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11 results for “atom probe tomography”
Atom probe tomography nomad-FAIR demonstrator dataset R76-23219-v01.epos.apth5
<p>This is the dataset of an atom probe tomography experiment which is provided open source for testing the possibility of implementing an open source encyclopedia for experimental materials science datasets, including techniques to begin with such as Scanning Transmission Electron Microscopy (STEM), Multidimensional Photo Emission Spectroscopy (MPES), and Atom Probe Tomography (APT) / Field Ion Microscopy (FIM).</p> <p><strong>This repository serves three aims:</strong></p> <p>1. The dataset is of scientific interest. Specifically, it captures the result of a cutting-edge APT experiment detailed exemplarily in DOI: 10.1038/s41467-018-03115-0 (Fig. 6a "Se+Na2Se treatment") by Torsten Schwarz and coworkers.</p> <p>2. The dataset contributes to tests of an extension to "The NOMAD Laboratory" (https://nomad-coe.eu/): nomad-FAIR. Specifically, to test various aspects of an automatized metadata parsing and processing pipeline to enable the extraction of domain-specific JSON metadata files into a NOMAD-conformant JSON file, ultimately aiming for searchable and repurposable dataset documentation. This serves two purposes: on the one hand to contextualize each dataset within NOMAD. On the other hand to serve as a starting point to parse potential interesting content from the heavy data HDF5 file to reduce unnecessary file access.<br> The implementation of nomad-FAIR is coordinated by Markus Scheidgen.<br> The APT domain-specific parser is developed by Markus Kühbach.</p> <p>3. The dataset constitutes further a test of an open format specification for storing atom probe tomography data using the Hierarchical Data Format (HDF5). This is a recent initiative of the International Field Emission Society's (IFES) atom probe tomography technical committee. In this repository it is detailed an exemplar proposal of how to store acquisition-side relevant results and context of an APT experiment into a HDF5 file and complementary metadata files such as JSON. Implementation of this HDF5-based storage solution for APT data is lead by Markus Kühbach.</p> <p><br> <strong>The organization of this repository with respect to above aims is as follows:</strong></p> <p>-The original EPOS file of the measured is contained in the compressed *.epos.tar.gz archive.</p> <p>-The *.apth5 file is a transcoded version of the EPOS file. Therein, x,y,z data columns are stripped.</p> <p>-The correspondingly named *.json file is the file which nomad-FAIR parses metadata from.</p> <p>-Other files constitute logs of the transcoding process.</p> <p><br> <strong>Funding:</strong><br> The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.</p>
Atom probe tomography nomad-FAIR demonstrator dataset R76-20231-v01.epos.apth5
<p>This is the dataset of an atom probe tomography experiment which is provided open source for testing the possibility of implementing an open source encyclopedia for experimental materials science datasets, including techniques to begin with such as Scanning Transmission Electron Microscopy (STEM), Multidimensional Photo Emission Spectroscopy (MPES), and Atom Probe Tomography (APT) / Field Ion Microscopy (FIM).</p> <p><strong>This repository serves three aims:</strong></p> <p>1. The dataset is of scientific interest. Specifically, it captures the result of a cutting-edge APT experiment detailed exemplarily in DOI 10.1017/S1431927616012654 Fig. 1d by Zirong Peng and coworkers.</p> <p>2. The dataset contributes to tests of an extension to "The NOMAD Laboratory" (https://nomad-coe.eu/): nomad-FAIR. Specifically, to test various aspects of an automatized metadata parsing and processing pipeline to enable the extraction of domain-specific JSON metadata files into a NOMAD-conformant JSON file, ultimately aiming for searchable and repurposable dataset documentation. This serves two purposes: on the one hand to contextualize each dataset within NOMAD. On the other hand to serve as a starting point to parse potential interesting content from the heavy data HDF5 file to reduce unnecessary file access.</p> <p>The implementation of nomad-FAIR is coordinated by Markus Scheidgen.<br> The APT domain-specific parser is developed by Markus Kühbach.</p> <p>3. The dataset constitutes further a test of an open format specification for storing atom probe tomography data using the Hierarchical Data Format (HDF5). This is a recent initiative of the International Field Emission Society's (IFES) atom probe tomography technical committee. In this repository it is detailed an exemplar proposal of how to store acquisition-side relevant results and context of an APT experiment into a HDF5 file and complementary metadata files such as JSON. Implementation of this HDF5-based storage solution for APT data is lead by Markus Kühbach.</p> <p><br> <strong>The organization of this repository with respect to above aims is as follows:</strong></p> <p>-The original EPOS file of the measured is contained in the compressed *.epos.tar.gz archive.</p> <p>-The *.apth5 file is a transcoded version of the EPOS file. Therein, x,y,z data columns are stripped.</p> <p>-The correspondingly named *.json file is the file which nomad-FAIR parses metadata from.</p> <p>-Other files constitute logs of the transcoding process.</p> <p><strong>Funding:</strong><br> The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.</p>
Atom probe tomography data collection from DIN 1.4970 (15-15Ti) austenitic stainless steel irradiated with Fe ions
<p>This dataset comprises a large collection of atom probe tomography datasets collected from DIN 1.4970 alloy that was irradiated with Fe ions at different conditions. The DIN 1.4970 alloy is an austenitic stainless steel with 15 wt% Cr, 15 wt% Ni, a small addition of Ti. The full composition and characterization of our material can be found published elsewhere [1,2].</p> <p>Some of our material was subjected to ageing heat treatments at different temperatures for different times. Small samples of our original material and aged material was irradiated at the Michigan Ion Beam Laboratory in 2017 with 4.5 MeV Fe ions up to 40 dpa at an average dose rate of <span class="math-tex">\(2 \times 10^{-4}\)</span> dpa/s. This was done at three different temperatures: 300, 450, and 600 ºC. Atom probe samples were made of the irradiated layers (approximately 1.5 micron deep) with focused ion beam and mounted on Microtip coupons. APT measurements took place on three CAMECA LEAP-HR systems located at CAES in Idaho Falls, USA (files beginning with R33), at Montanuniversität Leoben in Leoben, Austria (R21) and at Friedrich–Alexander University in Erlangen, Germany (R56).</p> <p>The contents of this archive are:</p> <ul> <li>A folder containing the raw RHIT files</li> <li>A folder containing all the reconstructions and miscelaneous analysis files made by the author</li> <li>An excel file which indicates which measurement number stands for what material</li> <li>A suggested range file</li> </ul> <p>The RHIT files can only be used if one has access to the full IVAS 3.x version in order to make new reconstructions.</p> <p>The reconstructions and analysis folder can be useful to anyone. The folder buildup structure is similar to a project folder created by IVAS and should be directly importable into IVAS. Most folders are simply named after the RHIT file they were constructed from, though some have slightly modified names to include date of creation, extra information,... Inside all these folders you will find the recons folder and inside multiple reconstructions. At the deepest level you will find .pos files which can be read into free software such as python or <a href="http://threedepict.sourceforge.net/">3depict</a>. The range file that will give decent results on all these measurements is given at the top level; slight modifications may need to be applied for each measurement. Inside all folders you will also find numerous files (csv, png, jpg, ...) that were created by analyzing the data in IVAS. Sometimes the file names are very descriptive, sometimes less so. Sometimes these files were not saved to the default analysis folder but elsewhere on my drive. To be complete, I have moved all of these files into the top level folder. Therefore, besides the imagoAnalysis and recons folders, you will sometimes find additional folders and files in the folder. By different merging procedures, there may be multiple copies of the same files present as well. Unfortunately, the reconstructions and analysis folder is rather chaotic, as is the nature of file creation by IVAS.</p> <p>It is most instructive to start with the excel file at the top level of the archive. The first sheet contains some information, mostly the same as mentioned here. The second sheet pertains to the ion irradiations that were performed. The table colunms are self explanatory. Each irradiated sample was given a particular alias (first column), which relates it to the slot in the storage box in which it is stored. 5 different materials appear in the irradiations:</p> <ul> <li>T24 = tube, 24% cold worked. This represents the material as it was received from the manufacturer.</li> <li>T24-800C2h = the as-received material with an ageing heat treatment of 2 hours for 800 ºC applied.</li> <li>T24-600C4h = the as-received material with an ageing heat treatment of 4 hours for 600 ºC applied.</li> <li>T24-600C2868h = the as-received material with an ageing heat treatment of 2868 hours for 600 ºC applied.</li> <li>T46 = tube 46% cold worked. This represents another material received from the manufacturer</li> <li>AIM1 = another related material with a higher P and Si content obtained from another research institute</li> </ul> <p>All these materials were irradiated under different conditions as given in the subsequent columns. The irradiation parameters were drawn directly from reports produced by the lab, but we suspect some typos slipped into the reports. We do know for certain that the samples were irradiated up to a surface dose of 40 dpa, at least according to a <a href="http://www.srim.org/">SRIM calculation</a> with the K-P model. Atom probe results only pertain to T24 and T24-800C2h. A few measurements were conducted on T24-600C4h material but this material was not irradiated.</p> <p>The last sheet gives an overview of all the APT measurements included in this archive. The first column pertains to the sample alias in sheet 2: the irradiated disc from which the samples were made. The sample detail column details the history of the sample for convenience: T24 - <heat treatment conditions> - <irradiation conditions>. When in doubt, one can look up the sample alias in sheet 2. The filename pertains to the APT measurement RHIT file. For the 3 measurements performed in Leoben, RHIT files are not included in this archive. Finally a few details such as approximate ion count and some comments are included for some measurements.</p> <p>Funding: This work was supported by ENGIE [contract number 2015-AC-007 e BSUEZ6900]; the U.S. Department of Energy, Office of Nuclear Energy under DOE Idaho Operations Office Contract DE-AC07- 051D14517 as part of a Nuclear Science User Facilities experiment; and by the MYRRHA program in development at SCK-CEN, Belgium. Funding of the Austrian BMVIT (846933) in the framework of the program "Production of the future" and the "BMVIT Professorship for Industry" is gratefully acknowledged.</p> <p> </p> <p><a href="https://www.sciencedirect.com/science/article/pii/S0022311518300485">[1] N. Cautaerts, R. Delville, E. Stergar, D. Schryvers, M. Verwerft, Tailoring the Ti-C Nanoprecipitate Population and Microstructure of Titanium Stabilized Austenitic Steels, J. Nucl. Mater. 507 (2018) 177–187. doi:10.1016/j.jnucmat.2018.04.041.</a></p> <p> </p> <p><a href="https://www.sciencedirect.com/science/article/pii/S1359645418308103">[2] N. Cautaerts, R. Delville, E. Stergar, D. Schryvers, M. Verwerft, Characterization of (Ti,Mo,Cr)C Nanoprecipitates in an Austenitic Stainless Steel on the Atomic Scale, Acta Mater. 164 (2018) 90–98. doi:10.1016/J.ACTAMAT.2018.10.018.</a></p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Atom Probe Tomography performed in a transmission electron microscope (JEOL F 200)
<p>Material: Fe-51.4at% Cr processed by high pressure torsion<br>Temperature of analysis: 78 K<br>Pulse repetition rate: 20 kHz<br>APT detector type: advanced delay line detector<br>Number of atoms collected: 1.235 millions<br>Volume size: 9 x 9 x 93 nm3</p>
Atom probe tomography nomad-FAIR demonstrator dataset R76-30057-v01.epos.apth5
<p>This is the dataset of an atom probe tomography experiment which is provided open source for testing the possibility of implementing an open source encyclopedia for experimental materials science datasets, including techniques to begin with such as Scanning Transmission Electron Microscopy (STEM), Multidimensional Photo Emission Spectroscopy (MPES), and Atom Probe Tomography (APT) / Field Ion Microscopy (FIM).</p> <p><strong>This repository serves three aims:</strong></p> <p>1. The dataset is of scientific interest. Specifically, it captures the result of a cutting-edge APT experiment whose details are going to be reported in an upcoming publication by Shyam Katnagallu and coworkers.</p> <p>2. The dataset contributes to tests of an extension to "The NOMAD Laboratory" (https://nomad-coe.eu/): nomad-FAIR. Specifically, to test various aspects of an automatized metadata parsing and processing pipeline to enable the extraction of domain-specific JSON metadata files into a NOMAD-conformant JSON file, ultimately aiming for searchable and repurposable dataset documentation. This serves two purposes: on the one hand to contextualize each dataset within NOMAD. On the other hand to serve as a starting point to parse potential interesting content from the heavy data HDF5 file to reduce unnecessary file access.<br> The implementation of nomad-FAIR is coordinated by Markus Scheidgen.<br> The APT domain-specific parser is developed by Markus Kühbach.</p> <p>3. The dataset constitutes further a test of an open format specification for storing atom probe tomography data using the Hierarchical Data Format (HDF5). This is a recent initiative of the International Field Emission Society's (IFES) atom probe tomography technical committee. In this repository it is detailed an exemplar proposal of how to store acquisition-side relevant results and context of an APT experiment into a HDF5 file and complementary metadata files such as JSON. Implementation of this HDF5-based storage solution for APT data is lead by Markus Kühbach.</p> <p><strong>The organization of this repository with respect to above aims is as follows:</strong></p> <p>-The original EPOS file of the measured is contained in the compressed *.epos.tar.gz archive.</p> <p>-The *.apth5 file is a transcoded version of the EPOS file. Therein, x,y,z data columns are stripped.</p> <p>-The correspondingly named *.json file is the file which nomad-FAIR parses metadata from.</p> <p>-Other files constitute logs of the transcoding process.</p> <p><br> <strong>Funding:</strong><br> The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.</p>
Atom probe tomography nomad-FAIR demonstrator dataset R76-31053-v01.epos.apth5
<p>This is the dataset of an atom probe tomography experiment which is provided open source for testing the possibility of implementing an open source encyclopedia for experimental materials science datasets, including techniques to begin with such as Scanning Transmission Electron Microscopy (STEM), Multidimensional Photo Emission Spectroscopy (MPES), and Atom Probe Tomography (APT) / Field Ion Microscopy (FIM).</p> <p><strong>This repository serves three aims:</strong></p> <p>1. The dataset is of scientific interest. Specifically, it captures the result of a cutting-edge APT experiment detailed in an upcoming paper by Ye Wei and coworkers.</p> <p>2. The dataset contributes to testing an extension of "The NOMAD Laboratory" (https://nomad-coe.eu/): nomad-FAIR. Specifically, to test various aspects of its automatized metadata parsing and processing pipeline to enable the extraction of domain-specific JSON metadata files into a NOMAD-conformant JSON file, ultimately aiming for searchable and repurposable dataset documentation. This serves two purposes: on the one hand to contextualize each dataset within NOMAD. On the other hand to serve as a starting point to parse potential interesting content from the heavy data HDF5 file to reduce unnecessary file access.<br> The implementation of nomad-FAIR is coordinated by Markus Scheidgen.<br> The APT domain-specific parser is developed by Markus Kühbach.</p> <p>2. The dataset constitutes further a test of an open format specification for storing atom probe tomography data using the Hierarchical Data Format (HDF5). This is a recent initiative of the International Field Emission Society's (IFES) atom probe tomography technical committee. In this repository it is detailed an exemplar proposal of how to store acquisition-side relevant results and context of an APT experiment into a HDF5 file and complementary metadata files such as JSON. Implementation of this HDF5-based storage solution for APT data is lead by Markus Kühbach.</p> <p><br> <strong>The organization of this repository with respect to above aims is as follows:</strong></p> <p>-The original EPOS file of the measured is contained in the compressed *.epos.tar.gz archive.</p> <p>-The *.apth5 file is a transcoded version of the EPOS file. Therein, x,y,z data columns are stripped.</p> <p>-The correspondingly named *.json file is the file which nomad-FAIR parses metadata from.</p> <p>-Other files constitute logs of the transcoding process.</p> <p><br> <strong>Funding:</strong><br> The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.</p>
Silica in Silico: a Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
<p>The .zip archive contains the trajectories of all the simulations performed and analysed within the manuscript. The water molecules were removed for control systems.</p>
Dataset for "Computer vision assisted decomposition analysis of atom probe tomography data"
<p>Dataset for the article "Computer vision assisted decomposition analysis of atom probe tomography data". APT measurements were performed by Marcus Hans at Materials Chemistry (RWTH Aachen University) using a CAMECA LEAP 4000X HR. Training data was created by Janis A. Sälker.</p> <p>Content:</p> <p>- 13 (V,Al)N and 3 (Ti,Al)N APT reconstructions (.epos file format) and the corresponding range file (.rrng file format).</p> <p>- Training data (images & masks) for 9 labeled (V,Al)N APT samples (h5 file format). Image data with key "image" of shape (2, number_of_slices, 608, 192), where 2 corresponds to the V- and Al-contribution/channel and 608/192 to the height/width of the images. Masks/labels with key "label" of shape (number_of_slices, 608, 192)</p> <p> </p>
Visualizing local fast ionic conduction pathways in nanocrystalline lanthanum manganite by isotope exchange-atom probe tomography - dataset
<p>Raw data for atom probe tomography 2D elemental reconstructions of 18O-exchanged La0.8Sr0.2MnO3 thin films. LSM thin films were deposited by large-area PLD (PVD Systems – PLD 5000) using a 248 nm KrF excimer laser (Lambda Physics – COMPex PRO 205). The layers were deposited on Al<sub>2</sub>O<sub>3</sub> (0001) single crystal substrate (Crystec GmbH). A thin barrier layer of Ce<sub>0.8</sub>Sm<sub>0.2</sub>O<sub>1.9</sub> (SDC) was deposited before the LSM film in order to avoid cationic intermixing at the interface. Both layers were deposited at 700 °C, under an oxygen pressure of 2.6 × 10<sup>−2</sup> mbar, target–substrate distance of 95 mm, laser fluency ≈1.2 J cm<sup>−2</sup> and 5 Hz of laser frequency. The thickness of LSM and SDC layers deposited was ≈45 nm and ≈35 nm, respectively, as measured by spectroscopy ellipsometry (UVISEL, Horiba scientific).The nominal oxygen exchange temperature and time were 550 °C and 1 h and 40 min, respectively. Instrument Cameca LEAP 4000X Si. APT performed at 45.5 K using a 30 pJ laser energy and 500 kHz pulse rate. The flight path length was 90 mm and the ion detection rate was set to 5 ions per 1000 pulses, resulting in a bias range of 5000–7400 V during the data collection. Reconstructions were generated in Cameca's IVAS 3.6.18 software. A systematic energy deficit correction was employed to improve the mass spectral resolution.</p>
On Strong Scaling and Open Source Tools for Analyzing Atom Probe Tomography Data
<p>This repository contains supplemental results to the paper "On Strong Scaling and Open Source Tools<br> for Analyzing Atom Probe Tomography Data".</p> <p>Specifically, the input parameter and result files from all synthetic benchmark studies.<br> The results file for all synthetic specimen benchmark studies are available from the<br> authors upon serious request.</p> <p><strong>The repository content is as follows:</strong></p> <p><strong>Real world data:<br> Three triplets of *.tar.gz archive files document the settings and analysis files for the real world case studies</strong><br> 3013902 is the incipient specimen,<br> 2763207 the intermediate specimen, and<br> 3345501 the mature specimen.</p> <p><strong>Scripts.zip</strong><br> Contains all batch scripts we used for performing the analyses as a queue</p> <p><strong>Synthetic data:</strong></p> <p><strong>APTCrystallography.zip</strong><br> Contains all results from the benchmarking of the reimplemented Vicente Araullo-Peters et al. method</p> <p><strong>FullVolumeTessellation.zip</strong><br> Contains all results from the benchmarking of the Voro++ Voronoi volume tessellation method except for the HDF5/XDMF volume tessellation files of the 200 and 2000 million ion datasets</p> <p><strong>TwoPointStatistics.zip</strong><br> Contains all results from benchmarking the computing of 2-point spatial statistics</p> <p><strong>TipSurfaceDescrSpatialStatistics.zip</strong><br> Contains all results from benchmarking the alpha shape computation, descriptive spatial statistics, and clustering analyses</p> <p><strong>PARAPROBE.Results.2Mio.tar.gz<br> PARAPROBE.Results.20Mio.tar.gz</strong><br> <strong>PARAPROBE.Results.200Mio.tar.gz</strong><br> Contains all settings files and some results from benchmarking the hybrid implementation.</p> <p><strong>Unpack the individual repositories using tar through Linux console as follows:</strong><br> tar -xvf <archivename> <br> where <archivename> is a placeholder for the respective tar gz compressed archives within the ZIP file.<br> Alternatively WinRAR can be used on a Windows system.</p> <p><strong>We would kindly like to ask you to use the following repository<br> to access source code of PARAPROBE in the future:</strong></p> <p><strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong><br> <br> <strong>Only above repository will be updated in the future! </strong><br> <strong>Only there new code additions and bugfixes are posted!<br> The examples folder of this repository contains a folder examples/tasks/paper14 which shows how<br> to run a workflow of paraprobe tools from this above repository to run analyses akin as reported in this paper.</strong></p> <p>Recommendations and bug reports to M. Kühbach are appreciated! Happy APT analyzing!</p> <p>------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br> <strong>The PARAPROBE source code version we used for analyzing the synthetic and real world APT<br> specimens in the paper used an earlier development version of the PARAPROBE tool, the source code</strong><br> <strong>is here:</strong></p> <p>PARAPROBE_20190117_VersionUsedForPaper.zip</p> <p>https://github.com/mkuehbach/PARAPROBE<br> https://paraprobe.readthedocs.io/en/latest/</p> <p> </p>
Atom Probe Tomography dataset of pure Aluminum (Raw data)
<p>Atom Probe Tomography dataset of pure Aluminum (Raw data). The experiment was done with Oxcart a custom-made APT instrument. The data was recorded by pyccapt control module.</p>
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