Atom probe tomography nomad-FAIR demonstrator dataset R76-20231-v01.epos.apth5

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). <strong>This repository serves three aims:</strong> 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. 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. The implementation of nomad-FAIR is coordinated by Markus Scheidgen.<br> The APT domain-specific parser is developed by Markus Kühbach. 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. <br> <strong>The organization of this repository with respect to above aims is as follows:</strong> -The original EPOS file of the measured is contained in the compressed *.epos.tar.gz archive. -The *.apth5 file is a transcoded version of the EPOS file. Therein, x,y,z data columns are stripped. -The correspondingly named *.json file is the file which nomad-FAIR parses metadata from. -Other files constitute logs of the transcoding process. <strong>Funding:</strong><br> The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.本数据集为原子探针层析成像（Atom Probe Tomography, APT）实验数据集，以开源形式发布，旨在测试搭建实验材料科学数据集开源百科全书的可行性，首批涵盖的技术包括扫描透射电子显微镜（Scanning Transmission Electron Microscopy, STEM）、多维光电子能谱（Multidimensional Photo Emission Spectroscopy, MPES）以及原子探针层析成像（APT）/场离子显微镜（Field Ion Microscopy, FIM）。 **本仓库旨在实现三大目标：** 1. 本数据集具备科学研究价值。具体而言，其记录了一项前沿原子探针层析成像实验的结果，该实验的详细示例可参见Zirong Peng及其合作者发表于DOI: 10.1017/S1431927616012654的论文中的图1d。 2. 本数据集可用于测试针对"NOMAD实验室（https://nomad-coe.eu/）"的扩展工具nomad-FAIR。具体来说，将对自动化元数据解析与处理流水线的各项功能进行测试，以实现将领域专属JSON元数据文件转换为符合NOMAD规范的JSON文件，最终目标是生成可检索、可复用的数据集文档。这一工作包含两大用途：一方面是将每个数据集在NOMAD平台中进行上下文关联；另一方面则是作为从海量HDF5数据文件中提取潜在有价值内容的起点，以减少不必要的文件访问操作。 nomad-FAIR的开发协调工作由Markus Scheidgen负责。原子探针层析成像领域专属解析器由Markus Kühbach开发。 3. 本数据集同时可用于测试基于分层数据格式（Hierarchical Data Format, HDF5）存储原子探针层析成像数据的开放格式规范。该规范是国际场发射学会（International Field Emission Society, IFES）原子探针层析成像技术委员会近期提出的倡议。本仓库将详细展示如何将APT实验中与采集端相关的结果及上下文信息存储至HDF5文件及配套的JSON等元数据文件中的示例性方案。基于HDF5的APT数据存储方案的开发工作由Markus Kühbach主导。 **针对上述三大目标，本仓库的组织结构如下：** - 实测数据的原始EPOS文件存储于压缩包*.epos.tar.gz中。 - *.apth5文件为EPOS文件的转码版本，其中已移除x、y、z三列数据。 - 与上述文件同名的*.json文件是nomad-FAIR用于解析元数据的文件。 - 其余文件为转码过程的日志文件。 **资助说明：** 本研究得到了马克斯·普朗克学会（Max Planck Society）旗下大数据驱动材料科学研究网络BiGmax的部分资助。