probe to detect the X tunnelling current in the GaAs-AlAs heterostructure, from which a new heterostructure intervalley transferred electron (HITE) device is obtained. In the 8 mm band, the highest pulse output power of these diodes is 2.65 W and the highest conversion efficiency is 18%. The dc and rf performance of the HITE devices was simulated by the band mixing resonant tunnelling theory and Monte Carlo transport simulation. The HITE effect has transformed the transit-time dipole-layer mode in the Gunn diode into a relaxation oscillation mode in the HITE device. From the comparison of simulated results to the measured data, the HITE effect is demonstrated straightforwardly.

Data analysis for pump-probe experiment with femtosecond pulses

Various analytical physical models are presented to extract the photodissociation dynamics information from the data obtained in the femtosecond pump-probe experiment. The single- and double-component models are employed to explain the single- and double-channel dissociation of parent molecules. Another single-component model for fragment dissociation or deexcitation is also presented. All cases are explanatorily demonstrated on the pump-probe experimental data.

Structural characterization of intermediate and metastable phases by electron microscopy

Structure characterization of nanocrystalline intermediates and metastable phases is of primary importance for a deep understanding of synthetic processes undergoing solid-to-solid state phase transitions. Understanding the evolution from the first nucleation stage to the final synthetic product supports not only the optimization of existing processes, but might assist in tailoring new synthetic paths. A systematic investigation of intermediates and metastable phases is hampered because it is impossible to produce large crystals and only in few cases a pure synthetic product can be obtained. Structure investigation by X-ray powder diffraction methods is still challenging on nanoscale, especially when the sample is polyphasic. Electron diffraction has the advantage to collect data from single nanoscopic crystals, but is limited by data incompleteness, dynamical effects and fast deterioration of the sample under the electron beam. Automated diffraction tomography (ADT), a recently developed technique, making possible to collect more complete three-dimensional electron diffraction data and to reduce at the same time dynamical scattering and beam damage, thus allowing to investigate even beam sensitive materials (f.e. hydrated phases and organics). At present, ADT is the only technique able to deliver complete three-dimensional structural information from single nanoscopic grains, independently from other surrounding phases. Thus, ADT is an ideal technique for the study of on-going processes where different phases exist at the same time and undergo several structural transitions. In this study ADT was used as the main technique for structural characterization for three different systems and combined subsequently with other techniques, among which high-resolution transmission electron microscopy (HRTEM), cryo-TEM imaging, X-ray powder diffraction (XRPD) and energy disperse X-ray spectroscopy (EDX).rnAs possible laser host materials, i.e. materials with a broad band emission in the near-infrared region, two unknown phases were investigated in the ternary oxide system M2O-Al2O3-WO3 (M = K, Na). Both phases exhibit low purity as well as non-homogeneous size distribution and particle morphology. The structures solved by ADT are also affected by pseudo-symmetry. rnSodium titanate nanotubes and nanowires are both intermediate products in the synthesis of TiO2 nanorods which are used as additives to colloidal TiO2 film for improving efficiency of dye-sensitized solar cells (DSSC). The structural transition from nantubes to nanowires was investigated in a step by step time-resolved study. Nanowires were discovered to consist of a hitherto unknown phase of sodium titanate. This new phase, typically affected by pervasive defects like mutual layer shift, was structurally determined ab-initio on the basis of ADT data. rnThe third system is related with calcium carbonate nucleation and early crystallization. The first part of this study is dedicated to the extensive investigations of calcium carbonate formation in a step by step analysis, up to the appearance of crystalline individua. The second part is dedicated to the structure determination by ADT of the first-to-form anhydrated phase of CaCO3: vaterite. An exhaustive structure analysis of vaterite had previously been hampered by diffuse scattering, extra periodicities and fast deterioration of the material under electron irradiation. rn

The structure of the acto-myosin subfragment 1 complex: Results of searches using data from electron microscopy and x-ray crystallography

Surmises of how myosin subfragment 1 (S1) interacts with actin filaments in muscle contraction rest upon knowing the relative arrangement of the two proteins. Although there exist crystallographic structures for both S1 and actin, as well as electron microscopy data for the acto–S1 complex (AS1), modeling of this arrangement has so far only been done “by eye.” Here we report fitted AS1 structures obtained using a quantitative method that is both more objective and makes more complete use of the data. Using undistorted crystallographic results, the best-fit AS1 structure shows significant differences from that obtained by visual fitting. The best fit is produced using the F-actin model of Holmes et al. [Holmes, K. C., Popp, D., Gebhard, W. & Kabsch, W. (1990) Nature (London) 347, 44–49]. S1 residues at the AS1 interface are now found at a higher radius as well as being translated axially and rotated azimuthally. Fits using S1 plus loops missing from the crystal structure were achieved using a homology search method to predict loop structures. These improved fits favor an arrangement in which the loop at the 50- to 20-kDa domain junction of S1 is located near the N terminus of actin. Rigid-body movements of the lower 50-kDa domain, which further improve the fit, produce closure of the large 50-kDa domain cleft and bring conserved residues in the lower 50-kDa domain into an apparently appropriate orientation for close interaction with actin. This finding supports the idea that binding of ATP to AS1 at the end of the ATPase cycle disrupts the actin binding site by changing the conformation of the 50-kDa cleft of S1.

Infrared spectra of Mg-SiO smokes : comparison with analytical electron microscopy studies

An important component of current models for interstellar and circumstellar evolution is the infrared (IR)spectral data collected from stellar outflows around oxygen-rich stars and from the general interstellar medium [1]. IR spectra from these celestial bodies are usually interpreted as showing the general properties of sub-micron sized silicate grains [2]. Two major features at 10 and 20 microns are reasonably attributed to amorphous olivine or pyroxene (e.g. Mg2Si04 or MgSi03) on the basis of comparisons with natural standards and vapor condensed silicates [3-6]. In an attempt to define crystallisation rates for spectrally amorphous condensates, Nuth and Donn [5] annealed experimentally produced amorphous magnesium silicate smokes at 1000K. On analysing these smokes at various annealing times, Nuth and Donn [5] showed that changes in crystallinity measured by bulk X-ray diffraction occured at longer annealing times (days) than changes measured by IR spectra (a few hours). To better define the onset of crystallinity in these magnesium silicates, we have examined each annealed product using a JEOL 1OOCX analytical electron microscope (AEM). In addition, the development of chemical diversity with annealing has been monitored using energy dispersive spectroscopy of individual grains from areas <20nm in diameter. Furthermore, the crystallisation kinetics of these smokes under ambient, room temperature conditions have been examined using bulk and fourier transform infrared (FTIR)spectra.

Analytical electron microscopy of Mg-SiO smokes; a comparison with infrared and XRD studies

Experimentally obtained Mg.SiO smokes were studied by analytical electron microscopy using the same samples that had been previously characterized by repeated infrared spectroscopy. Analytical electron microscopy shows that unannealed smokes contain some degree of microcrystallinity which increases with increased annealing for up to 30 hr. An SiO2 polymorph (tridymite) and MgO may form contemporaneously as a result of growth of forsterite (Mg2SiO4) microcrystallites in the initially nonstoichiometric smokes. After 4 hr annealing, forsterite and tridymite react to enstatite (MgSiO3). We suggest that infrared spectroscopy and X-ray diffraction analysis should be complemented by detailed analytical electron microscopy to detect budding crystallinity in vapor phase condensates.