Atom probe tomography nomad-FAIR demonstrator dataset R76-23219-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).

This repository serves three aims:

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.

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.
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.

The organization of this repository with respect to above aims is as follows:

-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.

Funding:
The work was partially supported by BiGmax, the Max Planck Society's Research Network on Big-Data-Driven Materials-Science.