Beyond filtered backprojection: a reconstruction software package for ion beam microtomography data

A new version of the TomoRebuild data reduction software package is presented, for the reconstruction of scanning transmission ion microscopy tomography (STIMT) and particle induced X-ray emission tomography (PIXET) images. First, we present a state of the art of the reconstruction codes available for ion beam microtomography. The algorithm proposed here brings several advantages. It is a portable, multi-platform code, designed in C++ with well-separated classes for easier use and evolution. Data reduction is separated in different steps and the intermediate results may be checked if necessary. Although no additional graphic library or numerical tool is required to run the program as a command line, a user friendly interface was designed in Java, as an ImageJ plugin. All experimental and reconstruction parameters may be entered either through this plugin or directly in text format files. A simple standard format is proposed for the input of experimental data. Optional graphic applications using the ROOT interface may be used separately to display and fit energy spectra. Regarding the reconstruction process, the filtered backprojection (FBP) algorithm, already present in the previous version of the code, was optimized so that it is about 10 times as fast. In addition, Maximum Likelihood Expectation Maximization (MLEM) and its accelerated version Ordered Subsets Expectation Maximization (OSEM) algorithms were implemented. A detailed user guide in English is available. A reconstruction example of experimental data from a biological sample is given. It shows the capability of the code to reduce noise in the sinograms and to deal with incomplete data, which puts a new perspective on tomography using low number of projections or limited angle.

Lifetime of silica final lenses subject to HiPER irradiation conditions

The goal of the European laser fusion project, is to build an engineering facility for repetitive laser operation (HiPER 4a) and later a fusion reactor (HiPER 4b). A key aspect for laser fusion energy is the final optics. At the moment, it is based on silica transmission lenses located 8 m away from the chamber center. Lens lifetime depends on the irradiation conditions. We have used a 48 MJ shock ignition target for calculations. We have studied the thermo-mechanical effects of ions and X-rays on the lenses. Ions lead to lens melting and must therefore be mitigated. On the other hand, X-rays (~1% of the energy) does not produce either a significant temperature rise or detrimental stresses. Finally, we calculated the neutron flux and gamma dose rate on the lenses. Next, based on a simple model we studied the formation of color centers in the sample, which lead to optical absorption. Calculations show that simultaneous neutron and gamma irradiation does not significantly increase the optical absorption during the expected lifetime of the HiPER 4a facility. Under severe conditions (HiPER 4b), operation above 800 K or lens refreshing by thermal annealing treatments seem to assure adequate behavior.

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Low-cost irradiance sensors for irradiation assessments inside tree canopies.

The solar irradiation that a crop receives is directly related to the physical and biological processes that affect the crop. However, the assessment of solar irradiation poses certain problems when it must be measured through fruit inside the canopy of a tree. In such cases, it is necessary to check many test points, which usually requires an expensive data acquisition system. The use of conventional irradiance sensors increases the cost of the experiment, making them unsuitable. Nevertheless, it is still possible to perform a precise irradiance test with a reduced price by using low-cost sensors based on the photovoltaic effect. The aim of this work is to develop a low-cost sensor that permits the measurement of the irradiance inside the tree canopy. Two different technologies of solar cells were analyzed for their use in the measurement of solar irradiation levels inside tree canopies. Two data acquisition system setups were also tested and compared. Experiments were performed in Ademuz (Valencia, Spain) in September 2011 and September 2012 to check the validity of low-cost sensors based on solar cells and their associated data acquisition systems. The observed difference between solar irradiation at high and low positions was of 18.5% ± 2.58% at a 95% confidence interval. Large differences were observed between the operations of the two tested sensors. In the case of a-Si cells based mini-modules, an effect of partial shadowing was detected due to the larger size of the devices, the use of individual c-Si cells is recommended over a-Si cells based mini-modules.

Ultrastructure of Plant Leaf Cuticles in relation to Sample Preparation as Observed by Transmission Electron Microscopy

The leaf cuticular ultrastructure of some plant species has been examined by transmission electron microscopy (TEM) in only few studies. Attending to the different cuticle layers and inner structure, plant cuticles have been grouped into six general morphological types. With the aim of critically examining the effect of cuticle isolation and preparation for TEM analysis on cuticular ultrastructure, adaxial leaf cuticles of blue-gum eucalypt, grey poplar, and European pear were assessed, following a membrane science approach. The embedding and staining protocols affected the ultrastructure of the cuticles analysed. The solubility parameter, surface tension, and contact angles with water of pure Spurr's and LR-White resins were within a similar range. Differences were however estimated for resin : solvent mixtures, since Spurr’s resin is combined with acetone and LR-White resin is mixed with ethanol. Given the composite hydrophilic and lipophilic nature of plant cuticles, the particular TEM tissue embedding and staining procedures employed may affect sample ultrastructure and the interpretation of the results in physicochemical and biological terms. It is concluded that tissue preparation procedures may be optimised to facilitate the observation of the micro- and nanostructure of cuticular layers and components with different degrees of polarity and hydrophobicity.

Detection of Biological CO2 and 1,3-Pentadiene Using Non-refrigerated Low-Cost MWIR Detectors

The early detection of spoiling metabolic products in contaminated food is a very important tool to control quality. Some volatile compounds produce unpleasant odours at very low concentrations, making their early detection very challenging. This is the case of 1,3-pentadiene produced by microorganisms through decarboxylation of the preservative sorbate. In this work, we have developed a methodology to use the data produced by a low-cost, compact MWIR (Mid-Wave IR) spectrometry device without moving parts, which is based on a linear array of 128 elements of VPD PbSe coupled to a linear variable filter (LVF) working in the spectral range between 3 and 4.6 ?m. This device is able to analyze food headspace gases through dedicated sample presentation setup. This methodology enables the detection of CO2 and the volatile compound 1,3-pentadiene, as compared to synthetic patrons. Data analysis is based on an automated multidimensional dynamic processing of the MWIR spectra. Principal component and discriminant analysis allow segregating between four yeast strains including producers and no producers. The segregation power is accounted as a measure of the discrimination quality.