Convert electron microscopy data and metadata to NeXus

Who is this tutorial for?

This document is for people who want to standardize their research data by converting these into a NeXus standardized format.

What should you know before this tutorial?

• You should have a basic understanding of FAIRmat NeXus and pynxtools
• You should have a basic understanding of using Python and Jupyter notebooks via JupyterLab

What you will know at the end of this tutorial?

You will have a basic understanding how to use pynxtools-apm for converting your APM data to a NeXus/HDF5 file.

Steps

Installation

See here for how to install pynxtools together with the APM reader plugin. Note that the reader is a combination of multiple readers each supporting a different set of versions of file formats used by key technology partners from the field of electron microscopy.

Running the reader from the command line

An example script to run the APM reader in pynxtools:

user@box:~$ dataconverter $<apm-file path> $<apm-file path> $<eln-file path> --reader apm --nxdl NXapm --output <output-file path>.nxs

Note that typically none of the supported file formats have data/values for all required and recommended fields and attributes in NXapm. In order for the validation step of the APM reader to pass, you need to provide an ELN file that contains the missing values if you would like to be fully compliant with the NXapm standard.

Examples

You can find examples how to use pynxtools-apm for your APM research data pipeline in src/pynxtools_apm/nomad/examples. These are designed for working with NOMAD and its NOMAD Remote Tools Hub (NORTH).

Congrats! You now have a FAIR NeXus file!