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Register a new userAn Interactive 3D Visualization Tool for Large Scale Data Sets for Quantitative Atom Probe Tomography
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Several visualization schemes have been developed for imaging materials at the atomic level through atom probe tomography. The main shortcoming of these tools is their inability to parallel process data using multi-core computing units to tackle the problem of larger data sets. This critically handicaps the ability to make a quantitative interpretation of spatial correlations in chemical composition, since a significant amount of the data is missed during subsequent analysis. In addition, since these visualization tools are not open-source software there is always a problem with developing a common language for the interpretation of data. In this contribution we present results of our work on using an open-source advanced interactive visualization software tool, which overcomes the difficulty of visualizing larger data sets by supporting parallel rendering on a graphical user interface or script user interface and permits quantitative analysis of atom probe tomography data in real time. This advancement allows materials scientists a codesign approach to making, measuring and modeling new and nanostructured materials by providing a direct feedback to the fabrication and designing of samples in real time.
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Atom probe tomography (APT) analysis conditions play a major role in the composition measurement accuracy. Preferential evaporation, which significantly biases apparent composition, more than other well-known phenomena in APT, is strongly connected to those analysis conditions. One way to optimize them, in order to have the most accurate measurement, is therefore to be able to predict and then to estimate their influence on the apparent composition. An analytical model is proposed to quantify the preferential evaporation. This model is applied to three different alloys: NiCu, FeCrNi and FeCu. The model explains not only the analysis temperature dependence, as in already existing model, but also the dependence to the pulse fraction and the pulse frequency. Moreover, the model can also provide energetic constant directly linked to energy barrier, required to field evaporate atom from the sample surface. 2
In todays world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a continuous feedback loop that seamlessly integrates experimental biology techniques and bioinformatics tools. High-performance computational facilities are capable of processing considerable volumes of data, yet often lack an easy-to-use interface to guide the user in supervising and adjusting bioinformatics analysis in real-time. Here we report the development of Telescope, a novel interactive tool that interfaces with high-performance computational clusters to deliver an intuitive user interface for controlling and monitoring bioinformatics analyses in real-time. Telescope was designed to natively operate with a simple and straightforward interface using Web 2.0 technology compatible with most modern devices (e.g., tablets and personal smartphones). Telescope provides a modern and elegant solution to integrate computational analyses into the experimental environment of biomedical research. Additionally, it allows biomedical researchers to leverage the power of large computational facilities in a user-friendly manner. Telescope is freely available at https://github.com/Mangul-Lab-USC/telescope.
We present a morphological analysis of atom probe data of nanoscale microstructural features, using methods developed by the astrophysics community to describe the shape of superclusters of galaxies. We describe second-phase regions using Minkowski functionals, representing the regions volume, surface area, mean curvature and Euler characteristic. The alloy data in this work show microstructures that can be described as sponge-like, filament-like, plate-like, and sphere-like at different concentration levels, and we find quantitative measurements of these features. To reduce user decision-making in constructing isosurfaces and to enhance the accuracy of the analysis a maximum likelihood based denoising filter was developed. We show that this filter performs significantly better than a simple Gaussian smoothing filter. We also interpolate the data using natural cubic splines, to refine voxel sizes and to refine the surface. We demonstrate that it is possible to find a mathematically well-defined, quantitative description of microstructure from atomistic datasets, to sub-voxel resolution, without user-tuneable parameters.
We present sample transfer instrumentation and integrated protocols for the preparation and correlative characterization of environmentally-sensitive materials by both atom probe tomography and electron microscopy. Ultra-high vacuum cryogenic suitcases allow specimen transfer between preparation, processing and several imaging platforms without exposure to atmospheric contamination. For expedient transfers, we installed a fast-docking station equipped with a cryogenic pump upon three systems; two atom probes, a scanning electron microscope / Xe-plasma focused ion beam and a N$_2$-atmosphere glovebox. We also installed a plasma FIB with a solid-state cooling stage to reduce beam damage and contamination, through reducing chemical activity and with the cryogenic components as passive cryogenic traps. We demonstrate the efficacy of the new laboratory protocols by the successful preparation and transfer of two highly contamination- and temperature-sensitive samples - water and ice. Analysing pure magnesium atom probe data, we show that surface oxidation can be effectively suppressed using an entirely cryogenic protocol (during specimen preparation and during transfer). Starting with the cryogenically-cooled plasma FIB, we also prepared and transferred frozen ice samples while avoiding significant melting or sublimation, suggesting that we may be able to measure the nanostructure of other normally-liquid or soft materials. Isolated cryogenic protocols within the N$_2$ glove box demonstrate the absence of ice condensation suggesting that environmental control can commence from fabrication until atom probe analysis.
The overall design of the Integrated Spectral Analysis Workbench (ISAW), being developed at Argonne, provides for an extensible, highly interactive, collaborating set of viewers for neutron scattering data. Large arbitrary collections of spectra from multiple detectors can be viewed as an image, a scrolled list of individual graphs, or using a 3D representation of the instrument showing the detector positions. Data from an area detector can be displayed using a contour or intensity map as well as an interactive table. Selected spectra can be displayed in tables or on a conventional graph. A unique characteristic of these viewers is their interactivity and coordination. The position pointed at by the user in one viewer is sent to other viewers of the same DataSet so they can track the position and display relevant information. Specialized viewers for single crystal neutron diffractometers are being developed. A proof-of-concept viewer that directly displays the 3D reciprocal lattice from a complete series of runs on a single crystal diffractometer has been implemented.
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