Post-processing Routines Research Articles

Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology

We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data.

Pseudocontinuous arterial spin labeling with optimized tagging efficiency

The adiabatic inversion of blood in pseudocontinuous arterial spin labeling (PCASL) is highly sensitive to off-resonance effects and gradient imperfections and this sensitivity can lead to tagging efficiency loss and unpredictable variations in cerebral blood flow estimates. This efficiency loss is caused by a phase tracking error between the RF pulses and the flowing spins. This article introduces a new method, referred to as Optimized PCASL (OptPCASL), that minimizes the phase tracking error by applying an additional compensation RF phase term and in-plane gradients to the PCASL pulse train. The optimal RF phase and gradient amplitudes are determined using a prescan procedure, which consists of a series of short scans interleaved with automated postprocessing routines integrated to the scanner console. The prescan procedure is shown to minimize the phase tracking error in a robust and time efficient manner. As an example of its application, the use of OptPCASL for the improved detection of functional activation in the visual cortex is demonstrated and temporal signal-to-noise ratio (SNR), image SNR, and baseline cerebral blood flow measures are compared to those acquired from conventional PCASL.

Spectral analysis software improves confidence in plant and soil water stable isotope analyses performed by isotope ratio infrared spectroscopy (IRIS)

Previous studies have demonstrated the potential for large errors to occur when analyzing waters containing organic contaminants using isotope ratio infrared spectroscopy (IRIS). In an attempt to address this problem, IRIS manufacturers now provide post-processing spectral analysis software capable of identifying samples with the types of spectral interference that compromises their stable isotope analysis. Here we report two independent tests of this post-processing spectral analysis software on two IRIS systems, OA-ICOS (Los Gatos Research Inc.) and WS-CRDS (Picarro Inc.). Following a similar methodology to a previous study, we cryogenically extracted plant leaf water and soil water and measured the δ(2)H and δ(18)O values of identical samples by isotope ratio mass spectrometry (IRMS) and IRIS. As an additional test, we analyzed plant stem waters and tap waters by IRMS and IRIS in an independent laboratory. For all tests we assumed that the IRMS value represented the "true" value against which we could compare the stable isotope results from the IRIS methods. Samples showing significant deviations from the IRMS value (>2σ) were considered to be contaminated and representative of spectral interference in the IRIS measurement. Over the two studies, 83% of plant species were considered contaminated on OA-ICOS and 58% on WS-CRDS. Post-analysis, spectra were analyzed using the manufacturer's spectral analysis software, in order to see if the software correctly identified contaminated samples. In our tests the software performed well, identifying all the samples with major errors. However, some false negatives indicate that user evaluation and testing of the software are necessary. Repeat sampling of plants showed considerable variation in the discrepancies between IRIS and IRMS. As such, we recommend that spectral analysis of IRIS data must be incorporated into standard post-processing routines. Furthermore, we suggest that the results from spectral analysis be included when reporting stable isotope data from IRIS.

Triangulation Method for Area-line Geometry-type Changes in Map Generalisation

<title/>Changes in object geometry-type such as area to line are necessary in terms of the requirements of cartographic generalisation, and also for the creation of the network topology in geographical information systems. Geometry-type changes that reduce dimension include area-line, area-point and line-point changes. This study focuses on area-line changes. Since the area objects have different shapes, there is no unique solution that works in all possible situations. Well-known methods for area-line changes include triangulation, water lining, straight skeletons, etc. In this paper, an approach based on triangulation is introduced for creating road centerlines from blocks of parcels. Spaghetti large-scale map data are taken into consideration in this approach in which blocks of parcels are captured as polygons and roads are represented by the space between them. In order to implement this approach, a subprogram (script) is developed under the NETCAD software package - a Turkish CAD-GIS software package - with the Visual Basic scripting language. This subprogram also includes post-processing routines for the relevant node creation at road crossings, and delivers acceptable results for the centerlines; however, the post-processing needs to be improved.

A Global/Local Finite Element Approach for Predicting Interlaminar and Intralaminar Damage Evolution in Composite Stiffened Panels Under Compressive Load

This paper addresses the prediction of intralaminar and interlaminar damage onset and evolution in composite structures through the use of a finite element based procedure. This procedure joins methodologies whose credibility has been already assessed in literature such as the Virtual Crack Closure Technique (for delamination) and the ply discount approach (for matrix/fiber failures). In order to establish the reliability of the procedure developed, comparisons with literature experimental results on a stiffened panel with an embedded delamination are illustrated. The methodology proposed, implemented in ANSYS © as post-processing routines, is combined with a finite element model of the panel, built by adopting both shell and solid elements within the frame of an embedded global/local approach to connect differently modelled substructures.

TU-EE-A4-02: Some Issues With Image Intensity Uniformity Test Performed On 3T MRI Scanners

Purpose: To investigate why Image Intensity Uniformity (IIU) tests performed on commercial 3T MRI systems according to the ACR MR Accreditation Program (MRAP) instructions are subject to frequent failures. Method and Materials: The phantom scanning instructions for ACR MRAP tests specify that a dedicated phantom (ACR phantom) must be used to assess the MRI scanners performance. As a part of required test, an assessment of IIU is performed by measuring the Percent Image Uniformity (PIU) according to the specified formula. The data used in calculation of PIU must be acquired for a rigidly defined scanning protocols, and the process of data collection is also precisely specified. For the 3T MRI scanner to pass the test, the measured PIU must be equal or greater than 82%. PIU tests were performed using the same ACR phantom on five different 3T MR scanners from two different vendors, following the ACR MRAP acquisition and measurement protocol exactly. The scanners tested were installed in routine clinical settings and all head coils, available on site, were tested independently. In addition, if scanner offered multiple gradient performance modes, all modes were tested. Finally, effects of image post-processing routines, designed to improve the image uniformity and installed on the scanners were investigated as well. Results: A vast majority of PIU tests using non-postprocessed images failed (more than 95%). All tests that used postprocessed images passed. Upon closer investigation, the likely cause of failures was linked to RF properties of the ACR phantom. Conclusion: The IIU test needs to be carefully reassessed to ensure that it provides a meaningful characterization of MRI scanner's performance, and is not hampered by the limitations imposed by the electromagnetic physics of scanning at 127 MHz, the resonant RF frequency of 3T MRI systems.

Fatigue damage of weld seams with and without postweld treatment under multiaxial loading*

Abstract The service durability of weld seams is one of the most challenging problems of component fatigue. Hereby, the complexity is due to several peculiarities of welded structures: the detailed weld seam geometry with macroscopic and microscopic notch effects and/or defects, the properties of the welded material, residual stresses and multiaxial proportional or non-proportional loading conditions. Non-experimental approaches to design against fatigue have to account for the difference between weld seams with and without post-weld treatment as well as proportional and non-proportional loading. The application of fracture mechanics parameters allows for a more realistic description of damage progression. This paper is intended to explain possible design approaches based on numerical fracture mechanics and their combination with stress and strain based approaches using clear and classified damage criteria (engineering crack size, fracture). All numerical approaches are presented with special regard to complexity and modeling requirements from the point of view of the practicing design engineer. Non-proportional loading is considered by the identification of a damage critical plane which requires special post-processing routines within the numerical analysis. Again, the question of practicability is raised.

Averaging Techniques for the Effective Numerical Solution of Symm's Integral Equation of the First Kind

Averaging techniques for finite element error control, occasionally called ZZ estimators for the gradient recovery, enjoy a high popularity in engineering because of their striking simplicity and universality: One does not even require a PDE to apply the nonexpensive post-processing routines. Recently, averaging techniques have been mathematically proved to be reliable and efficient for various applications of the finite element method. This paper establishes a class of averaging error estimators for boundary integral methods. Symm's integral equation of the first kind with a nonlocal single-layer integral operator serves as a model equation studied both theoretically and numerically. We introduce four new error estimators which are proven to be reliable and efficient up to terms of higher order. The higher-order terms depend on the regularity of the exact solution. Several numerical experiments illustrate the theoretical results and show that the [normally unknown] error is sharply estimated by the proposed estimators, i.e., error and estimators almost coincide.

Surface crystallography via electron microscopy

The study of atomic structure of surfaces is fundamental to the understanding of electronic, chemical and mechanical properties of surfaces and numerous techniques have been developed to this end. Transmission Electron Microscopy techniques, namely transmission electron imaging (TEM) and diffraction (TED), due to their ability to provide structural information at very high resolutions, have emerged as powerful tools for the study of surface structure. In this article we review the experimental method alongside the various post-processing routines that are necessary to extract vital structural information from experimental data.

Annual layers in polar firn detected by Borehole Optical Stratigraphy

We have developed a system called Borehole Optical Stratigraphy which can detect annual layers in boreholes in polar firn. Borehole Optical Stratigraphy consists of a downhole camera package and post‐processing routines, which allow us to measure the intensity of light emitted from an on‐board source and returned from the borehole wall. We manually identify the annual layers in this optical signal. We used this system at Siple Dome, Antarctica, in the 2001–2002 austral summer season. Our results agree well with counts of annual layers detected with two different methods in an ice core recovered 50 meters from our borehole.

On the computation of mixed-mode stress intensity factors in functionally graded materials

A new interaction energy integral method for the computation of mixed-mode stress intensity factors at the tips of arbitrarily oriented cracks in functionally graded materials is described. In the method, interaction energy contour integrals are defined and expressed in equivalent domain form. The interaction energy integrals involve products of the actual fields, that arise from solution to the boundary value problem, with known auxiliary fields. The auxiliary stress and displacement fields are chosen to be the asymptotic near-tip fields for a crack in a homogeneous material having the same elastic constants as those found at the crack tip in the functionally graded material. The auxiliary strain fields are obtained from the auxiliary stress fields using the constitutive relation for the functionally graded material. A consequence of our choice for the auxiliary strain field is lack of compatibility which leads to extra terms in the domain integrals that need to be evaluated for the sake of accuracy. The mixed-mode stress intensity factors are obtained from the domain integrals as a post-processing step in the extended finite element method. To assess the accuracy of the method, we consider the benchmark problems of an edge-cracked plate and an angled center crack for specimens with a functional gradient in material properties. Excellent agreement is obtained between the numerical results and the analytical solutions for both stress intensity factors in all cases. All numerical results for the stress intensity factors also exhibit domain independence. The pertinent post-processing routines are provided for download via the world wide web.

Measurement of flow mediated vasodilation (FMD) using kalman-filtering

Brachial artery flow-mediated vasodilation is increasingly used as a measure of endothelial function. High resolution ultrasound provides a noninvasive method to observe this flow-mediated vasodilation by monitoring the diameter of the artery over time. In the past, the diameter had to be measured in tedious postprocessing routines, usually by the examiner himself. We present a system, which is able to process ultrasound rf-data in realtime. On that system, we implemented a kalman filter, which makes the tracking of both vessel walls possible. The diameter can be calculated accurately, taking into account process noise as well as measurement noise.

Virtual reality and anthropology

Since the discovery of the Tyrolean Iceman in 1991 advanced imaging and post processing techniques were successfully applied in anthropology. Specific techniques include spiral computed tomography and 3-dimensional reconstructions including stereolithographic and fused deposition modeling of volume data sets. The Iceman’s skull was the first to be reproduced using stereolithography, before this method was successfully applied in preoperative planning. With the advent of high-end graphics workstations and biomedical image processing software packages, 3-dimensional reconstructions were established as a routine tool for analyzing volume data sets. These techniques opened totally new insights in the field of physical anthropology. Computed tomography became the ideal research tool to access the internal structures of various precious fossils without damaging or even touching them. Many of the most precious specimens from the species Autralopithecus (1.8–3.5 Myears), Homo heidelbergensis (200–600 kyears) or Homo neanderthalensis (40–100 kyears) were scanned during the last 5 years. Often the fossils are filled with a stone matrix or other materials. During the postprocessing routines highly advanced algorithms were used to remove virtually these incrustations. Thus it was possible to visualize the morphological structures that lie beneath the matrix. Some specimens were partially destroyed, so the missing parts were reconstructed on computer screen in order to get estimations of the brain volume and endocranial morphology, both major fields of interest in physical anthropology. Moreover the computerized form of the data allows new descriptions of morphologic structures by the means of ‘geometric morphometrics’. Some of the results may change aspects and interpretations in human evolution. The introduction of new imaging and post processing techniques created a new field of research: Virtual Anthropology.

Sputtering under ultrahigh vacuum environment : G. Peter, J. A. Koprio and R. Slepicka. Vacuum38(8–10), 795 (1988)

Thanks to finite elements simulation and dedicated post-processing routines, this paper explores stress induced mobility changes over three major bumping processes. A numerical comparative analysis over the assembly generations is carried out. In order to do so, models are built for solder flip chip, copper pillar flip chip and micro-copper pillar bumping. Design recommendations for MOSFET placement to include in conception tools are provided, which allow to ensure adherence to product specifications while technologies advance.It is demonstrated that stress effects on mobility are widely dependent on the integration flow, and transistor placements must be considered accordingly. Despite the fact that, qualitatively speaking, the generated stress states are quite similar for whole bumping schemes, the quantitative variations of each stress components in combination with the piezo resistive coefficients of silicon lead to distinct effective mobility variations. As a consequence, design rules and keep out zones can be optimized specifically for each assembly technology. More precisely, it is advised to avoid nMOS placement directly below the bump in flip chip devices, for which the mobility can be degraded by almost 5%. In these cases keep out zones must be considered. Reversely, in the case of 3DICs, the performances of nMOS are improved by more than 2% in that region, which means that no restriction is required and silicon area can hence be saved. As for the p type carriers, variability is sensitive to channel orientation rather than their location with respect to the bump: more precisely, the transport direction must be azimuthally oriented, and radially oriented pMOS are proscribed. Maximum variations of about ±5% are found for the copper pillar flip chip configuration. Thanks to a comprehensive analysis, FEoL designers will be able to integrate BEoL and packaging constraints during the conception phases of advanced semiconductor products.