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-em for converting your EM data to a NeXus/HDF5 file.

Steps

Installation

See here for how to install pynxtools together with the EM 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 EM reader in pynxtools:

user@box:~$ dataconverter $<em-file path> $<em-file path> $<eln-file path> --reader em --nxdl NXem --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 NXem. In order for the validation step of the EM 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 NXem standard.

Examples

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

Congrats! You now have a FAIR NeXus file!